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version 1.5, 2001/05/02 17:42:45 version 1.83, 2003/06/10 13:39:11
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.83  2003/06/10 13:39:11  lievre
   individuals from different ages are interviewed on their health status    *** empty log message ***
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.82  2003/06/05 15:57:20  brouard
   Health expectancies are computed from the transistions observed between    Add log in  imach.c and  fullversion number is now printed.
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to  */
   reach the Maximum Likelihood of the parameters involved in the model.  /*
   The simplest model is the multinomial logistic model where pij is     Interpolated Markov Chain
   the probabibility to be observed in state j at the second wave conditional  
   to be observed in state i at the first wave. Therefore the model is:    Short summary of the programme:
   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 complex model than "constant and    This program computes Healthy Life Expectancies from
   age", you should modify the program where the markup    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     *Covariates have to be included here again* invites you to do it.    first survey ("cross") where individuals from different ages are
   More covariates you add, less is the speed of the convergence.    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
   The advantage that this computer programme claims, comes from that if the    second wave of interviews ("longitudinal") which measure each change
   delay between waves is not identical for each individual, or if some    (if any) in individual health status.  Health expectancies are
   individual missed an interview, the information is not rounded or lost, but    computed from the time spent in each health state according to a
   taken into account using an interpolation or extrapolation.    model. More health states you consider, more time is necessary to reach the
   hPijx is the probability to be    Maximum Likelihood of the parameters involved in the model.  The
   observed in state i at age x+h conditional to the observed state i at age    simplest model is the multinomial logistic model where pij is the
   x. The delay 'h' can be split into an exact number (nh*stepm) of    probability to be observed in state j at the second wave
   unobserved intermediate  states. This elementary transition (by month or    conditional to be observed in state i at the first wave. Therefore
   quarter trimester, semester or year) is model as a multinomial logistic.    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    'age' is age and 'sex' is a covariate. If you want to have a more
   and the contribution of each individual to the likelihood is simply hPijx.    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
   Also this programme outputs the covariance matrix of the parameters but also    you to do it.  More covariates you add, slower the
   of the life expectancies. It also computes the prevalence limits.    convergence.
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    The advantage of this computer programme, compared to a simple
            Institut national d'études démographiques, Paris.    multinomial logistic model, is clear when the delay between waves is not
   This software have been partly granted by Euro-REVES, a concerted action    identical for each individual. Also, if a individual missed an
   from the European Union.    intermediate interview, the information is lost, but taken into
   It is copyrighted identically to a GNU software product, ie programme and    account using an interpolation or extrapolation.  
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    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
      split into an exact number (nh*stepm) of unobserved intermediate
 #include <math.h>    states. This elementary transition (by month, quarter,
 #include <stdio.h>    semester or year) is modelled as a multinomial logistic.  The hPx
 #include <stdlib.h>    matrix is simply the matrix product of nh*stepm elementary matrices
 #include <unistd.h>    and the contribution of each individual to the likelihood is simply
     hPijx.
 #define MAXLINE 256  
 #define FILENAMELENGTH 80    Also this programme outputs the covariance matrix of the parameters but also
 /*#define DEBUG*/    of the life expectancies. It also computes the stable prevalence. 
 #define windows    
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    software can be distributed freely for non commercial use. Latest version
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    can be accessed at http://euroreves.ined.fr/imach .
   
 #define NINTERVMAX 8    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    
 #define NCOVMAX 8 /* Maximum number of covariates */    **********************************************************************/
 #define MAXN 20000  /*
 #define YEARM 12. /* Number of months per year */    main
 #define AGESUP 130    read parameterfile
 #define AGEBASE 40    read datafile
     concatwav
     if (mle >= 1)
 int nvar;      mlikeli
 static int cptcov;    print results files
 int cptcovn;    if mle==1 
 int npar=NPARMAX;       computes hessian
 int nlstate=2; /* Number of live states */    read end of parameter file: agemin, agemax, bage, fage, estepm
 int ndeath=1; /* Number of dead states */        begin-prev-date,...
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    open gnuplot file
     open html file
 int *wav; /* Number of waves for this individuual 0 is possible */    stable prevalence
 int maxwav; /* Maxim number of waves */     for age prevalim()
 int mle, weightopt;    h Pij x
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    variance of p varprob
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    forecasting if prevfcast==1 prevforecast call prevalence()
 double **oldm, **newm, **savm; /* Working pointers to matrices */    health expectancies
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Variance-covariance of DFLE
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    prevalence()
 FILE *ficgp, *fichtm;     movingaverage()
 FILE *ficreseij;    varevsij() 
   char filerese[FILENAMELENGTH];    if popbased==1 varevsij(,popbased)
  FILE  *ficresvij;    total life expectancies
   char fileresv[FILENAMELENGTH];    Variance of stable prevalence
  FILE  *ficresvpl;   end
   char fileresvpl[FILENAMELENGTH];  */
   
   
   
    
 #define NR_END 1  #include <math.h>
 #define FREE_ARG char*  #include <stdio.h>
 #define FTOL 1.0e-10  #include <stdlib.h>
   #include <unistd.h>
 #define NRANSI  
 #define ITMAX 200  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 #define TOL 2.0e-4  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 80
 #define CGOLD 0.3819660  /*#define DEBUG*/
 #define ZEPS 1.0e-10  #define windows
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #define GOLD 1.618034  
 #define GLIMIT 100.0  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define TINY 1.0e-20  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 static double maxarg1,maxarg2;  #define NINTERVMAX 8
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    #define NCOVMAX 8 /* Maximum number of covariates */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define MAXN 20000
 #define rint(a) floor(a+0.5)  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 static double sqrarg;  #define AGEBASE 40
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #ifdef windows
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 int imx;  #else
 int stepm;  #define DIRSEPARATOR '/'
 /* Stepm, step in month: minimum step interpolation*/  #define ODIRSEPARATOR '\\'
   #endif
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;  /* $Id$ */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  /* $State$ */
 double **pmmij;  
   char version[]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 double *weight;  char fullversion[]="$Revision$ $Date$"; 
 int **s; /* Status */  int erreur; /* Error number */
 double *agedc, **covar, idx;  int nvar;
 int **nbcode, *Tcode, *Tvar, **codtab;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  int nlstate=2; /* Number of live states */
 double ftolhess; /* Tolerance for computing hessian */  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 static  int split( char *path, char *dirc, char *name )  
 {  int *wav; /* Number of waves for this individuual 0 is possible */
    char *s;                             /* pointer */  int maxwav; /* Maxim number of waves */
    int  l1, l2;                         /* length counters */  int jmin, jmax; /* min, max spacing between 2 waves */
   int mle, weightopt;
    l1 = strlen( path );                 /* length of path */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    s = strrchr( path, '\\' );           /* find last / */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
    if ( s == NULL ) {                   /* no directory, so use current */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 #if     defined(__bsd__)                /* get current working directory */  double jmean; /* Mean space between 2 waves */
       extern char       *getwd( );  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       if ( getwd( dirc ) == NULL ) {  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #else  FILE *ficlog, *ficrespow;
       extern char       *getcwd( );  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  FILE *fichtm; /* Html File */
 #endif  FILE *ficreseij;
          return( GLOCK_ERROR_GETCWD );  char filerese[FILENAMELENGTH];
       }  FILE  *ficresvij;
       strcpy( name, path );             /* we've got it */  char fileresv[FILENAMELENGTH];
    } else {                             /* strip direcotry from path */  FILE  *ficresvpl;
       s++;                              /* after this, the filename */  char fileresvpl[FILENAMELENGTH];
       l2 = strlen( s );                 /* length of filename */  char title[MAXLINE];
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       strcpy( name, s );                /* save file name */  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    }  char filelog[FILENAMELENGTH]; /* Log file */
    l1 = strlen( dirc );                 /* length of directory */  char filerest[FILENAMELENGTH];
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  char fileregp[FILENAMELENGTH];
    return( 0 );                         /* we're done */  char popfile[FILENAMELENGTH];
 }  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   
 /******************************************/  #define NR_END 1
   #define FREE_ARG char*
 void replace(char *s, char*t)  #define FTOL 1.0e-10
 {  
   int i;  #define NRANSI 
   int lg=20;  #define ITMAX 200 
   i=0;  
   lg=strlen(t);  #define TOL 2.0e-4 
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  #define CGOLD 0.3819660 
     if (t[i]== '\\') s[i]='/';  #define ZEPS 1.0e-10 
   }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 int nbocc(char *s, char occ)  #define GLIMIT 100.0 
 {  #define TINY 1.0e-20 
   int i,j=0;  
   int lg=20;  static double maxarg1,maxarg2;
   i=0;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   lg=strlen(s);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   for(i=0; i<= lg; i++) {    
   if  (s[i] == occ ) j++;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   }  #define rint(a) floor(a+0.5)
   return j;  
 }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 void cutv(char *u,char *v, char*t, char occ)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 {  
   int i,lg,j,p;  int imx; 
   i=0;  int stepm;
   for(j=0; j<=strlen(t)-1; j++) {  /* Stepm, step in month: minimum step interpolation*/
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   lg=strlen(t);  
   for(j=0; j<p; j++) {  int m,nb;
     (u[j] = t[j]);  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
     u[p]='\0';  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   }  double **pmmij, ***probs;
   double dateintmean=0;
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  double *weight;
   }  int **s; /* Status */
 }  double *agedc, **covar, idx;
   int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 /********************** nrerror ********************/  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 void nrerror(char error_text[])  double ftolhess; /* Tolerance for computing hessian */
 {  
   fprintf(stderr,"ERREUR ...\n");  /**************** split *************************/
   fprintf(stderr,"%s\n",error_text);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   exit(1);  {
 }    char  *ss;                            /* pointer */
 /*********************** vector *******************/    int   l1, l2;                         /* length counters */
 double *vector(int nl, int nh)  
 {    l1 = strlen(path );                   /* length of path */
   double *v;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   if (!v) nrerror("allocation failure in vector");    if ( ss == NULL ) {                   /* no directory, so use current */
   return v-nl+NR_END;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* get current working directory */
 /************************ free vector ******************/      /*    extern  char* getcwd ( char *buf , int len);*/
 void free_vector(double*v, int nl, int nh)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   free((FREE_ARG)(v+nl-NR_END));      }
 }      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 /************************ivector *******************************/      ss++;                               /* after this, the filename */
 int *ivector(long nl,long nh)      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   int *v;      strcpy( name, ss );         /* save file name */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   if (!v) nrerror("allocation failure in ivector");      dirc[l1-l2] = 0;                    /* add zero */
   return v-nl+NR_END;    }
 }    l1 = strlen( dirc );                  /* length of directory */
   #ifdef windows
 /******************free ivector **************************/    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 void free_ivector(int *v, long nl, long nh)  #else
 {    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   free((FREE_ARG)(v+nl-NR_END));  #endif
 }    ss = strrchr( name, '.' );            /* find last / */
     ss++;
 /******************* imatrix *******************************/    strcpy(ext,ss);                       /* save extension */
 int **imatrix(long nrl, long nrh, long ncl, long nch)    l1= strlen( name);
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    l2= strlen(ss)+1;
 {    strncpy( finame, name, l1-l2);
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    finame[l1-l2]= 0;
   int **m;    return( 0 );                          /* we're done */
    }
   /* 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;  
   m -= nrl;  void replace(char *s, char*t)
    {
      int i;
   /* allocate rows and set pointers to them */    int lg=20;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    i=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    lg=strlen(t);
   m[nrl] += NR_END;    for(i=0; i<= lg; i++) {
   m[nrl] -= ncl;      (s[i] = t[i]);
        if (t[i]== '\\') s[i]='/';
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    }
    }
   /* return pointer to array of pointers to rows */  
   return m;  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /****************** free_imatrix *************************/    int lg=20;
 void free_imatrix(m,nrl,nrh,ncl,nch)    i=0;
       int **m;    lg=strlen(s);
       long nch,ncl,nrh,nrl;    for(i=0; i<= lg; i++) {
      /* free an int matrix allocated by imatrix() */    if  (s[i] == occ ) j++;
 {    }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    return j;
   free((FREE_ARG) (m+nrl-NR_END));  }
 }  
   void cutv(char *u,char *v, char*t, char occ)
 /******************* matrix *******************************/  {
 double **matrix(long nrl, long nrh, long ncl, long nch)    /* cuts string t into u and v where u is ended by char occ excluding it
 {       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;       gives u="abcedf" and v="ghi2j" */
   double **m;    int i,lg,j,p=0;
     i=0;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    for(j=0; j<=strlen(t)-1; j++) {
   if (!m) nrerror("allocation failure 1 in matrix()");      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   m += NR_END;    }
   m -= nrl;  
     lg=strlen(t);
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    for(j=0; j<p; j++) {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      (u[j] = t[j]);
   m[nrl] += NR_END;    }
   m[nrl] -= ncl;       u[p]='\0';
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;     for(j=0; j<= lg; j++) {
   return m;      if (j>=(p+1))(v[j-p-1] = t[j]);
 }    }
   }
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  /********************** nrerror ********************/
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  void nrerror(char error_text[])
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 /******************* ma3x *******************************/    exit(EXIT_FAILURE);
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  }
 {  /*********************** vector *******************/
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  double *vector(int nl, int nh)
   double ***m;  {
     double *v;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!v) nrerror("allocation failure in vector");
   m += NR_END;    return v-nl+NR_END;
   m -= nrl;  }
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /************************ free vector ******************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  void free_vector(double*v, int nl, int nh)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    free((FREE_ARG)(v+nl-NR_END));
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /************************ivector *******************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  char *cvector(long nl,long nh)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  {
   m[nrl][ncl] += NR_END;    char *v;
   m[nrl][ncl] -= nll;    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   for (j=ncl+1; j<=nch; j++)    if (!v) nrerror("allocation failure in cvector");
     m[nrl][j]=m[nrl][j-1]+nlay;    return v-nl+NR_END;
    }
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /******************free ivector **************************/
     for (j=ncl+1; j<=nch; j++)  void free_cvector(char *v, long nl, long nh)
       m[i][j]=m[i][j-1]+nlay;  {
   }    free((FREE_ARG)(v+nl-NR_END));
   return m;  }
 }  
   /************************ivector *******************************/
 /*************************free ma3x ************************/  int *ivector(long nl,long nh)
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  {
 {    int *v;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!v) nrerror("allocation failure in ivector");
   free((FREE_ARG)(m+nrl-NR_END));    return v-nl+NR_END;
 }  }
   
 /***************** f1dim *************************/  /******************free ivector **************************/
 extern int ncom;  void free_ivector(int *v, long nl, long nh)
 extern double *pcom,*xicom;  {
 extern double (*nrfunc)(double []);    free((FREE_ARG)(v+nl-NR_END));
    }
 double f1dim(double x)  
 {  /******************* imatrix *******************************/
   int j;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   double f;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   double *xt;  { 
      long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   xt=vector(1,ncom);    int **m; 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    
   f=(*nrfunc)(xt);    /* allocate pointers to rows */ 
   free_vector(xt,1,ncom);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   return f;    if (!m) nrerror("allocation failure 1 in matrix()"); 
 }    m += NR_END; 
     m -= nrl; 
 /*****************brent *************************/    
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    
 {    /* allocate rows and set pointers to them */ 
   int iter;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double a,b,d,etemp;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double fu,fv,fw,fx;    m[nrl] += NR_END; 
   double ftemp;    m[nrl] -= ncl; 
   double p,q,r,tol1,tol2,u,v,w,x,xm;    
   double e=0.0;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
      
   a=(ax < cx ? ax : cx);    /* return pointer to array of pointers to rows */ 
   b=(ax > cx ? ax : cx);    return m; 
   x=w=v=bx;  } 
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  /****************** free_imatrix *************************/
     xm=0.5*(a+b);  void free_imatrix(m,nrl,nrh,ncl,nch)
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);        int **m;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/        long nch,ncl,nrh,nrl; 
     printf(".");fflush(stdout);       /* free an int matrix allocated by imatrix() */ 
 #ifdef DEBUG  { 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    free((FREE_ARG) (m+nrl-NR_END)); 
 #endif  } 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /******************* matrix *******************************/
       return fx;  double **matrix(long nrl, long nrh, long ncl, long nch)
     }  {
     ftemp=fu;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     if (fabs(e) > tol1) {    double **m;
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       p=(x-v)*q-(x-w)*r;    if (!m) nrerror("allocation failure 1 in matrix()");
       q=2.0*(q-r);    m += NR_END;
       if (q > 0.0) p = -p;    m -= nrl;
       q=fabs(q);  
       etemp=e;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       e=d;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m[nrl] += NR_END;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl] -= ncl;
       else {  
         d=p/q;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         u=x+d;    return m;
         if (u-a < tol2 || b-u < tol2)    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
           d=SIGN(tol1,xm-x);     */
       }  }
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  /*************************free matrix ************************/
     }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  {
     fu=(*f)(u);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     if (fu <= fx) {    free((FREE_ARG)(m+nrl-NR_END));
       if (u >= x) a=x; else b=x;  }
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  /******************* ma3x *******************************/
         } else {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
           if (u < x) a=u; else b=u;  {
           if (fu <= fw || w == x) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
             v=w;    double ***m;
             w=u;  
             fv=fw;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
             fw=fu;    if (!m) nrerror("allocation failure 1 in matrix()");
           } else if (fu <= fv || v == x || v == w) {    m += NR_END;
             v=u;    m -= nrl;
             fv=fu;  
           }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   }    m[nrl] += NR_END;
   nrerror("Too many iterations in brent");    m[nrl] -= ncl;
   *xmin=x;  
   return fx;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 }  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 /****************** mnbrak ***********************/    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    m[nrl][ncl] -= nll;
             double (*func)(double))    for (j=ncl+1; j<=nch; j++) 
 {      m[nrl][j]=m[nrl][j-1]+nlay;
   double ulim,u,r,q, dum;    
   double fu;    for (i=nrl+1; i<=nrh; i++) {
        m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   *fa=(*func)(*ax);      for (j=ncl+1; j<=nch; j++) 
   *fb=(*func)(*bx);        m[i][j]=m[i][j-1]+nlay;
   if (*fb > *fa) {    }
     SHFT(dum,*ax,*bx,dum)    return m; 
       SHFT(dum,*fb,*fa,dum)    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   *cx=(*bx)+GOLD*(*bx-*ax);    */
   *fc=(*func)(*cx);  }
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  /*************************free ma3x ************************/
     q=(*bx-*cx)*(*fb-*fa);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  {
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     ulim=(*bx)+GLIMIT*(*cx-*bx);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     if ((*bx-u)*(u-*cx) > 0.0) {    free((FREE_ARG)(m+nrl-NR_END));
       fu=(*func)(u);  }
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  /***************** f1dim *************************/
       if (fu < *fc) {  extern int ncom; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  extern double *pcom,*xicom;
           SHFT(*fb,*fc,fu,(*func)(u))  extern double (*nrfunc)(double []); 
           }   
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  double f1dim(double x) 
       u=ulim;  { 
       fu=(*func)(u);    int j; 
     } else {    double f;
       u=(*cx)+GOLD*(*cx-*bx);    double *xt; 
       fu=(*func)(u);   
     }    xt=vector(1,ncom); 
     SHFT(*ax,*bx,*cx,u)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       SHFT(*fa,*fb,*fc,fu)    f=(*nrfunc)(xt); 
       }    free_vector(xt,1,ncom); 
 }    return f; 
   } 
 /*************** linmin ************************/  
   /*****************brent *************************/
 int ncom;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 double *pcom,*xicom;  { 
 double (*nrfunc)(double []);    int iter; 
      double a,b,d,etemp;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    double fu,fv,fw,fx;
 {    double ftemp;
   double brent(double ax, double bx, double cx,    double p,q,r,tol1,tol2,u,v,w,x,xm; 
                double (*f)(double), double tol, double *xmin);    double e=0.0; 
   double f1dim(double x);   
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    a=(ax < cx ? ax : cx); 
               double *fc, double (*func)(double));    b=(ax > cx ? ax : cx); 
   int j;    x=w=v=bx; 
   double xx,xmin,bx,ax;    fw=fv=fx=(*f)(x); 
   double fx,fb,fa;    for (iter=1;iter<=ITMAX;iter++) { 
        xm=0.5*(a+b); 
   ncom=n;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   pcom=vector(1,n);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   xicom=vector(1,n);      printf(".");fflush(stdout);
   nrfunc=func;      fprintf(ficlog,".");fflush(ficlog);
   for (j=1;j<=n;j++) {  #ifdef DEBUG
     pcom[j]=p[j];      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);
     xicom[j]=xi[j];      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   ax=0.0;  #endif
   xx=1.0;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);        *xmin=x; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);        return fx; 
 #ifdef DEBUG      } 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      ftemp=fu;
 #endif      if (fabs(e) > tol1) { 
   for (j=1;j<=n;j++) {        r=(x-w)*(fx-fv); 
     xi[j] *= xmin;        q=(x-v)*(fx-fw); 
     p[j] += xi[j];        p=(x-v)*q-(x-w)*r; 
   }        q=2.0*(q-r); 
   free_vector(xicom,1,n);        if (q > 0.0) p = -p; 
   free_vector(pcom,1,n);        q=fabs(q); 
 }        etemp=e; 
         e=d; 
 /*************** powell ************************/        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             double (*func)(double []))        else { 
 {          d=p/q; 
   void linmin(double p[], double xi[], int n, double *fret,          u=x+d; 
               double (*func)(double []));          if (u-a < tol2 || b-u < tol2) 
   int i,ibig,j;            d=SIGN(tol1,xm-x); 
   double del,t,*pt,*ptt,*xit;        } 
   double fp,fptt;      } else { 
   double *xits;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   pt=vector(1,n);      } 
   ptt=vector(1,n);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   xit=vector(1,n);      fu=(*f)(u); 
   xits=vector(1,n);      if (fu <= fx) { 
   *fret=(*func)(p);        if (u >= x) a=x; else b=x; 
   for (j=1;j<=n;j++) pt[j]=p[j];        SHFT(v,w,x,u) 
   for (*iter=1;;++(*iter)) {          SHFT(fv,fw,fx,fu) 
     fp=(*fret);          } else { 
     ibig=0;            if (u < x) a=u; else b=u; 
     del=0.0;            if (fu <= fw || w == x) { 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);              v=w; 
     for (i=1;i<=n;i++)              w=u; 
       printf(" %d %.12f",i, p[i]);              fv=fw; 
     printf("\n");              fw=fu; 
     for (i=1;i<=n;i++) {            } else if (fu <= fv || v == x || v == w) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];              v=u; 
       fptt=(*fret);              fv=fu; 
 #ifdef DEBUG            } 
       printf("fret=%lf \n",*fret);          } 
 #endif    } 
       printf("%d",i);fflush(stdout);    nrerror("Too many iterations in brent"); 
       linmin(p,xit,n,fret,func);    *xmin=x; 
       if (fabs(fptt-(*fret)) > del) {    return fx; 
         del=fabs(fptt-(*fret));  } 
         ibig=i;  
       }  /****************** mnbrak ***********************/
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       for (j=1;j<=n;j++) {              double (*func)(double)) 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  { 
         printf(" x(%d)=%.12e",j,xit[j]);    double ulim,u,r,q, dum;
       }    double fu; 
       for(j=1;j<=n;j++)   
         printf(" p=%.12e",p[j]);    *fa=(*func)(*ax); 
       printf("\n");    *fb=(*func)(*bx); 
 #endif    if (*fb > *fa) { 
     }      SHFT(dum,*ax,*bx,dum) 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        SHFT(dum,*fb,*fa,dum) 
 #ifdef DEBUG        } 
       int k[2],l;    *cx=(*bx)+GOLD*(*bx-*ax); 
       k[0]=1;    *fc=(*func)(*cx); 
       k[1]=-1;    while (*fb > *fc) { 
       printf("Max: %.12e",(*func)(p));      r=(*bx-*ax)*(*fb-*fc); 
       for (j=1;j<=n;j++)      q=(*bx-*cx)*(*fb-*fa); 
         printf(" %.12e",p[j]);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       printf("\n");        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       for(l=0;l<=1;l++) {      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         for (j=1;j<=n;j++) {      if ((*bx-u)*(u-*cx) > 0.0) { 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        fu=(*func)(u); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         }        fu=(*func)(u); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        if (fu < *fc) { 
       }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 #endif            SHFT(*fb,*fc,fu,(*func)(u)) 
             } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       free_vector(xit,1,n);        u=ulim; 
       free_vector(xits,1,n);        fu=(*func)(u); 
       free_vector(ptt,1,n);      } else { 
       free_vector(pt,1,n);        u=(*cx)+GOLD*(*cx-*bx); 
       return;        fu=(*func)(u); 
     }      } 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      SHFT(*ax,*bx,*cx,u) 
     for (j=1;j<=n;j++) {        SHFT(*fa,*fb,*fc,fu) 
       ptt[j]=2.0*p[j]-pt[j];        } 
       xit[j]=p[j]-pt[j];  } 
       pt[j]=p[j];  
     }  /*************** linmin ************************/
     fptt=(*func)(ptt);  
     if (fptt < fp) {  int ncom; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  double *pcom,*xicom;
       if (t < 0.0) {  double (*nrfunc)(double []); 
         linmin(p,xit,n,fret,func);   
         for (j=1;j<=n;j++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           xi[j][ibig]=xi[j][n];  { 
           xi[j][n]=xit[j];    double brent(double ax, double bx, double cx, 
         }                 double (*f)(double), double tol, double *xmin); 
 #ifdef DEBUG    double f1dim(double x); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         for(j=1;j<=n;j++)                double *fc, double (*func)(double)); 
           printf(" %.12e",xit[j]);    int j; 
         printf("\n");    double xx,xmin,bx,ax; 
 #endif    double fx,fb,fa;
       }   
     }    ncom=n; 
   }    pcom=vector(1,n); 
 }    xicom=vector(1,n); 
     nrfunc=func; 
 /**** Prevalence limit ****************/    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      xicom[j]=xi[j]; 
 {    } 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    ax=0.0; 
      matrix by transitions matrix until convergence is reached */    xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   int i, ii,j,k;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   double min, max, maxmin, maxmax,sumnew=0.;  #ifdef DEBUG
   double **matprod2();    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double **out, cov[NCOVMAX], **pmij();    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double **newm;  #endif
   double agefin, delaymax=50 ; /* Max number of years to converge */    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
   for (ii=1;ii<=nlstate+ndeath;ii++)      p[j] += xi[j]; 
     for (j=1;j<=nlstate+ndeath;j++){    } 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    free_vector(xicom,1,n); 
     }    free_vector(pcom,1,n); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  } 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  /*************** powell ************************/
     /* Covariates have to be included here again */  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     cov[1]=1.;              double (*func)(double [])) 
     cov[2]=agefin;  { 
     if (cptcovn>0){    void linmin(double p[], double xi[], int n, double *fret, 
       for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}                double (*func)(double [])); 
     }    int i,ibig,j; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
     savm=oldm;    double *xits;
     oldm=newm;    pt=vector(1,n); 
     maxmax=0.;    ptt=vector(1,n); 
     for(j=1;j<=nlstate;j++){    xit=vector(1,n); 
       min=1.;    xits=vector(1,n); 
       max=0.;    *fret=(*func)(p); 
       for(i=1; i<=nlstate; i++) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
         sumnew=0;    for (*iter=1;;++(*iter)) { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      fp=(*fret); 
         prlim[i][j]= newm[i][j]/(1-sumnew);      ibig=0; 
         max=FMAX(max,prlim[i][j]);      del=0.0; 
         min=FMIN(min,prlim[i][j]);      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       maxmin=max-min;      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       maxmax=FMAX(maxmax,maxmin);      for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
     if(maxmax < ftolpl){        fprintf(ficlog," %d %.12lf",i, p[i]);
       return prlim;        fprintf(ficrespow," %.12lf", p[i]);
     }      }
   }      printf("\n");
 }      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");
 /*************** transition probabilities **********/      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        fptt=(*fret); 
 {  #ifdef DEBUG
   double s1, s2;        printf("fret=%lf \n",*fret);
   /*double t34;*/        fprintf(ficlog,"fret=%lf \n",*fret);
   int i,j,j1, nc, ii, jj;  #endif
         printf("%d",i);fflush(stdout);
     for(i=1; i<= nlstate; i++){        fprintf(ficlog,"%d",i);fflush(ficlog);
     for(j=1; j<i;j++){        linmin(p,xit,n,fret,func); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        if (fabs(fptt-(*fret)) > del) { 
         /*s2 += param[i][j][nc]*cov[nc];*/          del=fabs(fptt-(*fret)); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          ibig=i; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        } 
       }  #ifdef DEBUG
       ps[i][j]=s2;        printf("%d %.12e",i,(*fret));
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     for(j=i+1; j<=nlstate+ndeath;j++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          printf(" x(%d)=%.12e",j,xit[j]);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        }
       }        for(j=1;j<=n;j++) {
       ps[i][j]=s2;          printf(" p=%.12e",p[j]);
     }          fprintf(ficlog," p=%.12e",p[j]);
   }        }
   for(i=1; i<= nlstate; i++){        printf("\n");
      s1=0;        fprintf(ficlog,"\n");
     for(j=1; j<i; j++)  #endif
       s1+=exp(ps[i][j]);      } 
     for(j=i+1; j<=nlstate+ndeath; j++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       s1+=exp(ps[i][j]);  #ifdef DEBUG
     ps[i][i]=1./(s1+1.);        int k[2],l;
     for(j=1; j<i; j++)        k[0]=1;
       ps[i][j]= exp(ps[i][j])*ps[i][i];        k[1]=-1;
     for(j=i+1; j<=nlstate+ndeath; j++)        printf("Max: %.12e",(*func)(p));
       ps[i][j]= exp(ps[i][j])*ps[i][i];        fprintf(ficlog,"Max: %.12e",(*func)(p));
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        for (j=1;j<=n;j++) {
   } /* end i */          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        }
     for(jj=1; jj<= nlstate+ndeath; jj++){        printf("\n");
       ps[ii][jj]=0;        fprintf(ficlog,"\n");
       ps[ii][ii]=1;        for(l=0;l<=1;l++) {
     }          for (j=1;j<=n;j++) {
   }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for(jj=1; jj<= nlstate+ndeath; jj++){          }
      printf("%lf ",ps[ii][jj]);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
    }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     printf("\n ");        }
     }  #endif
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        free_vector(xit,1,n); 
   goto end;*/        free_vector(xits,1,n); 
     return ps;        free_vector(ptt,1,n); 
 }        free_vector(pt,1,n); 
         return; 
 /**************** Product of 2 matrices ******************/      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      for (j=1;j<=n;j++) { 
 {        ptt[j]=2.0*p[j]-pt[j]; 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        xit[j]=p[j]-pt[j]; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        pt[j]=p[j]; 
   /* in, b, out are matrice of pointers which should have been initialized      } 
      before: only the contents of out is modified. The function returns      fptt=(*func)(ptt); 
      a pointer to pointers identical to out */      if (fptt < fp) { 
   long i, j, k;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   for(i=nrl; i<= nrh; i++)        if (t < 0.0) { 
     for(k=ncolol; k<=ncoloh; k++)          linmin(p,xit,n,fret,func); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)          for (j=1;j<=n;j++) { 
         out[i][k] +=in[i][j]*b[j][k];            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
   return out;          }
 }  #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);
 /************* Higher Matrix Product ***************/          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            fprintf(ficlog," %.12e",xit[j]);
 {          }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          printf("\n");
      duration (i.e. until          fprintf(ficlog,"\n");
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  #endif
      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).      } 
      Model is determined by parameters x and covariates have to be    } 
      included manually here.  } 
   
      */  /**** Prevalence limit (stable prevalence)  ****************/
   
   int i, j, d, h, k;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   double **out, cov[NCOVMAX];  {
   double **newm;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)    int i, ii,j,k;
     for (j=1;j<=nlstate+ndeath;j++){    double min, max, maxmin, maxmax,sumnew=0.;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    double **matprod2();
       po[i][j][0]=(i==j ? 1.0 : 0.0);    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double agefin, delaymax=50 ; /* Max number of years to converge */
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){    for (ii=1;ii<=nlstate+ndeath;ii++)
       newm=savm;      for (j=1;j<=nlstate+ndeath;j++){
       /* Covariates have to be included here again */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       cov[1]=1.;      }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       if (cptcovn>0){     cov[1]=1.;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];   
     }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      newm=savm;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      /* Covariates have to be included here again */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));       cov[2]=agefin;
       savm=oldm;    
       oldm=newm;        for (k=1; k<=cptcovn;k++) {
     }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for(i=1; i<=nlstate+ndeath; i++)          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       for(j=1;j<=nlstate+ndeath;j++) {        }
         po[i][j][h]=newm[i][j];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        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]]];
       }  
   } /* end h */        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   return po;        /*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);
   
 /*************** log-likelihood *************/      savm=oldm;
 double func( double *x)      oldm=newm;
 {      maxmax=0.;
   int i, ii, j, k, mi, d;      for(j=1;j<=nlstate;j++){
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        min=1.;
   double **out;        max=0.;
   double sw; /* Sum of weights */        for(i=1; i<=nlstate; i++) {
   double lli; /* Individual log likelihood */          sumnew=0;
   long ipmx;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /*extern weight */          prlim[i][j]= newm[i][j]/(1-sumnew);
   /* We are differentiating ll according to initial status */          max=FMAX(max,prlim[i][j]);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          min=FMIN(min,prlim[i][j]);
   /*for(i=1;i<imx;i++)        }
 printf(" %d\n",s[4][i]);        maxmin=max-min;
   */        maxmax=FMAX(maxmax,maxmin);
       }
   for(k=1; k<=nlstate; k++) ll[k]=0.;      if(maxmax < ftolpl){
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        return prlim;
        for(mi=1; mi<= wav[i]-1; mi++){      }
       for (ii=1;ii<=nlstate+ndeath;ii++)    }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  }
             for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  /*************** transition probabilities ***************/ 
           cov[1]=1.;  
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
           if (cptcovn>0){  {
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];    double s1, s2;
             }    /*double t34;*/
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    int i,j,j1, nc, ii, jj;
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
           savm=oldm;      for(i=1; i<= nlstate; i++){
           oldm=newm;      for(j=1; j<i;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           /*s2 += param[i][j][nc]*cov[nc];*/
       } /* end mult */          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);*/
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        ps[i][j]=s2;
       ipmx +=1;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       sw += weight[i];      }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      for(j=i+1; j<=nlstate+ndeath;j++){
     } /* end of wave */        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   } /* end of individual */          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        ps[i][j]=s2;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      }
   return -l;    }
 }      /*ps[3][2]=1;*/
   
     for(i=1; i<= nlstate; i++){
 /*********** Maximum Likelihood Estimation ***************/       s1=0;
       for(j=1; j<i; j++)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        s1+=exp(ps[i][j]);
 {      for(j=i+1; j<=nlstate+ndeath; j++)
   int i,j, iter;        s1+=exp(ps[i][j]);
   double **xi,*delti;      ps[i][i]=1./(s1+1.);
   double fret;      for(j=1; j<i; j++)
   xi=matrix(1,npar,1,npar);        ps[i][j]= exp(ps[i][j])*ps[i][i];
   for (i=1;i<=npar;i++)      for(j=i+1; j<=nlstate+ndeath; j++)
     for (j=1;j<=npar;j++)        ps[i][j]= exp(ps[i][j])*ps[i][i];
       xi[i][j]=(i==j ? 1.0 : 0.0);      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   printf("Powell\n");    } /* end i */
   powell(p,xi,npar,ftol,&iter,&fret,func);  
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      for(jj=1; jj<= nlstate+ndeath; jj++){
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        ps[ii][jj]=0;
         ps[ii][ii]=1;
 }      }
     }
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  
 {    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   double  **a,**y,*x,pd;      for(jj=1; jj<= nlstate+ndeath; jj++){
   double **hess;       printf("%lf ",ps[ii][jj]);
   int i, j,jk;     }
   int *indx;      printf("\n ");
       }
   double hessii(double p[], double delta, int theta, double delti[]);      printf("\n ");printf("%lf ",cov[2]);*/
   double hessij(double p[], double delti[], int i, int j);  /*
   void lubksb(double **a, int npar, int *indx, double b[]) ;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   void ludcmp(double **a, int npar, int *indx, double *d) ;    goto end;*/
       return ps;
   }
   hess=matrix(1,npar,1,npar);  
   /**************** Product of 2 matrices ******************/
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     printf("%d",i);fflush(stdout);  {
     hess[i][i]=hessii(p,ftolhess,i,delti);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     /*printf(" %f ",p[i]);*/       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
   for (i=1;i<=npar;i++) {       a pointer to pointers identical to out */
     for (j=1;j<=npar;j++)  {    long i, j, k;
       if (j>i) {    for(i=nrl; i<= nrh; i++)
         printf(".%d%d",i,j);fflush(stdout);      for(k=ncolol; k<=ncoloh; k++)
         hess[i][j]=hessij(p,delti,i,j);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         hess[j][i]=hess[i][j];          out[i][k] +=in[i][j]*b[j][k];
       }  
     }    return out;
   }  }
   printf("\n");  
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /************* Higher Matrix Product ***************/
    
   a=matrix(1,npar,1,npar);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   y=matrix(1,npar,1,npar);  {
   x=vector(1,npar);    /* Computes the transition matrix starting at age 'age' over 
   indx=ivector(1,npar);       'nhstepm*hstepm*stepm' months (i.e. until
   for (i=1;i<=npar;i++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];       nhstepm*hstepm matrices. 
   ludcmp(a,npar,indx,&pd);       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=1;j<=npar;j++) {       for the memory).
     for (i=1;i<=npar;i++) x[i]=0;       Model is determined by parameters x and covariates have to be 
     x[j]=1;       included manually here. 
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){       */
       matcov[i][j]=x[i];  
     }    int i, j, d, h, k;
   }    double **out, cov[NCOVMAX];
     double **newm;
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {    /* Hstepm could be zero and should return the unit matrix */
     for (j=1;j<=npar;j++) {    for (i=1;i<=nlstate+ndeath;i++)
       printf("%.3e ",hess[i][j]);      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[i][j]=(i==j ? 1.0 : 0.0);
     printf("\n");        po[i][j][0]=(i==j ? 1.0 : 0.0);
   }      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   /* Recompute Inverse */    for(h=1; h <=nhstepm; h++){
   for (i=1;i<=npar;i++)      for(d=1; d <=hstepm; d++){
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        newm=savm;
   ludcmp(a,npar,indx,&pd);        /* Covariates have to be included here again */
         cov[1]=1.;
   /*  printf("\n#Hessian matrix recomputed#\n");        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for (j=1;j<=npar;j++) {        for (k=1; k<=cptcovage;k++)
     for (i=1;i<=npar;i++) x[i]=0;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     x[j]=1;        for (k=1; k<=cptcovprod;k++)
     lubksb(a,npar,indx,x);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     printf("\n");        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   */        savm=oldm;
         oldm=newm;
   free_matrix(a,1,npar,1,npar);      }
   free_matrix(y,1,npar,1,npar);      for(i=1; i<=nlstate+ndeath; i++)
   free_vector(x,1,npar);        for(j=1;j<=nlstate+ndeath;j++) {
   free_ivector(indx,1,npar);          po[i][j][h]=newm[i][j];
   free_matrix(hess,1,npar,1,npar);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
            */
         }
 }    } /* end h */
     return po;
 /*************** hessian matrix ****************/  }
 double hessii( double x[], double delta, int theta, double delti[])  
 {  
   int i;  /*************** log-likelihood *************/
   int l=1, lmax=20;  double func( double *x)
   double k1,k2;  {
   double p2[NPARMAX+1];    int i, ii, j, k, mi, d, kk;
   double res;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double **out;
   double fx;    double sw; /* Sum of weights */
   int k=0,kmax=10;    double lli; /* Individual log likelihood */
   double l1;    int s1, s2;
     double bbh, survp;
   fx=func(x);    long ipmx;
   for (i=1;i<=npar;i++) p2[i]=x[i];    /*extern weight */
   for(l=0 ; l <=lmax; l++){    /* We are differentiating ll according to initial status */
     l1=pow(10,l);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     delts=delt;    /*for(i=1;i<imx;i++) 
     for(k=1 ; k <kmax; k=k+1){      printf(" %d\n",s[4][i]);
       delt = delta*(l1*k);    */
       p2[theta]=x[theta] +delt;    cov[1]=1.;
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;    for(k=1; k<=nlstate; k++) ll[k]=0.;
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */    if(mle==1){
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
              for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 #ifdef DEBUG        for(mi=1; mi<= wav[i]-1; mi++){
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          for (ii=1;ii<=nlstate+ndeath;ii++)
 #endif            for (j=1;j<=nlstate+ndeath;j++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         k=kmax;            }
       }          for(d=0; d<dh[mi][i]; d++){
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            newm=savm;
         k=kmax; l=lmax*10.;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         delts=delt;            }
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   delti[theta]=delts;            oldm=newm;
   return res;          } /* end mult */
          
 }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias and large stepm.
 double hessij( double x[], double delti[], int thetai,int thetaj)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 {           * (in months) between two waves is not a multiple of stepm, we rounded to 
   int i;           * the nearest (and in case of equal distance, to the lowest) interval but now
   int l=1, l1, lmax=20;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double k1,k2,k3,k4,res,fx;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   double p2[NPARMAX+1];           * probability in order to take into account the bias as a fraction of the way
   int k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
   fx=func(x);           * For stepm=1 the results are the same as for previous versions of Imach.
   for (k=1; k<=2; k++) {           * For stepm > 1 the results are less biased than in previous versions. 
     for (i=1;i<=npar;i++) p2[i]=x[i];           */
     p2[thetai]=x[thetai]+delti[thetai]/k;          s1=s[mw[mi][i]][i];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          s2=s[mw[mi+1][i]][i];
     k1=func(p2)-fx;          bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias is positive if real duration
     p2[thetai]=x[thetai]+delti[thetai]/k;           * is higher than the multiple of stepm and negative otherwise.
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           */
     k2=func(p2)-fx;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
            if( s2 > nlstate){ 
     p2[thetai]=x[thetai]-delti[thetai]/k;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;               to the likelihood is the probability to die between last step unit time and current 
     k3=func(p2)-fx;               step unit time, which is also the differences between probability to die before dh 
                 and probability to die before dh-stepm . 
     p2[thetai]=x[thetai]-delti[thetai]/k;               In version up to 0.92 likelihood was computed
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          as if date of death was unknown. Death was treated as any other
     k4=func(p2)-fx;          health state: the date of the interview describes the actual state
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          and not the date of a change in health state. The former idea was
 #ifdef DEBUG          to consider that at each interview the state was recorded
     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);          (healthy, disable or death) and IMaCh was corrected; but when we
 #endif          introduced the exact date of death then we should have modified
   }          the contribution of an exact death to the likelihood. This new
   return res;          contribution is smaller and very dependent of the step unit
 }          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
 /************** Inverse of matrix **************/          interview up to one month before death multiplied by the
 void ludcmp(double **a, int n, int *indx, double *d)          probability to die within a month. Thanks to Chris
 {          Jackson for correcting this bug.  Former versions increased
   int i,imax,j,k;          mortality artificially. The bad side is that we add another loop
   double big,dum,sum,temp;          which slows down the processing. The difference can be up to 10%
   double *vv;          lower mortality.
              */
   vv=vector(1,n);            lli=log(out[s1][s2] - savm[s1][s2]);
   *d=1.0;          }else{
   for (i=1;i<=n;i++) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     big=0.0;            /*  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 */
     for (j=1;j<=n;j++)          } 
       if ((temp=fabs(a[i][j])) > big) big=temp;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          /*if(lli ==000.0)*/
     vv[i]=1.0/big;          /*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;
   for (j=1;j<=n;j++) {          sw += weight[i];
     for (i=1;i<j;i++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       sum=a[i][j];        } /* end of wave */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      } /* end of individual */
       a[i][j]=sum;    }  else if(mle==2){
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     big=0.0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (i=j;i<=n;i++) {        for(mi=1; mi<= wav[i]-1; mi++){
       sum=a[i][j];          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (k=1;k<j;k++)            for (j=1;j<=nlstate+ndeath;j++){
         sum -= a[i][k]*a[k][j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       a[i][j]=sum;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if ( (dum=vv[i]*fabs(sum)) >= big) {            }
         big=dum;          for(d=0; d<=dh[mi][i]; d++){
         imax=i;            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
     if (j != imax) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for (k=1;k<=n;k++) {            }
         dum=a[imax][k];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         a[imax][k]=a[j][k];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         a[j][k]=dum;            savm=oldm;
       }            oldm=newm;
       *d = -(*d);          } /* end mult */
       vv[imax]=vv[j];        
     }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     indx[j]=imax;          /* But now since version 0.9 we anticipate for bias and large stepm.
     if (a[j][j] == 0.0) a[j][j]=TINY;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     if (j != n) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
       dum=1.0/(a[j][j]);           * the nearest (and in case of equal distance, to the lowest) interval but now
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     }           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   }           * probability in order to take into account the bias as a fraction of the way
   free_vector(vv,1,n);  /* Doesn't work */           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 ;           * -stepm/2 to stepm/2 .
 }           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
 void lubksb(double **a, int n, int *indx, double b[])           */
 {          s1=s[mw[mi][i]][i];
   int i,ii=0,ip,j;          s2=s[mw[mi+1][i]][i];
   double sum;          bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias is positive if real duration
   for (i=1;i<=n;i++) {           * is higher than the multiple of stepm and negative otherwise.
     ip=indx[i];           */
     sum=b[ip];          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 */
     b[ip]=b[i];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     if (ii)          /*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 */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     else if (sum) ii=i;          /*if(lli ==000.0)*/
     b[i]=sum;          /*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;
   for (i=n;i>=1;i--) {          sw += weight[i];
     sum=b[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        } /* end of wave */
     b[i]=sum/a[i][i];      } /* end of individual */
   }    }  else if(mle==3){  /* exponential inter-extrapolation */
 }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 /************ Frequencies ********************/        for(mi=1; mi<= wav[i]-1; mi++){
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)          for (ii=1;ii<=nlstate+ndeath;ii++)
 {  /* Some frequencies */            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ***freq; /* Frequencies */            }
   double *pp;          for(d=0; d<dh[mi][i]; d++){
   double pos;            newm=savm;
   FILE *ficresp;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   char fileresp[FILENAMELENGTH];            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   pp=vector(1,nlstate);            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   strcpy(fileresp,"p");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   strcat(fileresp,fileres);            savm=oldm;
   if((ficresp=fopen(fileresp,"w"))==NULL) {            oldm=newm;
     printf("Problem with prevalence resultfile: %s\n", fileresp);          } /* end mult */
     exit(0);        
   }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          /* But now since version 0.9 we anticipate for bias and large stepm.
   j1=0;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
   j=cptcovn;           * the nearest (and in case of equal distance, to the lowest) interval but now
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * 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(k1=1; k1<=j;k1++){           * probability in order to take into account the bias as a fraction of the way
    for(i1=1; i1<=ncodemax[k1];i1++){           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
        j1++;           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
         for (i=-1; i<=nlstate+ndeath; i++)             * For stepm > 1 the results are less biased than in previous versions. 
          for (jk=-1; jk<=nlstate+ndeath; jk++)             */
            for(m=agemin; m <= agemax+3; m++)          s1=s[mw[mi][i]][i];
              freq[i][jk][m]=0;          s2=s[mw[mi+1][i]][i];
                  bbh=(double)bh[mi][i]/(double)stepm; 
        for (i=1; i<=imx; i++) {          /* bias is positive if real duration
          bool=1;           * is higher than the multiple of stepm and negative otherwise.
          if  (cptcovn>0) {           */
            for (z1=1; z1<=cptcovn; z1++)          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=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 */
          }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           if (bool==1) {          /*if(lli ==000.0)*/
            for(m=firstpass; m<=lastpass-1; m++){          /*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(agev[m][i]==0) agev[m][i]=agemax+1;          ipmx +=1;
              if(agev[m][i]==1) agev[m][i]=agemax+2;          sw += weight[i];
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        } /* end of wave */
            }      } /* end of individual */
          }    }else{  /* ml=4 no inter-extrapolation */
        }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if  (cptcovn>0) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          fprintf(ficresp, "\n#Variable");        for(mi=1; mi<= wav[i]-1; mi++){
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);          for (ii=1;ii<=nlstate+ndeath;ii++)
        }            for (j=1;j<=nlstate+ndeath;j++){
        fprintf(ficresp, "\n#");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        for(i=1; i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);            }
        fprintf(ficresp, "\n");          for(d=0; d<dh[mi][i]; d++){
                    newm=savm;
   for(i=(int)agemin; i <= (int)agemax+3; i++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if(i==(int)agemax+3)            for (kk=1; kk<=cptcovage;kk++) {
       printf("Total");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     else            }
       printf("Age %d", i);          
     for(jk=1; jk <=nlstate ; jk++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         pp[jk] += freq[jk][m][i];            savm=oldm;
     }            oldm=newm;
     for(jk=1; jk <=nlstate ; jk++){          } /* end mult */
       for(m=-1, pos=0; m <=0 ; m++)        
         pos += freq[jk][m][i];          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       if(pp[jk]>=1.e-10)          ipmx +=1;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          sw += weight[i];
       else          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        } /* end of wave */
     }      } /* end of individual */
     for(jk=1; jk <=nlstate ; jk++){    } /* End of if */
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         pp[jk] += freq[jk][m][i];    /* 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 */
     for(jk=1,pos=0; jk <=nlstate ; jk++)    return -l;
       pos += pp[jk];  }
     for(jk=1; jk <=nlstate ; jk++){  
       if(pos>=1.e-5)  
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  /*********** Maximum Likelihood Estimation ***************/
       else  
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       if( i <= (int) agemax){  {
         if(pos>=1.e-5)    int i,j, iter;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    double **xi;
       else    double fret;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    char filerespow[FILENAMELENGTH];
       }    xi=matrix(1,npar,1,npar);
     }    for (i=1;i<=npar;i++)
     for(jk=-1; jk <=nlstate+ndeath; jk++)      for (j=1;j<=npar;j++)
       for(m=-1; m <=nlstate+ndeath; m++)        xi[i][j]=(i==j ? 1.0 : 0.0);
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     if(i <= (int) agemax)    strcpy(filerespow,"pow"); 
       fprintf(ficresp,"\n");    strcat(filerespow,fileres);
     printf("\n");    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", filerespow);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
  }    }
      fprintf(ficrespow,"# Powell\n# iter -2*LL");
   fclose(ficresp);    for (i=1;i<=nlstate;i++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for(j=1;j<=nlstate+ndeath;j++)
   free_vector(pp,1,nlstate);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
 }  /* End of Freq */    powell(p,xi,npar,ftol,&iter,&fret,func);
   
 /************* Waves Concatenation ***************/    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  
      Death is a valid wave (if date is known).  }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  /**** Computes Hessian and covariance matrix ***/
      and mw[mi+1][i]. dh depends on stepm.  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
      */  {
     double  **a,**y,*x,pd;
   int i, mi, m;    double **hess;
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    int i, j,jk;
 float sum=0.;    int *indx;
   
   for(i=1; i<=imx; i++){    double hessii(double p[], double delta, int theta, double delti[]);
     mi=0;    double hessij(double p[], double delti[], int i, int j);
     m=firstpass;    void lubksb(double **a, int npar, int *indx, double b[]) ;
     while(s[m][i] <= nlstate){    void ludcmp(double **a, int npar, int *indx, double *d) ;
       if(s[m][i]>=1)  
         mw[++mi][i]=m;    hess=matrix(1,npar,1,npar);
       if(m >=lastpass)  
         break;    printf("\nCalculation of the hessian matrix. Wait...\n");
       else    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         m++;    for (i=1;i<=npar;i++){
     }/* end while */      printf("%d",i);fflush(stdout);
     if (s[m][i] > nlstate){      fprintf(ficlog,"%d",i);fflush(ficlog);
       mi++;     /* Death is another wave */      hess[i][i]=hessii(p,ftolhess,i,delti);
       /* if(mi==0)  never been interviewed correctly before death */      /*printf(" %f ",p[i]);*/
          /* Only death is a correct wave */      /*printf(" %lf ",hess[i][i]);*/
       mw[mi][i]=m;    }
     }    
     for (i=1;i<=npar;i++) {
     wav[i]=mi;      for (j=1;j<=npar;j++)  {
     if(mi==0)        if (j>i) { 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          printf(".%d%d",i,j);fflush(stdout);
   }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j);
   for(i=1; i<=imx; i++){          hess[j][i]=hess[i][j];    
     for(mi=1; mi<wav[i];mi++){          /*printf(" %lf ",hess[i][j]);*/
       if (stepm <=0)        }
         dh[mi][i]=1;      }
       else{    }
         if (s[mw[mi+1][i]][i] > nlstate) {    printf("\n");
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    fprintf(ficlog,"\n");
           if(j=0) j=1;  /* Survives at least one month after exam */  
         }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         else{    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    
           k=k+1;    a=matrix(1,npar,1,npar);
           if (j >= jmax) jmax=j;    y=matrix(1,npar,1,npar);
           else if (j <= jmin)jmin=j;    x=vector(1,npar);
           sum=sum+j;    indx=ivector(1,npar);
         }    for (i=1;i<=npar;i++)
         jk= j/stepm;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         jl= j -jk*stepm;    ludcmp(a,npar,indx,&pd);
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)    for (j=1;j<=npar;j++) {
           dh[mi][i]=jk;      for (i=1;i<=npar;i++) x[i]=0;
         else      x[j]=1;
           dh[mi][i]=jk+1;      lubksb(a,npar,indx,x);
         if(dh[mi][i]==0)      for (i=1;i<=npar;i++){ 
           dh[mi][i]=1; /* At least one step */        matcov[i][j]=x[i];
       }      }
     }    }
   }  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);    printf("\n#Hessian matrix#\n");
 }    fprintf(ficlog,"\n#Hessian matrix#\n");
 /*********** Tricode ****************************/    for (i=1;i<=npar;i++) { 
 void tricode(int *Tvar, int **nbcode, int imx)      for (j=1;j<=npar;j++) { 
 {        printf("%.3e ",hess[i][j]);
   int Ndum[80],ij, k, j, i;        fprintf(ficlog,"%.3e ",hess[i][j]);
   int cptcode=0;      }
   for (k=0; k<79; k++) Ndum[k]=0;      printf("\n");
   for (k=1; k<=7; k++) ncodemax[k]=0;      fprintf(ficlog,"\n");
      }
   for (j=1; j<=cptcovn; j++) {  
     for (i=1; i<=imx; i++) {    /* Recompute Inverse */
       ij=(int)(covar[Tvar[j]][i]);    for (i=1;i<=npar;i++)
       Ndum[ij]++;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       if (ij > cptcode) cptcode=ij;    ludcmp(a,npar,indx,&pd);
     }  
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/    /*  printf("\n#Hessian matrix recomputed#\n");
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;    for (j=1;j<=npar;j++) {
     }      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
     ij=1;      lubksb(a,npar,indx,x);
     for (i=1; i<=ncodemax[j]; i++) {      for (i=1;i<=npar;i++){ 
       for (k=0; k<=79; k++) {        y[i][j]=x[i];
         if (Ndum[k] != 0) {        printf("%.3e ",y[i][j]);
           nbcode[Tvar[j]][ij]=k;        fprintf(ficlog,"%.3e ",y[i][j]);
           ij++;      }
         }      printf("\n");
         if (ij > ncodemax[j]) break;      fprintf(ficlog,"\n");
       }      }
     }    */
   }    
     free_matrix(a,1,npar,1,npar);
   }    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
 /*********** Health Expectancies ****************/    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  
 {  
   /* Health expectancies */  }
   int i, j, nhstepm, hstepm, h;  
   double age, agelim,hf;  /*************** hessian matrix ****************/
   double ***p3mat;  double hessii( double x[], double delta, int theta, double delti[])
    {
   fprintf(ficreseij,"# Health expectancies\n");    int i;
   fprintf(ficreseij,"# Age");    int l=1, lmax=20;
   for(i=1; i<=nlstate;i++)    double k1,k2;
     for(j=1; j<=nlstate;j++)    double p2[NPARMAX+1];
       fprintf(ficreseij," %1d-%1d",i,j);    double res;
   fprintf(ficreseij,"\n");    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
   hstepm=1*YEARM; /*  Every j years of age (in month) */    int k=0,kmax=10;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double l1;
   
   agelim=AGESUP;    fx=func(x);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (i=1;i<=npar;i++) p2[i]=x[i];
     /* nhstepm age range expressed in number of stepm */    for(l=0 ; l <=lmax; l++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);      l1=pow(10,l);
     /* Typically if 20 years = 20*12/6=40 stepm */      delts=delt;
     if (stepm >= YEARM) hstepm=1;      for(k=1 ; k <kmax; k=k+1){
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        delt = delta*(l1*k);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        p2[theta]=x[theta] +delt;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        k1=func(p2)-fx;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        p2[theta]=x[theta]-delt;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     for(i=1; i<=nlstate;i++)        
       for(j=1; j<=nlstate;j++)  #ifdef DEBUG
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        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);
           eij[i][j][(int)age] +=p3mat[i][j][h];        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         }  #endif
            /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     hf=1;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     if (stepm >= YEARM) hf=stepm/YEARM;          k=kmax;
     fprintf(ficreseij,"%.0f",age );        }
     for(i=1; i<=nlstate;i++)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       for(j=1; j<=nlstate;j++){          k=kmax; l=lmax*10.;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);        }
       }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     fprintf(ficreseij,"\n");          delts=delt;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
   }      }
 }    }
     delti[theta]=delts;
 /************ Variance ******************/    return res; 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    
 {  }
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  double hessij( double x[], double delti[], int thetai,int thetaj)
   double **newm;  {
   double **dnewm,**doldm;    int i;
   int i, j, nhstepm, hstepm, h;    int l=1, l1, lmax=20;
   int k, cptcode;    double k1,k2,k3,k4,res,fx;
    double *xp;    double p2[NPARMAX+1];
   double **gp, **gm;    int k;
   double ***gradg, ***trgradg;  
   double ***p3mat;    fx=func(x);
   double age,agelim;    for (k=1; k<=2; k++) {
   int theta;      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
    fprintf(ficresvij,"# Covariances of life expectancies\n");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   fprintf(ficresvij,"# Age");      k1=func(p2)-fx;
   for(i=1; i<=nlstate;i++)    
     for(j=1; j<=nlstate;j++)      p2[thetai]=x[thetai]+delti[thetai]/k;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   fprintf(ficresvij,"\n");      k2=func(p2)-fx;
     
   xp=vector(1,npar);      p2[thetai]=x[thetai]-delti[thetai]/k;
   dnewm=matrix(1,nlstate,1,npar);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   doldm=matrix(1,nlstate,1,nlstate);      k3=func(p2)-fx;
      
   hstepm=1*YEARM; /* Every year of age */      p2[thetai]=x[thetai]-delti[thetai]/k;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   agelim = AGESUP;      k4=func(p2)-fx;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  #ifdef DEBUG
     if (stepm >= YEARM) hstepm=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);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      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);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #endif
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    }
     gp=matrix(0,nhstepm,1,nlstate);    return res;
     gm=matrix(0,nhstepm,1,nlstate);  }
   
     for(theta=1; theta <=npar; theta++){  /************** Inverse of matrix **************/
       for(i=1; i<=npar; i++){ /* Computes gradient */  void ludcmp(double **a, int n, int *indx, double *d) 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  { 
       }    int i,imax,j,k; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double big,dum,sum,temp; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double *vv; 
       for(j=1; j<= nlstate; j++){   
         for(h=0; h<=nhstepm; h++){    vv=vector(1,n); 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    *d=1.0; 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    for (i=1;i<=n;i++) { 
         }      big=0.0; 
       }      for (j=1;j<=n;j++) 
            if ((temp=fabs(a[i][j])) > big) big=temp; 
       for(i=1; i<=npar; i++) /* Computes gradient */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      vv[i]=1.0/big; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (j=1;j<=n;j++) { 
       for(j=1; j<= nlstate; j++){      for (i=1;i<j;i++) { 
         for(h=0; h<=nhstepm; h++){        sum=a[i][j]; 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        a[i][j]=sum; 
         }      } 
       }      big=0.0; 
       for(j=1; j<= nlstate; j++)      for (i=j;i<=n;i++) { 
         for(h=0; h<=nhstepm; h++){        sum=a[i][j]; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        for (k=1;k<j;k++) 
         }          sum -= a[i][k]*a[k][j]; 
     } /* End theta */        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          big=dum; 
           imax=i; 
     for(h=0; h<=nhstepm; h++)        } 
       for(j=1; j<=nlstate;j++)      } 
         for(theta=1; theta <=npar; theta++)      if (j != imax) { 
           trgradg[h][j][theta]=gradg[h][theta][j];        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
     for(i=1;i<=nlstate;i++)          a[imax][k]=a[j][k]; 
       for(j=1;j<=nlstate;j++)          a[j][k]=dum; 
         vareij[i][j][(int)age] =0.;        } 
     for(h=0;h<=nhstepm;h++){        *d = -(*d); 
       for(k=0;k<=nhstepm;k++){        vv[imax]=vv[j]; 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      } 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      indx[j]=imax; 
         for(i=1;i<=nlstate;i++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
           for(j=1;j<=nlstate;j++)      if (j != n) { 
             vareij[i][j][(int)age] += doldm[i][j];        dum=1.0/(a[j][j]); 
       }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     }      } 
     h=1;    } 
     if (stepm >= YEARM) h=stepm/YEARM;    free_vector(vv,1,n);  /* Doesn't work */
     fprintf(ficresvij,"%.0f ",age );  ;
     for(i=1; i<=nlstate;i++)  } 
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  void lubksb(double **a, int n, int *indx, double b[]) 
       }  { 
     fprintf(ficresvij,"\n");    int i,ii=0,ip,j; 
     free_matrix(gp,0,nhstepm,1,nlstate);    double sum; 
     free_matrix(gm,0,nhstepm,1,nlstate);   
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    for (i=1;i<=n;i++) { 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      ip=indx[i]; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      sum=b[ip]; 
   } /* End age */      b[ip]=b[i]; 
        if (ii) 
   free_vector(xp,1,npar);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   free_matrix(doldm,1,nlstate,1,npar);      else if (sum) ii=i; 
   free_matrix(dnewm,1,nlstate,1,nlstate);      b[i]=sum; 
     } 
 }    for (i=n;i>=1;i--) { 
       sum=b[i]; 
 /************ Variance of prevlim ******************/      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 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)      b[i]=sum/a[i][i]; 
 {    } 
   /* Variance of prevalence limit */  } 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;  /************ Frequencies ********************/
   double **dnewm,**doldm;  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)
   int i, j, nhstepm, hstepm;  {  /* Some frequencies */
   int k, cptcode;    
   double *xp;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   double *gp, *gm;    int first;
   double **gradg, **trgradg;    double ***freq; /* Frequencies */
   double age,agelim;    double *pp, **prop;
   int theta;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
        FILE *ficresp;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    char fileresp[FILENAMELENGTH];
   fprintf(ficresvpl,"# Age");    
   for(i=1; i<=nlstate;i++)    pp=vector(1,nlstate);
       fprintf(ficresvpl," %1d-%1d",i,i);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   fprintf(ficresvpl,"\n");    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
   xp=vector(1,npar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   dnewm=matrix(1,nlstate,1,npar);      printf("Problem with prevalence resultfile: %s\n", fileresp);
   doldm=matrix(1,nlstate,1,nlstate);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
        exit(0);
   hstepm=1*YEARM; /* Every year of age */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   agelim = AGESUP;    j1=0;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    j=cptcoveff;
     if (stepm >= YEARM) hstepm=1;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);    first=1;
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
     for(theta=1; theta <=npar; theta++){        j1++;
       for(i=1; i<=npar; i++){ /* Computes gradient */        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          scanf("%d", i);*/
       }        for (i=-1; i<=nlstate+ndeath; i++)  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       for(i=1;i<=nlstate;i++)            for(m=iagemin; m <= iagemax+3; m++)
         gp[i] = prlim[i][i];              freq[i][jk][m]=0;
      
       for(i=1; i<=npar; i++) /* Computes gradient */      for (i=1; i<=nlstate; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for(m=iagemin; m <= iagemax+3; m++)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          prop[i][m]=0;
       for(i=1;i<=nlstate;i++)        
         gm[i] = prlim[i][i];        dateintsum=0;
         k2cpt=0;
       for(i=1;i<=nlstate;i++)        for (i=1; i<=imx; i++) {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          bool=1;
     } /* End theta */          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
     trgradg =matrix(1,nlstate,1,npar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
     for(j=1; j<=nlstate;j++)          }
       for(theta=1; theta <=npar; theta++)          if (bool==1){
         trgradg[j][theta]=gradg[theta][j];            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
     for(i=1;i<=nlstate;i++)              if ((k2>=dateprev1) && (k2<=dateprev2)) {
       varpl[i][(int)age] =0.;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     for(i=1;i<=nlstate;i++)                if (m<lastpass) {
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */                  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];
     fprintf(ficresvpl,"%.0f ",age );                }
     for(i=1; i<=nlstate;i++)                
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     fprintf(ficresvpl,"\n");                  dateintsum=dateintsum+k2;
     free_vector(gp,1,nlstate);                  k2cpt++;
     free_vector(gm,1,nlstate);                }
     free_matrix(gradg,1,npar,1,nlstate);              }
     free_matrix(trgradg,1,nlstate,1,npar);            }
   } /* End age */          }
         }
   free_vector(xp,1,npar);         
   free_matrix(doldm,1,nlstate,1,npar);        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   free_matrix(dnewm,1,nlstate,1,nlstate);  
         if  (cptcovn>0) {
 }          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
         }
 /***********************************************/        for(i=1; i<=nlstate;i++) 
 /**************** Main Program *****************/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 /***********************************************/        fprintf(ficresp, "\n");
         
 /*int main(int argc, char *argv[])*/        for(i=iagemin; i <= iagemax+3; i++){
 int main()          if(i==iagemax+3){
 {            fprintf(ficlog,"Total");
           }else{
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;            if(first==1){
   double agedeb, agefin,hf;              first=0;
   double agemin=1.e20, agemax=-1.e20;              printf("See log file for details...\n");
             }
   double fret;            fprintf(ficlog,"Age %d", i);
   double **xi,tmp,delta;          }
           for(jk=1; jk <=nlstate ; jk++){
   double dum; /* Dummy variable */            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   double ***p3mat;              pp[jk] += freq[jk][m][i]; 
   int *indx;          }
   char line[MAXLINE], linepar[MAXLINE];          for(jk=1; jk <=nlstate ; jk++){
   char title[MAXLINE];            for(m=-1, pos=0; m <=0 ; m++)
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];              pos += freq[jk][m][i];
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];            if(pp[jk]>=1.e-10){
   char filerest[FILENAMELENGTH];              if(first==1){
   char fileregp[FILENAMELENGTH];              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];              }
   int firstobs=1, lastobs=10;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   int sdeb, sfin; /* Status at beginning and end */            }else{
   int c,  h , cpt,l;              if(first==1)
   int ju,jl, mi;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            }
            }
   int hstepm, nhstepm;  
   double bage, fage, age, agelim, agebase;          for(jk=1; jk <=nlstate ; jk++){
   double ftolpl=FTOL;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   double **prlim;              pp[jk] += freq[jk][m][i];
   double *severity;          }       
   double ***param; /* Matrix of parameters */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double  *p;            pos += pp[jk];
   double **matcov; /* Matrix of covariance */            posprop += prop[jk][i];
   double ***delti3; /* Scale */          }
   double *delti; /* Scale */          for(jk=1; jk <=nlstate ; jk++){
   double ***eij, ***vareij;            if(pos>=1.e-5){
   double **varpl; /* Variances of prevalence limits by age */              if(first==1)
   double *epj, vepp;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   char *alph[]={"a","a","b","c","d","e"}, str[4];            }else{
               if(first==1)
   char z[1]="c", occ;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 #include <sys/time.h>              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 #include <time.h>            }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            if( i <= iagemax){
   /* long total_usecs;              if(pos>=1.e-5){
   struct timeval start_time, end_time;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                  probs[i][jk][j1]= pp[jk]/pos;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
               else
   printf("\nIMACH, Version 0.64a");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   printf("\nEnter the parameter file name: ");            }
           }
 #ifdef windows          
   scanf("%s",pathtot);          for(jk=-1; jk <=nlstate+ndeath; jk++)
   getcwd(pathcd, size);            for(m=-1; m <=nlstate+ndeath; m++)
   /*cygwin_split_path(pathtot,path,optionfile);              if(freq[jk][m][i] !=0 ) {
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/              if(first==1)
   /* cutv(path,optionfile,pathtot,'\\');*/                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
 split(pathtot, path,optionfile);              }
   chdir(path);          if(i <= iagemax)
   replace(pathc,path);            fprintf(ficresp,"\n");
 #endif          if(first==1)
 #ifdef unix            printf("Others in log...\n");
   scanf("%s",optionfile);          fprintf(ficlog,"\n");
 #endif        }
       }
 /*-------- arguments in the command line --------*/    }
     dateintmean=dateintsum/k2cpt; 
   strcpy(fileres,"r");   
   strcat(fileres, optionfile);    fclose(ficresp);
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   /*---------arguments file --------*/    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    /* End of Freq */
     printf("Problem with optionfile %s\n",optionfile);  }
     goto end;  
   }  /************ Prevalence ********************/
   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)
   strcpy(filereso,"o");  {  
   strcat(filereso,fileres);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   if((ficparo=fopen(filereso,"w"))==NULL) {       in each health status at the date of interview (if between dateprev1 and dateprev2).
     printf("Problem with Output resultfile: %s\n", filereso);goto end;       We still use firstpass and lastpass as another selection.
   }    */
    
   /* Reads comments: lines beginning with '#' */    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   while((c=getc(ficpar))=='#' && c!= EOF){    double ***freq; /* Frequencies */
     ungetc(c,ficpar);    double *pp, **prop;
     fgets(line, MAXLINE, ficpar);    double pos,posprop; 
     puts(line);    double  y2; /* in fractional years */
     fputs(line,ficparo);    int iagemin, iagemax;
   }  
   ungetc(c,ficpar);    iagemin= (int) agemin;
     iagemax= (int) agemax;
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    /*pp=vector(1,nlstate);*/
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
   covar=matrix(1,NCOVMAX,1,n);        
   if (strlen(model)<=1) cptcovn=0;    j=cptcoveff;
   else {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     j=0;    
     j=nbocc(model,'+');    for(k1=1; k1<=j;k1++){
     cptcovn=j+1;      for(i1=1; i1<=ncodemax[k1];i1++){
   }        j1++;
         
   ncovmodel=2+cptcovn;        for (i=1; i<=nlstate; i++)  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          for(m=iagemin; m <= iagemax+3; m++)
              prop[i][m]=0.0;
   /* Read guess parameters */       
   /* Reads comments: lines beginning with '#' */        for (i=1; i<=imx; i++) { /* Each individual */
   while((c=getc(ficpar))=='#' && c!= EOF){          bool=1;
     ungetc(c,ficpar);          if  (cptcovn>0) {
     fgets(line, MAXLINE, ficpar);            for (z1=1; z1<=cptcoveff; z1++) 
     puts(line);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     fputs(line,ficparo);                bool=0;
   }          } 
   ungetc(c,ficpar);          if (bool==1) { 
              for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     for(i=1; i <=nlstate; i++)              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     for(j=1; j <=nlstate+ndeath-1; j++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fprintf(ficparo,"%1d%1d",i1,j1);                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); 
       printf("%1d%1d",i,j);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       for(k=1; k<=ncovmodel;k++){                  /*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]]);*/
         fscanf(ficpar," %lf",&param[i][j][k]);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         printf(" %lf",param[i][j][k]);                  prop[s[m][i]][iagemax+3] += weight[i]; 
         fprintf(ficparo," %lf",param[i][j][k]);                } 
       }              }
       fscanf(ficpar,"\n");            } /* end selection of waves */
       printf("\n");          }
       fprintf(ficparo,"\n");        }
     }        for(i=iagemin; i <= iagemax+3; i++){  
            
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   p=param[1][1];            posprop += prop[jk][i]; 
            } 
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){          for(jk=1; jk <=nlstate ; jk++){     
     ungetc(c,ficpar);            if( i <=  iagemax){ 
     fgets(line, MAXLINE, ficpar);              if(posprop>=1.e-5){ 
     puts(line);                probs[i][jk][j1]= prop[jk][i]/posprop;
     fputs(line,ficparo);              } 
   }            } 
   ungetc(c,ficpar);          }/* end jk */ 
         }/* end i */ 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      } /* end i1 */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    } /* end k1 */
   for(i=1; i <=nlstate; i++){    
     for(j=1; j <=nlstate+ndeath-1; j++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       fscanf(ficpar,"%1d%1d",&i1,&j1);    /*free_vector(pp,1,nlstate);*/
       printf("%1d%1d",i,j);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       fprintf(ficparo,"%1d%1d",i1,j1);  }  /* End of prevalence */
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);  /************* Waves Concatenation ***************/
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);  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)
       }  {
       fscanf(ficpar,"\n");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       printf("\n");       Death is a valid wave (if date is known).
       fprintf(ficparo,"\n");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   }       and mw[mi+1][i]. dh depends on stepm.
   delti=delti3[1][1];       */
    
   /* Reads comments: lines beginning with '#' */    int i, mi, m;
   while((c=getc(ficpar))=='#' && c!= EOF){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     ungetc(c,ficpar);       double sum=0., jmean=0.;*/
     fgets(line, MAXLINE, ficpar);    int first;
     puts(line);    int j, k=0,jk, ju, jl;
     fputs(line,ficparo);    double sum=0.;
   }    first=0;
   ungetc(c,ficpar);    jmin=1e+5;
      jmax=-1;
   matcov=matrix(1,npar,1,npar);    jmean=0.;
   for(i=1; i <=npar; i++){    for(i=1; i<=imx; i++){
     fscanf(ficpar,"%s",&str);      mi=0;
     printf("%s",str);      m=firstpass;
     fprintf(ficparo,"%s",str);      while(s[m][i] <= nlstate){
     for(j=1; j <=i; j++){        if(s[m][i]>=1)
       fscanf(ficpar," %le",&matcov[i][j]);          mw[++mi][i]=m;
       printf(" %.5le",matcov[i][j]);        if(m >=lastpass)
       fprintf(ficparo," %.5le",matcov[i][j]);          break;
     }        else
     fscanf(ficpar,"\n");          m++;
     printf("\n");      }/* end while */
     fprintf(ficparo,"\n");      if (s[m][i] > nlstate){
   }        mi++;     /* Death is another wave */
   for(i=1; i <=npar; i++)        /* if(mi==0)  never been interviewed correctly before death */
     for(j=i+1;j<=npar;j++)           /* Only death is a correct wave */
       matcov[i][j]=matcov[j][i];        mw[mi][i]=m;
          }
   printf("\n");  
       wav[i]=mi;
       if(mi==0){
    if(mle==1){        if(first==0){
     /*-------- data file ----------*/          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
     if((ficres =fopen(fileres,"w"))==NULL) {          first=1;
       printf("Problem with resultfile: %s\n", fileres);goto end;        }
     }        if(first==1){
     fprintf(ficres,"#%s\n",version);          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
            }
     if((fic=fopen(datafile,"r"))==NULL)    {      } /* end mi==0 */
       printf("Problem with datafile: %s\n", datafile);goto end;    } /* End individuals */
     }  
     for(i=1; i<=imx; i++){
     n= lastobs;      for(mi=1; mi<wav[i];mi++){
     severity = vector(1,maxwav);        if (stepm <=0)
     outcome=imatrix(1,maxwav+1,1,n);          dh[mi][i]=1;
     num=ivector(1,n);        else{
     moisnais=vector(1,n);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     annais=vector(1,n);            if (agedc[i] < 2*AGESUP) {
     moisdc=vector(1,n);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     andc=vector(1,n);            if(j==0) j=1;  /* Survives at least one month after exam */
     agedc=vector(1,n);            k=k+1;
     cod=ivector(1,n);            if (j >= jmax) jmax=j;
     weight=vector(1,n);            if (j <= jmin) jmin=j;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            sum=sum+j;
     mint=matrix(1,maxwav,1,n);            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     anint=matrix(1,maxwav,1,n);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     s=imatrix(1,maxwav+1,1,n);            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]);
     adl=imatrix(1,maxwav+1,1,n);                }
     tab=ivector(1,NCOVMAX);          }
     ncodemax=ivector(1,8);          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     i=1;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     while (fgets(line, MAXLINE, fic) != NULL)    {            k=k+1;
       if ((i >= firstobs) && (i <=lastobs)) {            if (j >= jmax) jmax=j;
                    else if (j <= jmin)jmin=j;
         for (j=maxwav;j>=1;j--){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            /*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(line,stra);            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]);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            sum=sum+j;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          }
         }          jk= j/stepm;
                  jl= j -jk*stepm;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          ju= j -(jk+1)*stepm;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          if(mle <=1){ 
             if(jl==0){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              dh[mi][i]=jk;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                    * at the price of an extra matrix product in likelihood */
         for (j=ncov;j>=1;j--){              dh[mi][i]=jk+1;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=ju;
         }            }
         num[i]=atol(stra);          }else{
             if(jl <= -ju){
         /*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]));*/              dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
         i=i+1;                                   * is higher than the multiple of stepm and negative otherwise.
       }                                   */
     }            }
             else{
     /*scanf("%d",i);*/              dh[mi][i]=jk+1;
   imx=i-1; /* Number of individuals */              bh[mi][i]=ju;
             }
   /* Calculation of the number of parameter from char model*/            if(dh[mi][i]==0){
   Tvar=ivector(1,8);                  dh[mi][i]=1; /* At least one step */
                  bh[mi][i]=ju; /* At least one step */
   if (strlen(model) >1){              /*  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);*/
     j=0;            }
     j=nbocc(model,'+');          }
     cptcovn=j+1;        } /* end if mle */
          } /* end wave */
     strcpy(modelsav,model);    }
     if (j==0) {    jmean=sum/k;
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);    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);
     else {   }
       for(i=j; i>=1;i--){  
         cutv(stra,strb,modelsav,'+');  /*********** Tricode ****************************/
         if (strchr(strb,'*')) {  void tricode(int *Tvar, int **nbcode, int imx)
           cutv(strd,strc,strb,'*');  {
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;    
           cutv(strb,strc,strd,'V');    int Ndum[20],ij=1, k, j, i, maxncov=19;
           for (k=1; k<=lastobs;k++)    int cptcode=0;
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    cptcoveff=0; 
         }   
         else {cutv(strd,strc,strb,'V');    for (k=0; k<maxncov; k++) Ndum[k]=0;
         Tvar[i+1]=atoi(strc);    for (k=1; k<=7; k++) ncodemax[k]=0;
         }  
         strcpy(modelsav,stra);      for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       cutv(strd,strc,stra,'V');                                 modality*/ 
       Tvar[1]=atoi(strc);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     }        Ndum[ij]++; /*store the modality */
   }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   /*printf("tvar=%d ",Tvar[1]);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   scanf("%d ",i);*/                                         Tvar[j]. If V=sex and male is 0 and 
     fclose(fic);                                         female is 1, then  cptcode=1.*/
       }
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;      for (i=0; i<=cptcode; i++) {
     }        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
     /*-calculation of age at interview from date of interview and age at death -*/      }
     agev=matrix(1,maxwav,1,imx);  
          ij=1; 
     for (i=1; i<=imx; i++)  {      for (i=1; i<=ncodemax[j]; i++) {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for (k=0; k<= maxncov; k++) {
       for(m=1; (m<= maxwav); m++){          if (Ndum[k] != 0) {
         if(s[m][i] >0){            nbcode[Tvar[j]][ij]=k; 
           if (s[m][i] == nlstate+1) {            /* 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; */
             if(agedc[i]>0)            
               if(moisdc[i]!=99 && andc[i]!=9999)            ij++;
               agev[m][i]=agedc[i];          }
             else{          if (ij > ncodemax[j]) break; 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        }  
               agev[m][i]=-1;      } 
             }    }  
           }  
           else if(s[m][i] !=9){ /* Should no more exist */   for (k=0; k< maxncov; k++) Ndum[k]=0;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)   for (i=1; i<=ncovmodel-2; i++) { 
               agev[m][i]=1;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
             else if(agev[m][i] <agemin){     ij=Tvar[i];
               agemin=agev[m][i];     Ndum[ij]++;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/   }
             }  
             else if(agev[m][i] >agemax){   ij=1;
               agemax=agev[m][i];   for (i=1; i<= maxncov; i++) {
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/     if((Ndum[i]!=0) && (i<=ncovcol)){
             }       Tvaraff[ij]=i; /*For printing */
             /*agev[m][i]=anint[m][i]-annais[i];*/       ij++;
             /*   agev[m][i] = age[i]+2*m;*/     }
           }   }
           else { /* =9 */   
             agev[m][i]=1;   cptcoveff=ij-1; /*Number of simple covariates*/
             s[m][i]=-1;  }
           }  
         }  /*********** Health Expectancies ****************/
         else /*= 0 Unknown */  
           agev[m][i]=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 )
       }  
      {
     }    /* Health expectancies */
     for (i=1; i<=imx; i++)  {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       for(m=1; (m<= maxwav); m++){    double age, agelim, hf;
         if (s[m][i] > (nlstate+ndeath)) {    double ***p3mat,***varhe;
           printf("Error: Wrong value in nlstate or ndeath\n");      double **dnewm,**doldm;
           goto end;    double *xp;
         }    double **gp, **gm;
       }    double ***gradg, ***trgradg;
     }    int theta;
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     free_vector(severity,1,maxwav);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     free_imatrix(outcome,1,maxwav+1,1,n);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     free_vector(moisnais,1,n);    
     free_vector(annais,1,n);    fprintf(ficreseij,"# Health expectancies\n");
     free_matrix(mint,1,maxwav,1,n);    fprintf(ficreseij,"# Age");
     free_matrix(anint,1,maxwav,1,n);    for(i=1; i<=nlstate;i++)
     free_vector(moisdc,1,n);      for(j=1; j<=nlstate;j++)
     free_vector(andc,1,n);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
      
     wav=ivector(1,imx);    if(estepm < stepm){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      printf ("Problem %d lower than %d\n",estepm, stepm);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    }
        else  hstepm=estepm;   
     /* Concatenates waves */    /* We compute the life expectancy from trapezoids spaced every estepm months
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);     * 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 
 Tcode=ivector(1,100);     * progression in between and thus overestimating or underestimating according
    nbcode=imatrix(1,nvar,1,8);       * to the curvature of the survival function. If, for the same date, we 
    ncodemax[1]=1;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);     * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
    codtab=imatrix(1,100,1,10);     * curvature will be obtained if estepm is as small as stepm. */
    h=0;  
    m=pow(2,cptcovn);    /* 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(k=1;k<=cptcovn; k++){       nhstepm is the number of hstepm from age to agelim 
      for(i=1; i <=(m/pow(2,k));i++){       nstepm is the number of stepm from age to agelin. 
        for(j=1; j <= ncodemax[k]; j++){       Look at hpijx to understand the reason of that which relies in memory size
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){       and note for a fixed period like estepm months */
            h++;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
            if (h>m) h=1;codtab[h][k]=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
        }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
      }       results. So we changed our mind and took the option of the best precision.
    }    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    /*for(i=1; i <=m ;i++){  
      for(k=1; k <=cptcovn; k++){    agelim=AGESUP;
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      }      /* nhstepm age range expressed in number of stepm */
      printf("\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
    }*/      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
    /*scanf("%d",i);*/      /* if (stepm >= YEARM) hstepm=1;*/
          nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
    /* Calculates basic frequencies. Computes observed prevalence at single age      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        and prints on file fileres'p'. */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       gm=matrix(0,nhstepm,1,nlstate*nlstate);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */   
      
     /* For Powell, parameters are in a vector p[] starting at p[1]      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */  
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      /* Computing Variances of health expectancies */
      
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
              xp[i] = x[i] + (i==theta ?delti[theta]:0);
     /*--------- results files --------------*/        }
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        
    jk=1;        cptj=0;
    fprintf(ficres,"# Parameters\n");        for(j=1; j<= nlstate; j++){
    printf("# Parameters\n");          for(i=1; i<=nlstate; i++){
    for(i=1,jk=1; i <=nlstate; i++){            cptj=cptj+1;
      for(k=1; k <=(nlstate+ndeath); k++){            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
        if (k != i)              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
          {            }
            printf("%d%d ",i,k);          }
            fprintf(ficres,"%1d%1d ",i,k);        }
            for(j=1; j <=ncovmodel; j++){       
              printf("%f ",p[jk]);       
              fprintf(ficres,"%f ",p[jk]);        for(i=1; i<=npar; i++) 
              jk++;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
            printf("\n");        
            fprintf(ficres,"\n");        cptj=0;
          }        for(j=1; j<= nlstate; j++){
      }          for(i=1;i<=nlstate;i++){
    }            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     hesscov(matcov, p, npar, delti, ftolhess, func);            }
     fprintf(ficres,"# Scales\n");          }
     printf("# Scales\n");        }
      for(i=1,jk=1; i <=nlstate; i++){        for(j=1; j<= nlstate*nlstate; j++)
       for(j=1; j <=nlstate+ndeath; j++){          for(h=0; h<=nhstepm-1; h++){
         if (j!=i) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           fprintf(ficres,"%1d%1d",i,j);          }
           printf("%1d%1d",i,j);       } 
           for(k=1; k<=ncovmodel;k++){     
             printf(" %.5e",delti[jk]);  /* End theta */
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           }  
           printf("\n");       for(h=0; h<=nhstepm-1; h++)
           fprintf(ficres,"\n");        for(j=1; j<=nlstate*nlstate;j++)
         }          for(theta=1; theta <=npar; theta++)
       }            trgradg[h][j][theta]=gradg[h][theta][j];
       }       
      
     k=1;       for(i=1;i<=nlstate*nlstate;i++)
     fprintf(ficres,"# Covariance\n");        for(j=1;j<=nlstate*nlstate;j++)
     printf("# Covariance\n");          varhe[i][j][(int)age] =0.;
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;       printf("%d|",(int)age);fflush(stdout);
       i1=(i-1)/(ncovmodel*nlstate)+1;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);       for(h=0;h<=nhstepm-1;h++){
       printf("%s%d%d",alph[k],i1,tab[i]);*/        for(k=0;k<=nhstepm-1;k++){
       fprintf(ficres,"%3d",i);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       printf("%3d",i);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       for(j=1; j<=i;j++){          for(i=1;i<=nlstate*nlstate;i++)
         fprintf(ficres," %.5e",matcov[i][j]);            for(j=1;j<=nlstate*nlstate;j++)
         printf(" %.5e",matcov[i][j]);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
       fprintf(ficres,"\n");      }
       printf("\n");      /* Computing expectancies */
       k++;      for(i=1; i<=nlstate;i++)
     }        for(j=1; j<=nlstate;j++)
              for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     while((c=getc(ficpar))=='#' && c!= EOF){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       ungetc(c,ficpar);            
       fgets(line, MAXLINE, ficpar);  /* 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]);*/
       puts(line);  
       fputs(line,ficparo);          }
     }  
     ungetc(c,ficpar);      fprintf(ficreseij,"%3.0f",age );
        cptj=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++){
     if (fage <= 2) {          cptj++;
       bage = agemin;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       fage = agemax;        }
     }      fprintf(ficreseij,"\n");
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
 /*------------ gnuplot -------------*/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
 chdir(pathcd);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   if((ficgp=fopen("graph.plt","w"))==NULL) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with file graph.gp");goto end;    }
   }    printf("\n");
 #ifdef windows    fprintf(ficlog,"\n");
   fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif    free_vector(xp,1,npar);
 m=pow(2,cptcovn);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
  /* 1eme*/    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   for (cpt=1; cpt<= nlstate ; cpt ++) {  }
    for (k1=1; k1<= m ; k1 ++) {  
   /************ Variance ******************/
 #ifdef windows  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)
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);  {
 #endif    /* Variance of health expectancies */
 #ifdef unix    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    /* double **newm;*/
 #endif    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
 for (i=1; i<= nlstate ; i ++) {    int i, j, nhstepm, hstepm, h, nstepm ;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    int k, cptcode;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double *xp;
 }    double **gp, **gm;  /* for var eij */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    double ***gradg, ***trgradg; /*for var eij */
     for (i=1; i<= nlstate ; i ++) {    double **gradgp, **trgradgp; /* for var p point j */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double *gpp, *gmp; /* for var p point j */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 }    double ***p3mat;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    double age,agelim, hf;
      for (i=1; i<= nlstate ; i ++) {    double ***mobaverage;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    int theta;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    char digit[4];
 }      char digitp[25];
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix    char fileresprobmorprev[FILENAMELENGTH];
 fprintf(ficgp,"\nset ter gif small size 400,300");  
 #endif    if(popbased==1){
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      if(mobilav!=0)
    }        strcpy(digitp,"-populbased-mobilav-");
   }      else strcpy(digitp,"-populbased-nomobil-");
   /*2 eme*/    }
     else 
   for (k1=1; k1<= m ; k1 ++) {      strcpy(digitp,"-stablbased-");
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  
        if (mobilav!=0) {
     for (i=1; i<= nlstate+1 ; i ++) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       k=2*i;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       for (j=1; j<= nlstate+1 ; j ++) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    strcpy(fileresprobmorprev,"prmorprev"); 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    sprintf(digit,"%-d",ij);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       for (j=1; j<= nlstate+1 ; j ++) {    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         else fprintf(ficgp," \%%*lf (\%%*lf)");    strcat(fileresprobmorprev,fileres);
 }      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       fprintf(ficgp,"\" t\"\" w l 0,");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       for (j=1; j<= nlstate+1 ; j ++) {    }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 }      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       else fprintf(ficgp,"\" t\"\" w l 0,");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     }      fprintf(ficresprobmorprev," p.%-d SE",j);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
   /*3eme*/    fprintf(ficresprobmorprev,"\n");
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   for (k1=1; k1<= m ; k1 ++) {      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     for (cpt=1; cpt<= nlstate ; cpt ++) {      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       k=2+nlstate*(cpt-1);      exit(0);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);    }
       for (i=1; i< nlstate ; i ++) {    else{
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);      fprintf(ficgp,"\n# Routine varevsij");
       }    }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     }      printf("Problem with html file: %s\n", optionfilehtm);
   }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
        exit(0);
   /* CV preval stat */    }
   for (k1=1; k1<= m ; k1 ++) {    else{
     for (cpt=1; cpt<nlstate ; cpt ++) {      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");
       k=3;      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    }
       for (i=1; i< nlstate ; i ++)    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
          fprintf(ficresvij,"# Age");
       l=3+(nlstate+ndeath)*cpt;    for(i=1; i<=nlstate;i++)
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      for(j=1; j<=nlstate;j++)
       for (i=1; i< nlstate ; i ++) {        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
         l=3+(nlstate+ndeath)*cpt;    fprintf(ficresvij,"\n");
         fprintf(ficgp,"+$%d",l+i+1);  
       }    xp=vector(1,npar);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      dnewm=matrix(1,nlstate,1,npar);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    doldm=matrix(1,nlstate,1,nlstate);
     }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   /* proba elementaires */    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
    for(i=1,jk=1; i <=nlstate; i++){    gpp=vector(nlstate+1,nlstate+ndeath);
     for(k=1; k <=(nlstate+ndeath); k++){    gmp=vector(nlstate+1,nlstate+ndeath);
       if (k != i) {    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         for(j=1; j <=ncovmodel; j++){    
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    if(estepm < stepm){
           /*fprintf(ficgp,"%s",alph[1]);*/      printf ("Problem %d lower than %d\n",estepm, stepm);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    }
           jk++;    else  hstepm=estepm;   
           fprintf(ficgp,"\n");    /* 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 
     }       nstepm is the number of stepm from age to agelin. 
     }       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
   for(jk=1; jk <=m; jk++) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);       survival function given by stepm (the optimization length). Unfortunately it
    i=1;       means that if the survival funtion is printed every two years of age and if
    for(k2=1; k2<=nlstate; k2++) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
      k3=i;       results. So we changed our mind and took the option of the best precision.
      for(k=1; k<=(nlstate+ndeath); k++) {    */
        if (k != k2){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         for(j=3; j <=ncovmodel; j++)      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         fprintf(ficgp,")/(1");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         for(k1=1; k1 <=nlstate+1; k1=k1+2){        gp=matrix(0,nhstepm,1,nlstate);
             fprintf(ficgp,"+exp(p%d+p%d*x",k1+k3-1,k1+k3);      gm=matrix(0,nhstepm,1,nlstate);
   
             for(j=3; j <=ncovmodel; j++)  
               fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for(theta=1; theta <=npar; theta++){
             fprintf(ficgp,")");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
         }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     i=i+ncovmodel;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        }  
      }        if (popbased==1) {
    }          if(mobilav ==0){
   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            for(i=1; i<=nlstate;i++)
    }              prlim[i][i]=probs[(int)age][i][ij];
              }else{ /* mobilav */ 
   fclose(ficgp);            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=mobaverage[(int)age][i][ij];
 chdir(path);          }
     free_matrix(agev,1,maxwav,1,imx);        }
     free_ivector(wav,1,imx);    
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        for(j=1; j<= nlstate; j++){
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          for(h=0; h<=nhstepm; h++){
                for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     free_imatrix(s,1,maxwav+1,1,n);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
              }
            }
     free_ivector(num,1,n);        /* This for computing probability of death (h=1 means
     free_vector(agedc,1,n);           computed over hstepm matrices product = hstepm*stepm months) 
     free_vector(weight,1,n);           as a weighted average of prlim.
     /*free_matrix(covar,1,NCOVMAX,1,n);*/        */
     fclose(ficparo);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fclose(ficres);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
    }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
            }    
    /*________fin mle=1_________*/        /* end probability of death */
      
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
     /* No more information from the sample is required now */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /* Reads comments: lines beginning with '#' */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   while((c=getc(ficpar))=='#' && c!= EOF){   
     ungetc(c,ficpar);        if (popbased==1) {
     fgets(line, MAXLINE, ficpar);          if(mobilav ==0){
     puts(line);            for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
   ungetc(c,ficpar);            for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          }
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
 /*--------- index.htm --------*/        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   if((fichtm=fopen("index.htm","w"))==NULL)    {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     printf("Problem with index.htm \n");goto end;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
         }
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n        /* This for computing probability of death (h=1 means
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n           computed over hstepm matrices product = hstepm*stepm months) 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>           as a weighted average of prlim.
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        */
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          for(i=1,gmp[j]=0.; i<= nlstate; i++)
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>        }    
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>        /* end probability of death */
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  
         for(j=1; j<= nlstate; j++) /* vareij */
  fprintf(fichtm," <li>Graphs</li>\n<p>");          for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
  m=cptcovn;          }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
  j1=0;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
  for(k1=1; k1<=m;k1++){        }
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;      } /* End theta */
        if (cptcovn > 0) {  
          fprintf(fichtm,"<hr>************ Results for covariates");      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
          for (cpt=1; cpt<=cptcovn;cpt++)  
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);      for(h=0; h<=nhstepm; h++) /* veij */
          fprintf(fichtm," ************\n<hr>");        for(j=1; j<=nlstate;j++)
        }          for(theta=1; theta <=npar; theta++)
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>            trgradg[h][j][theta]=gradg[h][theta][j];
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      
        for(cpt=1; cpt<nlstate;cpt++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        for(theta=1; theta <=npar; theta++)
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          trgradgp[j][theta]=gradgp[theta][j];
        }    
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 interval) in state (%d): v%s%d%d.gif <br>      for(i=1;i<=nlstate;i++)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for(j=1;j<=nlstate;j++)
      }          vareij[i][j][(int)age] =0.;
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      for(h=0;h<=nhstepm;h++){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for(k=0;k<=nhstepm;k++){
      }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 health expectancies in states (1) and (2): e%s%d.gif<br>          for(i=1;i<=nlstate;i++)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            for(j=1;j<=nlstate;j++)
 fprintf(fichtm,"\n</body>");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
    }        }
  }      }
 fclose(fichtm);    
       /* pptj */
   /*--------------- Prevalence limit --------------*/      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);
   strcpy(filerespl,"pl");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   strcat(filerespl,fileres);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          varppt[j][i]=doldmp[j][i];
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      /* end ppptj */
   }      /*  x centered again */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   fprintf(ficrespl,"#Prevalence limit\n");      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   fprintf(ficrespl,"#Age ");   
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      if (popbased==1) {
   fprintf(ficrespl,"\n");        if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
   prlim=matrix(1,nlstate,1,nlstate);            prlim[i][i]=probs[(int)age][i][ij];
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }else{ /* mobilav */ 
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(i=1; i<=nlstate;i++)
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            prlim[i][i]=mobaverage[(int)age][i][ij];
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      }
   k=0;               
   agebase=agemin;      /* This for computing probability of death (h=1 means
   agelim=agemax;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   ftolpl=1.e-10;         as a weighted average of prlim.
   i1=cptcovn;      */
   if (cptcovn < 1){i1=1;}      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   for(cptcov=1;cptcov<=i1;cptcov++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }    
         k=k+1;      /* end probability of death */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#****** ");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         for(j=1;j<=cptcovn;j++)      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         fprintf(ficrespl,"******\n");        for(i=1; i<=nlstate;i++){
                  fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         for (age=agebase; age<=agelim; age++){        }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      } 
           fprintf(ficrespl,"%.0f",age );      fprintf(ficresprobmorprev,"\n");
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);      fprintf(ficresvij,"%.0f ",age );
           fprintf(ficrespl,"\n");      for(i=1; i<=nlstate;i++)
         }        for(j=1; j<=nlstate;j++){
       }          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     }        }
   fclose(ficrespl);      fprintf(ficresvij,"\n");
   /*------------- h Pij x at various ages ------------*/      free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    } /* End age */
   printf("Computing pij: result on file '%s' \n", filerespij);    free_vector(gpp,nlstate+1,nlstate+ndeath);
      free_vector(gmp,nlstate+1,nlstate+ndeath);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   if (stepm<=24) stepsize=2;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   agelim=AGESUP;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   hstepm=stepsize*YEARM; /* Every year of age */    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   k=0;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
       k=k+1;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
         fprintf(ficrespij,"\n#****** ");    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
         for(j=1;j<=cptcovn;j++)    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
         fprintf(ficrespij,"******\n");  */
            fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_vector(xp,1,npar);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    free_matrix(doldm,1,nlstate,1,nlstate);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(dnewm,1,nlstate,1,npar);
           oldm=oldms;savm=savms;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           fprintf(ficrespij,"# Age");    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           for(i=1; i<=nlstate;i++)    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             for(j=1; j<=nlstate+ndeath;j++)    fclose(ficresprobmorprev);
               fprintf(ficrespij," %1d-%1d",i,j);    fclose(ficgp);
           fprintf(ficrespij,"\n");    fclose(fichtm);
           for (h=0; h<=nhstepm; h++){  }  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)  /************ Variance of prevlim ******************/
               for(j=1; j<=nlstate+ndeath;j++)  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  {
             fprintf(ficrespij,"\n");    /* Variance of prevalence limit */
           }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **newm;
           fprintf(ficrespij,"\n");    double **dnewm,**doldm;
         }    int i, j, nhstepm, hstepm;
     }    int k, cptcode;
   }    double *xp;
     double *gp, *gm;
   fclose(ficrespij);    double **gradg, **trgradg;
     double age,agelim;
   /*---------- Health expectancies and variances ------------*/    int theta;
      
   strcpy(filerest,"t");    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   strcat(filerest,fileres);    fprintf(ficresvpl,"# Age");
   if((ficrest=fopen(filerest,"w"))==NULL) {    for(i=1; i<=nlstate;i++)
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficresvpl," %1d-%1d",i,i);
   }    fprintf(ficresvpl,"\n");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   strcpy(filerese,"e");    doldm=matrix(1,nlstate,1,nlstate);
   strcat(filerese,fileres);    
   if((ficreseij=fopen(filerese,"w"))==NULL) {    hstepm=1*YEARM; /* Every year of age */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   }    agelim = AGESUP;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  strcpy(fileresv,"v");      if (stepm >= YEARM) hstepm=1;
   strcat(fileresv,fileres);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      gradg=matrix(1,npar,1,nlstate);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      gp=vector(1,nlstate);
   }      gm=vector(1,nlstate);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
       for(theta=1; theta <=npar; theta++){
   k=0;        for(i=1; i<=npar; i++){ /* Computes gradient */
   for(cptcov=1;cptcov<=i1;cptcov++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
       k=k+1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fprintf(ficrest,"\n#****** ");        for(i=1;i<=nlstate;i++)
       for(j=1;j<=cptcovn;j++)          gp[i] = prlim[i][i];
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);      
       fprintf(ficrest,"******\n");        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficreseij,"\n#****** ");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for(j=1;j<=cptcovn;j++)        for(i=1;i<=nlstate;i++)
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          gm[i] = prlim[i][i];
       fprintf(ficreseij,"******\n");  
         for(i=1;i<=nlstate;i++)
       fprintf(ficresvij,"\n#****** ");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       for(j=1;j<=cptcovn;j++)      } /* End theta */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficresvij,"******\n");      trgradg =matrix(1,nlstate,1,npar);
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      for(j=1; j<=nlstate;j++)
       oldm=oldms;savm=savms;        for(theta=1; theta <=npar; theta++)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            trgradg[j][theta]=gradg[theta][j];
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;      for(i=1;i<=nlstate;i++)
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        varpl[i][(int)age] =0.;
            matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      for(i=1;i<=nlstate;i++)
       fprintf(ficrest,"\n");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
          
       hf=1;      fprintf(ficresvpl,"%.0f ",age );
       if (stepm >= YEARM) hf=stepm/YEARM;      for(i=1; i<=nlstate;i++)
       epj=vector(1,nlstate+1);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       for(age=bage; age <=fage ;age++){      fprintf(ficresvpl,"\n");
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      free_vector(gp,1,nlstate);
         fprintf(ficrest," %.0f",age);      free_vector(gm,1,nlstate);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      free_matrix(gradg,1,npar,1,nlstate);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      free_matrix(trgradg,1,nlstate,1,npar);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    } /* End age */
           }  
           epj[nlstate+1] +=epj[j];    free_vector(xp,1,npar);
         }    free_matrix(doldm,1,nlstate,1,npar);
         for(i=1, vepp=0.;i <=nlstate;i++)    free_matrix(dnewm,1,nlstate,1,nlstate);
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];  }
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  
         for(j=1;j <=nlstate;j++){  /************ Variance of one-step probabilities  ******************/
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
         }  {
         fprintf(ficrest,"\n");    int i, j=0,  i1, k1, l1, t, tj;
       }    int k2, l2, j1,  z1;
     }    int k=0,l, cptcode;
   }    int first=1, first1;
            double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
  fclose(ficreseij);    double **dnewm,**doldm;
  fclose(ficresvij);    double *xp;
   fclose(ficrest);    double *gp, *gm;
   fclose(ficpar);    double **gradg, **trgradg;
   free_vector(epj,1,nlstate+1);    double **mu;
   /*  scanf("%d ",i); */    double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   /*------- Variance limit prevalence------*/      int theta;
     char fileresprob[FILENAMELENGTH];
 strcpy(fileresvpl,"vpl");    char fileresprobcov[FILENAMELENGTH];
   strcat(fileresvpl,fileres);    char fileresprobcor[FILENAMELENGTH];
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    double ***varpij;
     exit(0);  
   }    strcpy(fileresprob,"prob"); 
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
  k=0;      printf("Problem with resultfile: %s\n", fileresprob);
  for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
      k=k+1;    strcpy(fileresprobcov,"probcov"); 
      fprintf(ficresvpl,"\n#****** ");    strcat(fileresprobcov,fileres);
      for(j=1;j<=cptcovn;j++)    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);      printf("Problem with resultfile: %s\n", fileresprobcov);
      fprintf(ficresvpl,"******\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
          }
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    strcpy(fileresprobcor,"probcor"); 
      oldm=oldms;savm=savms;    strcat(fileresprobcor,fileres);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
    }      printf("Problem with resultfile: %s\n", fileresprobcor);
  }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
   fclose(ficresvpl);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   /*---------- End : free ----------------*/    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    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);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    
      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficresprobcov,"# Age");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficresprobcov,"# Age");
    
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    for(i=1; i<=nlstate;i++)
        for(j=1; j<=(nlstate+ndeath);j++){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
   printf("End of Imach\n");        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      }  
     /* fprintf(ficresprob,"\n");
   /* 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);*/    fprintf(ficresprobcov,"\n");
   /*printf("Total time was %d uSec.\n", total_usecs);*/    fprintf(ficresprobcor,"\n");
   /*------ End -----------*/   */
    xp=vector(1,npar);
  end:    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 #ifdef windows    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
  chdir(pathcd);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
 #endif    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
  system("wgnuplot graph.plt");    first=1;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 #ifdef windows      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   while (z[0] != 'q') {      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     chdir(pathcd);      exit(0);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    }
     scanf("%s",z);    else{
     if (z[0] == 'c') system("./imach");      fprintf(ficgp,"\n# Routine varprob");
     else if (z[0] == 'e') {    }
       chdir(path);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       system("index.htm");      printf("Problem with html file: %s\n", optionfilehtm);
     }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     else if (z[0] == 'q') exit(0);      exit(0);
   }    }
 #endif    else{
 }      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(fichtm,"\n");
   
       fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       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");
   
     }
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           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]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     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);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                       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);
                       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);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fclose(ficgp);
     fclose(fichtm);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
     if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     }
   
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
    - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
    - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
    - Life expectancies by age and initial health status (estepm=%2d months): 
      <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(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* 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>
   <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
   <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
    - 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
    - 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); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and period prevalence (with confident
   interval) in state (%d): v%s%d%d.png <br>
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   fclose(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   
     /*#ifdef windows */
       fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   m=pow(2,cptcoveff);
     
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        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 ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         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);
           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 ; i ++) {
           fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          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);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fclose(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* 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
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             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);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1;
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
Removed from v.1.5  
changed lines
  Added in v.1.83

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