Diff for /imach/src/imach.c between versions 1.15 and 1.84

version 1.15, 2002/02/20 17:08:52 version 1.84, 2003/06/13 21:44:43
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 1.84  2003/06/13 21:44:43  brouard
   individuals from different ages are interviewed on their health status    * imach.c (Repository): Replace "freqsummary" at a correct
   or degree of  disability. At least a second wave of interviews    place. It differs from routine "prevalence" which may be called
   ("longitudinal") should  measure each new individual health status.    many times. Probs is memory consuming and must be used with
   Health expectancies are computed from the transistions observed between    parcimony.
   waves and are computed for each degree of severity of disability (number    Version 0.95a2 (should output exactly the same maximization than 0.8a2)
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.83  2003/06/10 13:39:11  lievre
   The simplest model is the multinomial logistic model where pij is    *** empty log message ***
   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:    Revision 1.82  2003/06/05 15:57:20  brouard
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Add log in  imach.c and  fullversion number is now printed.
   is a covariate. If you want to have a more complex model than "constant and  
   age", you should modify the program where the markup  */
     *Covariates have to be included here again* invites you to do it.  /*
   More covariates you add, less is the speed of the convergence.     Interpolated Markov Chain
   
   The advantage that this computer programme claims, comes from that if the    Short summary of the programme:
   delay between waves is not identical for each individual, or if some    
   individual missed an interview, the information is not rounded or lost, but    This program computes Healthy Life Expectancies from
   taken into account using an interpolation or extrapolation.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   hPijx is the probability to be    first survey ("cross") where individuals from different ages are
   observed in state i at age x+h conditional to the observed state i at age    interviewed on their health status or degree of disability (in the
   x. The delay 'h' can be split into an exact number (nh*stepm) of    case of a health survey which is our main interest) -2- at least a
   unobserved intermediate  states. This elementary transition (by month or    second wave of interviews ("longitudinal") which measure each change
   quarter trimester, semester or year) is model as a multinomial logistic.    (if any) in individual health status.  Health expectancies are
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    computed from the time spent in each health state according to a
   and the contribution of each individual to the likelihood is simply hPijx.    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
   Also this programme outputs the covariance matrix of the parameters but also    simplest model is the multinomial logistic model where pij is the
   of the life expectancies. It also computes the prevalence limits.    probability to be observed in state j at the second wave
      conditional to be observed in state i at the first wave. Therefore
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
            Institut national d'études démographiques, Paris.    'age' is age and 'sex' is a covariate. If you want to have a more
   This software have been partly granted by Euro-REVES, a concerted action    complex model than "constant and age", you should modify the program
   from the European Union.    where the markup *Covariates have to be included here again* invites
   It is copyrighted identically to a GNU software product, ie programme and    you to do it.  More covariates you add, slower the
   software can be distributed freely for non commercial use. Latest version    convergence.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    The advantage of this computer programme, compared to a simple
      multinomial logistic model, is clear when the delay between waves is not
 #include <math.h>    identical for each individual. Also, if a individual missed an
 #include <stdio.h>    intermediate interview, the information is lost, but taken into
 #include <stdlib.h>    account using an interpolation or extrapolation.  
 #include <unistd.h>  
     hPijx is the probability to be observed in state i at age x+h
 #define MAXLINE 256    conditional to the observed state i at age x. The delay 'h' can be
 #define FILENAMELENGTH 80    split into an exact number (nh*stepm) of unobserved intermediate
 /*#define DEBUG*/    states. This elementary transition (by month, quarter,
 #define windows    semester or year) is modelled as a multinomial logistic.  The hPx
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    matrix is simply the matrix product of nh*stepm elementary matrices
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    and the contribution of each individual to the likelihood is simply
     hPijx.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the stable prevalence. 
 #define NINTERVMAX 8    
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */             Institut national d'études démographiques, Paris.
 #define NCOVMAX 8 /* Maximum number of covariates */    This software have been partly granted by Euro-REVES, a concerted action
 #define MAXN 20000    from the European Union.
 #define YEARM 12. /* Number of months per year */    It is copyrighted identically to a GNU software product, ie programme and
 #define AGESUP 130    software can be distributed freely for non commercial use. Latest version
 #define AGEBASE 40    can be accessed at http://euroreves.ined.fr/imach .
   
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int nvar;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    
 int npar=NPARMAX;    **********************************************************************/
 int nlstate=2; /* Number of live states */  /*
 int ndeath=1; /* Number of dead states */    main
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    read parameterfile
 int popbased=0;    read datafile
     concatwav
 int *wav; /* Number of waves for this individuual 0 is possible */    freqsummary
 int maxwav; /* Maxim number of waves */    if (mle >= 1)
 int jmin, jmax; /* min, max spacing between 2 waves */      mlikeli
 int mle, weightopt;    print results files
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    if mle==1 
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */       computes hessian
 double jmean; /* Mean space between 2 waves */    read end of parameter file: agemin, agemax, bage, fage, estepm
 double **oldm, **newm, **savm; /* Working pointers to matrices */        begin-prev-date,...
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    open gnuplot file
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    open html file
 FILE *ficgp, *fichtm,*ficresprob;    stable prevalence
 FILE *ficreseij;     for age prevalim()
   char filerese[FILENAMELENGTH];    h Pij x
  FILE  *ficresvij;    variance of p varprob
   char fileresv[FILENAMELENGTH];    forecasting if prevfcast==1 prevforecast call prevalence()
  FILE  *ficresvpl;    health expectancies
   char fileresvpl[FILENAMELENGTH];    Variance-covariance of DFLE
     prevalence()
 #define NR_END 1     movingaverage()
 #define FREE_ARG char*    varevsij() 
 #define FTOL 1.0e-10    if popbased==1 varevsij(,popbased)
     total life expectancies
 #define NRANSI    Variance of stable prevalence
 #define ITMAX 200   end
   */
 #define TOL 2.0e-4  
   
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10   
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #include <math.h>
   #include <stdio.h>
 #define GOLD 1.618034  #include <stdlib.h>
 #define GLIMIT 100.0  #include <unistd.h>
 #define TINY 1.0e-20  
   #define MAXLINE 256
 static double maxarg1,maxarg2;  #define GNUPLOTPROGRAM "gnuplot"
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define FILENAMELENGTH 80
    /*#define DEBUG*/
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define windows
 #define rint(a) floor(a+0.5)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 int imx;  #define NINTERVMAX 8
 int stepm;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 /* Stepm, step in month: minimum step interpolation*/  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 int m,nb;  #define MAXN 20000
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define YEARM 12. /* Number of months per year */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define AGESUP 130
 double **pmmij, ***probs, ***mobaverage;  #define AGEBASE 40
   #ifdef windows
 double *weight;  #define DIRSEPARATOR '\\'
 int **s; /* Status */  #define ODIRSEPARATOR '/'
 double *agedc, **covar, idx;  #else
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #endif
 double ftolhess; /* Tolerance for computing hessian */  
   /* $Id$ */
 /**************** split *************************/  /* $State$ */
 static  int split( char *path, char *dirc, char *name )  
 {  char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
    char *s;                             /* pointer */  char fullversion[]="$Revision$ $Date$"; 
    int  l1, l2;                         /* length counters */  int erreur; /* Error number */
   int nvar;
    l1 = strlen( path );                 /* length of path */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  int npar=NPARMAX;
    s = strrchr( path, '\\' );           /* find last / */  int nlstate=2; /* Number of live states */
    if ( s == NULL ) {                   /* no directory, so use current */  int ndeath=1; /* Number of dead states */
 #if     defined(__bsd__)                /* get current working directory */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       extern char       *getwd( );  int popbased=0;
   
       if ( getwd( dirc ) == NULL ) {  int *wav; /* Number of waves for this individuual 0 is possible */
 #else  int maxwav; /* Maxim number of waves */
       extern char       *getcwd( );  int jmin, jmax; /* min, max spacing between 2 waves */
   int mle, weightopt;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #endif  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
          return( GLOCK_ERROR_GETCWD );  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       strcpy( name, path );             /* we've got it */  double jmean; /* Mean space between 2 waves */
    } else {                             /* strip direcotry from path */  double **oldm, **newm, **savm; /* Working pointers to matrices */
       s++;                              /* after this, the filename */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       l2 = strlen( s );                 /* length of filename */  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  FILE *ficlog, *ficrespow;
       strcpy( name, s );                /* save file name */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  FILE *ficresprobmorprev;
       dirc[l1-l2] = 0;                  /* add zero */  FILE *fichtm; /* Html File */
    }  FILE *ficreseij;
    l1 = strlen( dirc );                 /* length of directory */  char filerese[FILENAMELENGTH];
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  FILE  *ficresvij;
    return( 0 );                         /* we're done */  char fileresv[FILENAMELENGTH];
 }  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 /******************************************/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 void replace(char *s, char*t)  
 {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   int i;  char filelog[FILENAMELENGTH]; /* Log file */
   int lg=20;  char filerest[FILENAMELENGTH];
   i=0;  char fileregp[FILENAMELENGTH];
   lg=strlen(t);  char popfile[FILENAMELENGTH];
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
     if (t[i]== '\\') s[i]='/';  
   }  #define NR_END 1
 }  #define FREE_ARG char*
   #define FTOL 1.0e-10
 int nbocc(char *s, char occ)  
 {  #define NRANSI 
   int i,j=0;  #define ITMAX 200 
   int lg=20;  
   i=0;  #define TOL 2.0e-4 
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  #define CGOLD 0.3819660 
   if  (s[i] == occ ) j++;  #define ZEPS 1.0e-10 
   }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   return j;  
 }  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 void cutv(char *u,char *v, char*t, char occ)  #define TINY 1.0e-20 
 {  
   int i,lg,j,p=0;  static double maxarg1,maxarg2;
   i=0;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   for(j=0; j<=strlen(t)-1; j++) {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    
   }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
   lg=strlen(t);  
   for(j=0; j<p; j++) {  static double sqrarg;
     (u[j] = t[j]);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
      u[p]='\0';  
   int imx; 
    for(j=0; j<= lg; j++) {  int stepm;
     if (j>=(p+1))(v[j-p-1] = t[j]);  /* Stepm, step in month: minimum step interpolation*/
   }  
 }  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 /********************** nrerror ********************/  
   int m,nb;
 void nrerror(char error_text[])  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   fprintf(stderr,"ERREUR ...\n");  double **pmmij, ***probs;
   fprintf(stderr,"%s\n",error_text);  double dateintmean=0;
   exit(1);  
 }  double *weight;
 /*********************** vector *******************/  int **s; /* Status */
 double *vector(int nl, int nh)  double *agedc, **covar, idx;
 {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   if (!v) nrerror("allocation failure in vector");  double ftolhess; /* Tolerance for computing hessian */
   return v-nl+NR_END;  
 }  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 /************************ free vector ******************/  {
 void free_vector(double*v, int nl, int nh)    char  *ss;                            /* pointer */
 {    int   l1, l2;                         /* length counters */
   free((FREE_ARG)(v+nl-NR_END));  
 }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 /************************ivector *******************************/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 int *ivector(long nl,long nh)    if ( ss == NULL ) {                   /* no directory, so use current */
 {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   int *v;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));      /* get current working directory */
   if (!v) nrerror("allocation failure in ivector");      /*    extern  char* getcwd ( char *buf , int len);*/
   return v-nl+NR_END;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 }        return( GLOCK_ERROR_GETCWD );
       }
 /******************free ivector **************************/      strcpy( name, path );               /* we've got it */
 void free_ivector(int *v, long nl, long nh)    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   free((FREE_ARG)(v+nl-NR_END));      l2 = strlen( ss );                  /* length of filename */
 }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 /******************* imatrix *******************************/      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 int **imatrix(long nrl, long nrh, long ncl, long nch)      dirc[l1-l2] = 0;                    /* add zero */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    }
 {    l1 = strlen( dirc );                  /* length of directory */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #ifdef windows
   int **m;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
    #else
   /* allocate pointers to rows */    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #endif
   if (!m) nrerror("allocation failure 1 in matrix()");    ss = strrchr( name, '.' );            /* find last / */
   m += NR_END;    ss++;
   m -= nrl;    strcpy(ext,ss);                       /* save extension */
      l1= strlen( name);
      l2= strlen(ss)+1;
   /* allocate rows and set pointers to them */    strncpy( finame, name, l1-l2);
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    finame[l1-l2]= 0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    return( 0 );                          /* we're done */
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  /******************************************/
    
   /* return pointer to array of pointers to rows */  void replace(char *s, char*t)
   return m;  {
 }    int i;
     int lg=20;
 /****************** free_imatrix *************************/    i=0;
 void free_imatrix(m,nrl,nrh,ncl,nch)    lg=strlen(t);
       int **m;    for(i=0; i<= lg; i++) {
       long nch,ncl,nrh,nrl;      (s[i] = t[i]);
      /* free an int matrix allocated by imatrix() */      if (t[i]== '\\') s[i]='/';
 {    }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  }
   free((FREE_ARG) (m+nrl-NR_END));  
 }  int nbocc(char *s, char occ)
   {
 /******************* matrix *******************************/    int i,j=0;
 double **matrix(long nrl, long nrh, long ncl, long nch)    int lg=20;
 {    i=0;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    lg=strlen(s);
   double **m;    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");    return j;
   m += NR_END;  }
   m -= nrl;  
   void cutv(char *u,char *v, char*t, char occ)
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    /* cuts string t into u and v where u is ended by char occ excluding it
   m[nrl] += NR_END;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   m[nrl] -= ncl;       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    i=0;
   return m;    for(j=0; j<=strlen(t)-1; j++) {
 }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    lg=strlen(t);
 {    for(j=0; j<p; j++) {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      (u[j] = t[j]);
   free((FREE_ARG)(m+nrl-NR_END));    }
 }       u[p]='\0';
   
 /******************* ma3x *******************************/     for(j=0; j<= lg; j++) {
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)      if (j>=(p+1))(v[j-p-1] = t[j]);
 {    }
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  }
   double ***m;  
   /********************** nrerror ********************/
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  void nrerror(char error_text[])
   m += NR_END;  {
   m -= nrl;    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    exit(EXIT_FAILURE);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  }
   m[nrl] += NR_END;  /*********************** vector *******************/
   m[nrl] -= ncl;  double *vector(int nl, int nh)
   {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    if (!v) nrerror("allocation failure in vector");
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    return v-nl+NR_END;
   m[nrl][ncl] += NR_END;  }
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  /************************ free vector ******************/
     m[nrl][j]=m[nrl][j-1]+nlay;  void free_vector(double*v, int nl, int nh)
    {
   for (i=nrl+1; i<=nrh; i++) {    free((FREE_ARG)(v+nl-NR_END));
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  }
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  /************************ivector *******************************/
   }  char *cvector(long nl,long nh)
   return m;  {
 }    char *v;
     v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
 /*************************free ma3x ************************/    if (!v) nrerror("allocation failure in cvector");
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    return v-nl+NR_END;
 {  }
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /******************free ivector **************************/
   free((FREE_ARG)(m+nrl-NR_END));  void free_cvector(char *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /***************** f1dim *************************/  }
 extern int ncom;  
 extern double *pcom,*xicom;  /************************ivector *******************************/
 extern double (*nrfunc)(double []);  int *ivector(long nl,long nh)
    {
 double f1dim(double x)    int *v;
 {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   int j;    if (!v) nrerror("allocation failure in ivector");
   double f;    return v-nl+NR_END;
   double *xt;  }
    
   xt=vector(1,ncom);  /******************free ivector **************************/
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  void free_ivector(int *v, long nl, long nh)
   f=(*nrfunc)(xt);  {
   free_vector(xt,1,ncom);    free((FREE_ARG)(v+nl-NR_END));
   return f;  }
 }  
   /******************* imatrix *******************************/
 /*****************brent *************************/  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 {  { 
   int iter;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   double a,b,d,etemp;    int **m; 
   double fu,fv,fw,fx;    
   double ftemp;    /* allocate pointers to rows */ 
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double e=0.0;    if (!m) nrerror("allocation failure 1 in matrix()"); 
      m += NR_END; 
   a=(ax < cx ? ax : cx);    m -= nrl; 
   b=(ax > cx ? ax : cx);    
   x=w=v=bx;    
   fw=fv=fx=(*f)(x);    /* allocate rows and set pointers to them */ 
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     xm=0.5*(a+b);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    m[nrl] += NR_END; 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m[nrl] -= ncl; 
     printf(".");fflush(stdout);    
 #ifdef DEBUG    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    /* return pointer to array of pointers to rows */ 
 #endif    return m; 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  } 
       *xmin=x;  
       return fx;  /****************** free_imatrix *************************/
     }  void free_imatrix(m,nrl,nrh,ncl,nch)
     ftemp=fu;        int **m;
     if (fabs(e) > tol1) {        long nch,ncl,nrh,nrl; 
       r=(x-w)*(fx-fv);       /* free an int matrix allocated by imatrix() */ 
       q=(x-v)*(fx-fw);  { 
       p=(x-v)*q-(x-w)*r;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       q=2.0*(q-r);    free((FREE_ARG) (m+nrl-NR_END)); 
       if (q > 0.0) p = -p;  } 
       q=fabs(q);  
       etemp=e;  /******************* matrix *******************************/
       e=d;  double **matrix(long nrl, long nrh, long ncl, long nch)
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  {
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       else {    double **m;
         d=p/q;  
         u=x+d;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         if (u-a < tol2 || b-u < tol2)    if (!m) nrerror("allocation failure 1 in matrix()");
           d=SIGN(tol1,xm-x);    m += NR_END;
       }    m -= nrl;
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    m[nrl] += NR_END;
     fu=(*f)(u);    m[nrl] -= ncl;
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       SHFT(v,w,x,u)    return m;
         SHFT(fv,fw,fx,fu)    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
         } else {     */
           if (u < x) a=u; else b=u;  }
           if (fu <= fw || w == x) {  
             v=w;  /*************************free matrix ************************/
             w=u;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
             fv=fw;  {
             fw=fu;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
           } else if (fu <= fv || v == x || v == w) {    free((FREE_ARG)(m+nrl-NR_END));
             v=u;  }
             fv=fu;  
           }  /******************* ma3x *******************************/
         }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   }  {
   nrerror("Too many iterations in brent");    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   *xmin=x;    double ***m;
   return fx;  
 }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /****************** mnbrak ***********************/    m += NR_END;
     m -= nrl;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double ulim,u,r,q, dum;    m[nrl] += NR_END;
   double fu;    m[nrl] -= ncl;
    
   *fa=(*func)(*ax);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   *fb=(*func)(*bx);  
   if (*fb > *fa) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     SHFT(dum,*ax,*bx,dum)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       SHFT(dum,*fb,*fa,dum)    m[nrl][ncl] += NR_END;
       }    m[nrl][ncl] -= nll;
   *cx=(*bx)+GOLD*(*bx-*ax);    for (j=ncl+1; j<=nch; j++) 
   *fc=(*func)(*cx);      m[nrl][j]=m[nrl][j-1]+nlay;
   while (*fb > *fc) {    
     r=(*bx-*ax)*(*fb-*fc);    for (i=nrl+1; i<=nrh; i++) {
     q=(*bx-*cx)*(*fb-*fa);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      for (j=ncl+1; j<=nch; j++) 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        m[i][j]=m[i][j-1]+nlay;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    }
     if ((*bx-u)*(u-*cx) > 0.0) {    return m; 
       fu=(*func)(u);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     } else if ((*cx-u)*(u-ulim) > 0.0) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       fu=(*func)(u);    */
       if (fu < *fc) {  }
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  /*************************free ma3x ************************/
           }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  {
       u=ulim;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       fu=(*func)(u);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     } else {    free((FREE_ARG)(m+nrl-NR_END));
       u=(*cx)+GOLD*(*cx-*bx);  }
       fu=(*func)(u);  
     }  /***************** f1dim *************************/
     SHFT(*ax,*bx,*cx,u)  extern int ncom; 
       SHFT(*fa,*fb,*fc,fu)  extern double *pcom,*xicom;
       }  extern double (*nrfunc)(double []); 
 }   
   double f1dim(double x) 
 /*************** linmin ************************/  { 
     int j; 
 int ncom;    double f;
 double *pcom,*xicom;    double *xt; 
 double (*nrfunc)(double []);   
      xt=vector(1,ncom); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 {    f=(*nrfunc)(xt); 
   double brent(double ax, double bx, double cx,    free_vector(xt,1,ncom); 
                double (*f)(double), double tol, double *xmin);    return f; 
   double f1dim(double x);  } 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  /*****************brent *************************/
   int j;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   double xx,xmin,bx,ax;  { 
   double fx,fb,fa;    int iter; 
      double a,b,d,etemp;
   ncom=n;    double fu,fv,fw,fx;
   pcom=vector(1,n);    double ftemp;
   xicom=vector(1,n);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   nrfunc=func;    double e=0.0; 
   for (j=1;j<=n;j++) {   
     pcom[j]=p[j];    a=(ax < cx ? ax : cx); 
     xicom[j]=xi[j];    b=(ax > cx ? ax : cx); 
   }    x=w=v=bx; 
   ax=0.0;    fw=fv=fx=(*f)(x); 
   xx=1.0;    for (iter=1;iter<=ITMAX;iter++) { 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      xm=0.5*(a+b); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 #ifdef DEBUG      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      printf(".");fflush(stdout);
 #endif      fprintf(ficlog,".");fflush(ficlog);
   for (j=1;j<=n;j++) {  #ifdef DEBUG
     xi[j] *= xmin;      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);
     p[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)))) { */
   free_vector(xicom,1,n);  #endif
   free_vector(pcom,1,n);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 }        *xmin=x; 
         return fx; 
 /*************** powell ************************/      } 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      ftemp=fu;
             double (*func)(double []))      if (fabs(e) > tol1) { 
 {        r=(x-w)*(fx-fv); 
   void linmin(double p[], double xi[], int n, double *fret,        q=(x-v)*(fx-fw); 
               double (*func)(double []));        p=(x-v)*q-(x-w)*r; 
   int i,ibig,j;        q=2.0*(q-r); 
   double del,t,*pt,*ptt,*xit;        if (q > 0.0) p = -p; 
   double fp,fptt;        q=fabs(q); 
   double *xits;        etemp=e; 
   pt=vector(1,n);        e=d; 
   ptt=vector(1,n);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   xit=vector(1,n);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   xits=vector(1,n);        else { 
   *fret=(*func)(p);          d=p/q; 
   for (j=1;j<=n;j++) pt[j]=p[j];          u=x+d; 
   for (*iter=1;;++(*iter)) {          if (u-a < tol2 || b-u < tol2) 
     fp=(*fret);            d=SIGN(tol1,xm-x); 
     ibig=0;        } 
     del=0.0;      } else { 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for (i=1;i<=n;i++)      } 
       printf(" %d %.12f",i, p[i]);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     printf("\n");      fu=(*f)(u); 
     for (i=1;i<=n;i++) {      if (fu <= fx) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        if (u >= x) a=x; else b=x; 
       fptt=(*fret);        SHFT(v,w,x,u) 
 #ifdef DEBUG          SHFT(fv,fw,fx,fu) 
       printf("fret=%lf \n",*fret);          } else { 
 #endif            if (u < x) a=u; else b=u; 
       printf("%d",i);fflush(stdout);            if (fu <= fw || w == x) { 
       linmin(p,xit,n,fret,func);              v=w; 
       if (fabs(fptt-(*fret)) > del) {              w=u; 
         del=fabs(fptt-(*fret));              fv=fw; 
         ibig=i;              fw=fu; 
       }            } else if (fu <= fv || v == x || v == w) { 
 #ifdef DEBUG              v=u; 
       printf("%d %.12e",i,(*fret));              fv=fu; 
       for (j=1;j<=n;j++) {            } 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);          } 
         printf(" x(%d)=%.12e",j,xit[j]);    } 
       }    nrerror("Too many iterations in brent"); 
       for(j=1;j<=n;j++)    *xmin=x; 
         printf(" p=%.12e",p[j]);    return fx; 
       printf("\n");  } 
 #endif  
     }  /****************** mnbrak ***********************/
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       int k[2],l;              double (*func)(double)) 
       k[0]=1;  { 
       k[1]=-1;    double ulim,u,r,q, dum;
       printf("Max: %.12e",(*func)(p));    double fu; 
       for (j=1;j<=n;j++)   
         printf(" %.12e",p[j]);    *fa=(*func)(*ax); 
       printf("\n");    *fb=(*func)(*bx); 
       for(l=0;l<=1;l++) {    if (*fb > *fa) { 
         for (j=1;j<=n;j++) {      SHFT(dum,*ax,*bx,dum) 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        SHFT(dum,*fb,*fa,dum) 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        } 
         }    *cx=(*bx)+GOLD*(*bx-*ax); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    *fc=(*func)(*cx); 
       }    while (*fb > *fc) { 
 #endif      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       free_vector(xit,1,n);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       free_vector(xits,1,n);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       free_vector(ptt,1,n);      if ((*bx-u)*(u-*cx) > 0.0) { 
       free_vector(pt,1,n);        fu=(*func)(u); 
       return;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     }        fu=(*func)(u); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        if (fu < *fc) { 
     for (j=1;j<=n;j++) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       ptt[j]=2.0*p[j]-pt[j];            SHFT(*fb,*fc,fu,(*func)(u)) 
       xit[j]=p[j]-pt[j];            } 
       pt[j]=p[j];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     }        u=ulim; 
     fptt=(*func)(ptt);        fu=(*func)(u); 
     if (fptt < fp) {      } else { 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        u=(*cx)+GOLD*(*cx-*bx); 
       if (t < 0.0) {        fu=(*func)(u); 
         linmin(p,xit,n,fret,func);      } 
         for (j=1;j<=n;j++) {      SHFT(*ax,*bx,*cx,u) 
           xi[j][ibig]=xi[j][n];        SHFT(*fa,*fb,*fc,fu) 
           xi[j][n]=xit[j];        } 
         }  } 
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /*************** linmin ************************/
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  int ncom; 
         printf("\n");  double *pcom,*xicom;
 #endif  double (*nrfunc)(double []); 
       }   
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   }  { 
 }    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
 /**** Prevalence limit ****************/    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)                double *fc, double (*func)(double)); 
 {    int j; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    double xx,xmin,bx,ax; 
      matrix by transitions matrix until convergence is reached */    double fx,fb,fa;
    
   int i, ii,j,k;    ncom=n; 
   double min, max, maxmin, maxmax,sumnew=0.;    pcom=vector(1,n); 
   double **matprod2();    xicom=vector(1,n); 
   double **out, cov[NCOVMAX], **pmij();    nrfunc=func; 
   double **newm;    for (j=1;j<=n;j++) { 
   double agefin, delaymax=50 ; /* Max number of years to converge */      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
   for (ii=1;ii<=nlstate+ndeath;ii++)    } 
     for (j=1;j<=nlstate+ndeath;j++){    ax=0.0; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    xx=1.0; 
     }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
    cov[1]=1.;  #ifdef DEBUG
      printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #endif
     newm=savm;    for (j=1;j<=n;j++) { 
     /* Covariates have to be included here again */      xi[j] *= xmin; 
      cov[2]=agefin;      p[j] += xi[j]; 
      } 
       for (k=1; k<=cptcovn;k++) {    free_vector(xicom,1,n); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    free_vector(pcom,1,n); 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  } 
       }  
       for (k=1; k<=cptcovage;k++)  /*************** powell ************************/
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for (k=1; k<=cptcovprod;k++)              double (*func)(double [])) 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  { 
     void linmin(double p[], double xi[], int n, double *fret, 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/                double (*func)(double [])); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    double fp,fptt;
     double *xits;
     savm=oldm;    pt=vector(1,n); 
     oldm=newm;    ptt=vector(1,n); 
     maxmax=0.;    xit=vector(1,n); 
     for(j=1;j<=nlstate;j++){    xits=vector(1,n); 
       min=1.;    *fret=(*func)(p); 
       max=0.;    for (j=1;j<=n;j++) pt[j]=p[j]; 
       for(i=1; i<=nlstate; i++) {    for (*iter=1;;++(*iter)) { 
         sumnew=0;      fp=(*fret); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      ibig=0; 
         prlim[i][j]= newm[i][j]/(1-sumnew);      del=0.0; 
         max=FMAX(max,prlim[i][j]);      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         min=FMIN(min,prlim[i][j]);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       }      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       maxmin=max-min;      for (i=1;i<=n;i++) {
       maxmax=FMAX(maxmax,maxmin);        printf(" %d %.12f",i, p[i]);
     }        fprintf(ficlog," %d %.12lf",i, p[i]);
     if(maxmax < ftolpl){        fprintf(ficrespow," %.12lf", p[i]);
       return prlim;      }
     }      printf("\n");
   }      fprintf(ficlog,"\n");
 }      fprintf(ficrespow,"\n");
       for (i=1;i<=n;i++) { 
 /*************** transition probabilities ***************/        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #ifdef DEBUG
 {        printf("fret=%lf \n",*fret);
   double s1, s2;        fprintf(ficlog,"fret=%lf \n",*fret);
   /*double t34;*/  #endif
   int i,j,j1, nc, ii, jj;        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
     for(i=1; i<= nlstate; i++){        linmin(p,xit,n,fret,func); 
     for(j=1; j<i;j++){        if (fabs(fptt-(*fret)) > del) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          del=fabs(fptt-(*fret)); 
         /*s2 += param[i][j][nc]*cov[nc];*/          ibig=i; 
         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);*/  #ifdef DEBUG
       }        printf("%d %.12e",i,(*fret));
       ps[i][j]=s2;        fprintf(ficlog,"%d %.12e",i,(*fret));
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        for (j=1;j<=n;j++) {
     }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for(j=i+1; j<=nlstate+ndeath;j++){          printf(" x(%d)=%.12e",j,xit[j]);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         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(j=1;j<=n;j++) {
       }          printf(" p=%.12e",p[j]);
       ps[i][j]=(s2);          fprintf(ficlog," p=%.12e",p[j]);
     }        }
   }        printf("\n");
     /*ps[3][2]=1;*/        fprintf(ficlog,"\n");
   #endif
   for(i=1; i<= nlstate; i++){      } 
      s1=0;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     for(j=1; j<i; j++)  #ifdef DEBUG
       s1+=exp(ps[i][j]);        int k[2],l;
     for(j=i+1; j<=nlstate+ndeath; j++)        k[0]=1;
       s1+=exp(ps[i][j]);        k[1]=-1;
     ps[i][i]=1./(s1+1.);        printf("Max: %.12e",(*func)(p));
     for(j=1; j<i; j++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
       ps[i][j]= exp(ps[i][j])*ps[i][i];        for (j=1;j<=n;j++) {
     for(j=i+1; j<=nlstate+ndeath; j++)          printf(" %.12e",p[j]);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          fprintf(ficlog," %.12e",p[j]);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        }
   } /* end i */        printf("\n");
         fprintf(ficlog,"\n");
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        for(l=0;l<=1;l++) {
     for(jj=1; jj<= nlstate+ndeath; jj++){          for (j=1;j<=n;j++) {
       ps[ii][jj]=0;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       ps[ii][ii]=1;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   }          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        }
     for(jj=1; jj<= nlstate+ndeath; jj++){  #endif
      printf("%lf ",ps[ii][jj]);  
    }  
     printf("\n ");        free_vector(xit,1,n); 
     }        free_vector(xits,1,n); 
     printf("\n ");printf("%lf ",cov[2]);*/        free_vector(ptt,1,n); 
 /*        free_vector(pt,1,n); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        return; 
   goto end;*/      } 
     return ps;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 }      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
 /**************** Product of 2 matrices ******************/        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      } 
 {      fptt=(*func)(ptt); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      if (fptt < fp) { 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   /* in, b, out are matrice of pointers which should have been initialized        if (t < 0.0) { 
      before: only the contents of out is modified. The function returns          linmin(p,xit,n,fret,func); 
      a pointer to pointers identical to out */          for (j=1;j<=n;j++) { 
   long i, j, k;            xi[j][ibig]=xi[j][n]; 
   for(i=nrl; i<= nrh; i++)            xi[j][n]=xit[j]; 
     for(k=ncolol; k<=ncoloh; k++)          }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  #ifdef DEBUG
         out[i][k] +=in[i][j]*b[j][k];          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);
   return out;          for(j=1;j<=n;j++){
 }            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
           }
 /************* Higher Matrix Product ***************/          printf("\n");
           fprintf(ficlog,"\n");
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  #endif
 {        }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      } 
      duration (i.e. until    } 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  } 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).  /**** Prevalence limit (stable prevalence)  ****************/
      Model is determined by parameters x and covariates have to be  
      included manually here.  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
      */    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];    int i, ii,j,k;
   double **newm;    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
   /* Hstepm could be zero and should return the unit matrix */    double **out, cov[NCOVMAX], **pmij();
   for (i=1;i<=nlstate+ndeath;i++)    double **newm;
     for (j=1;j<=nlstate+ndeath;j++){    double agefin, delaymax=50 ; /* Max number of years to converge */
       oldm[i][j]=(i==j ? 1.0 : 0.0);  
       po[i][j][0]=(i==j ? 1.0 : 0.0);    for (ii=1;ii<=nlstate+ndeath;ii++)
     }      for (j=1;j<=nlstate+ndeath;j++){
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(h=1; h <=nhstepm; h++){      }
     for(d=1; d <=hstepm; d++){  
       newm=savm;     cov[1]=1.;
       /* Covariates have to be included here again */   
       cov[1]=1.;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      newm=savm;
       for (k=1; k<=cptcovage;k++)      /* Covariates have to be included here again */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       cov[2]=agefin;
       for (k=1; k<=cptcovprod;k++)    
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        for (k=1; k<=cptcovprod;k++)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       savm=oldm;  
       oldm=newm;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for(i=1; i<=nlstate+ndeath; i++)        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       for(j=1;j<=nlstate+ndeath;j++) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      savm=oldm;
          */      oldm=newm;
       }      maxmax=0.;
   } /* end h */      for(j=1;j<=nlstate;j++){
   return po;        min=1.;
 }        max=0.;
         for(i=1; i<=nlstate; i++) {
           sumnew=0;
 /*************** log-likelihood *************/          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 double func( double *x)          prlim[i][j]= newm[i][j]/(1-sumnew);
 {          max=FMAX(max,prlim[i][j]);
   int i, ii, j, k, mi, d, kk;          min=FMIN(min,prlim[i][j]);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        }
   double **out;        maxmin=max-min;
   double sw; /* Sum of weights */        maxmax=FMAX(maxmax,maxmin);
   double lli; /* Individual log likelihood */      }
   long ipmx;      if(maxmax < ftolpl){
   /*extern weight */        return prlim;
   /* We are differentiating ll according to initial status */      }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    }
   /*for(i=1;i<imx;i++)  }
     printf(" %d\n",s[4][i]);  
   */  /*************** transition probabilities ***************/ 
   cov[1]=1.;  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   for(k=1; k<=nlstate; k++) ll[k]=0.;  {
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    double s1, s2;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    /*double t34;*/
     for(mi=1; mi<= wav[i]-1; mi++){    int i,j,j1, nc, ii, jj;
       for (ii=1;ii<=nlstate+ndeath;ii++)  
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      for(i=1; i<= nlstate; i++){
       for(d=0; d<dh[mi][i]; d++){      for(j=1; j<i;j++){
         newm=savm;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          /*s2 += param[i][j][nc]*cov[nc];*/
         for (kk=1; kk<=cptcovage;kk++) {          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }        }
                ps[i][j]=s2;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      }
         savm=oldm;      for(j=i+1; j<=nlstate+ndeath;j++){
         oldm=newm;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
                  s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
                  /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       } /* end mult */        }
              ps[i][j]=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]]);*/    }
       ipmx +=1;      /*ps[3][2]=1;*/
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    for(i=1; i<= nlstate; i++){
     } /* end of wave */       s1=0;
   } /* end of individual */      for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      for(j=i+1; j<=nlstate+ndeath; j++)
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        s1+=exp(ps[i][j]);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      ps[i][i]=1./(s1+1.);
   return -l;      for(j=1; j<i; j++)
 }        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
 /*********** Maximum Likelihood Estimation ***************/      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     } /* end i */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   int i,j, iter;      for(jj=1; jj<= nlstate+ndeath; jj++){
   double **xi,*delti;        ps[ii][jj]=0;
   double fret;        ps[ii][ii]=1;
   xi=matrix(1,npar,1,npar);      }
   for (i=1;i<=npar;i++)    }
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   powell(p,xi,npar,ftol,&iter,&fret,func);      for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));     }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));      printf("\n ");
       }
 }      printf("\n ");printf("%lf ",cov[2]);*/
   /*
 /**** Computes Hessian and covariance matrix ***/    for(i=1; i<= npar; i++) printf("%f ",x[i]);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    goto end;*/
 {      return ps;
   double  **a,**y,*x,pd;  }
   double **hess;  
   int i, j,jk;  /**************** Product of 2 matrices ******************/
   int *indx;  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   double hessii(double p[], double delta, int theta, double delti[]);  {
   double hessij(double p[], double delti[], int i, int j);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   void lubksb(double **a, int npar, int *indx, double b[]) ;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   void ludcmp(double **a, int npar, int *indx, double *d) ;    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
   hess=matrix(1,npar,1,npar);       a pointer to pointers identical to out */
     long i, j, k;
   printf("\nCalculation of the hessian matrix. Wait...\n");    for(i=nrl; i<= nrh; i++)
   for (i=1;i<=npar;i++){      for(k=ncolol; k<=ncoloh; k++)
     printf("%d",i);fflush(stdout);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     hess[i][i]=hessii(p,ftolhess,i,delti);          out[i][k] +=in[i][j]*b[j][k];
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/    return out;
   }  }
    
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {  /************* Higher Matrix Product ***************/
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         hess[i][j]=hessij(p,delti,i,j);  {
         hess[j][i]=hess[i][j];        /* Computes the transition matrix starting at age 'age' over 
         /*printf(" %lf ",hess[i][j]);*/       'nhstepm*hstepm*stepm' months (i.e. until
       }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     }       nhstepm*hstepm matrices. 
   }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   printf("\n");       (typically every 2 years instead of every month which is too big 
        for the memory).
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");       Model is determined by parameters x and covariates have to be 
         included manually here. 
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);       */
   x=vector(1,npar);  
   indx=ivector(1,npar);    int i, j, d, h, k;
   for (i=1;i<=npar;i++)    double **out, cov[NCOVMAX];
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    double **newm;
   ludcmp(a,npar,indx,&pd);  
     /* Hstepm could be zero and should return the unit matrix */
   for (j=1;j<=npar;j++) {    for (i=1;i<=nlstate+ndeath;i++)
     for (i=1;i<=npar;i++) x[i]=0;      for (j=1;j<=nlstate+ndeath;j++){
     x[j]=1;        oldm[i][j]=(i==j ? 1.0 : 0.0);
     lubksb(a,npar,indx,x);        po[i][j][0]=(i==j ? 1.0 : 0.0);
     for (i=1;i<=npar;i++){      }
       matcov[i][j]=x[i];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    for(h=1; h <=nhstepm; h++){
   }      for(d=1; d <=hstepm; d++){
         newm=savm;
   printf("\n#Hessian matrix#\n");        /* Covariates have to be included here again */
   for (i=1;i<=npar;i++) {        cov[1]=1.;
     for (j=1;j<=npar;j++) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       printf("%.3e ",hess[i][j]);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     }        for (k=1; k<=cptcovage;k++)
     printf("\n");          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]]];
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   ludcmp(a,npar,indx,&pd);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   /*  printf("\n#Hessian matrix recomputed#\n");                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
   for (j=1;j<=npar;j++) {        oldm=newm;
     for (i=1;i<=npar;i++) x[i]=0;      }
     x[j]=1;      for(i=1; i<=nlstate+ndeath; i++)
     lubksb(a,npar,indx,x);        for(j=1;j<=nlstate+ndeath;j++) {
     for (i=1;i<=npar;i++){          po[i][j][h]=newm[i][j];
       y[i][j]=x[i];          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       printf("%.3e ",y[i][j]);           */
     }        }
     printf("\n");    } /* end h */
   }    return po;
   */  }
   
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);  /*************** log-likelihood *************/
   free_vector(x,1,npar);  double func( double *x)
   free_ivector(indx,1,npar);  {
   free_matrix(hess,1,npar,1,npar);    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
 }    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
 /*************** hessian matrix ****************/    int s1, s2;
 double hessii( double x[], double delta, int theta, double delti[])    double bbh, survp;
 {    long ipmx;
   int i;    /*extern weight */
   int l=1, lmax=20;    /* We are differentiating ll according to initial status */
   double k1,k2;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double p2[NPARMAX+1];    /*for(i=1;i<imx;i++) 
   double res;      printf(" %d\n",s[4][i]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    */
   double fx;    cov[1]=1.;
   int k=0,kmax=10;  
   double l1;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   fx=func(x);    if(mle==1){
   for (i=1;i<=npar;i++) p2[i]=x[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for(l=0 ; l <=lmax; l++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     l1=pow(10,l);        for(mi=1; mi<= wav[i]-1; mi++){
     delts=delt;          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(k=1 ; k <kmax; k=k+1){            for (j=1;j<=nlstate+ndeath;j++){
       delt = delta*(l1*k);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       p2[theta]=x[theta] +delt;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       k1=func(p2)-fx;            }
       p2[theta]=x[theta]-delt;          for(d=0; d<dh[mi][i]; d++){
       k2=func(p2)-fx;            newm=savm;
       /*res= (k1-2.0*fx+k2)/delt/delt; */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */            for (kk=1; kk<=cptcovage;kk++) {
                    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 #ifdef DEBUG            }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 #endif                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            savm=oldm;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            oldm=newm;
         k=kmax;          } /* end mult */
       }        
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         k=kmax; l=lmax*10.;          /* But now since version 0.9 we anticipate for bias and large stepm.
       }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){           * (in months) between two waves is not a multiple of stepm, we rounded to 
         delts=delt;           * the nearest (and in case of equal distance, to the lowest) interval but now
       }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     }           * (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
   delti[theta]=delts;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   return res;           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
 }           * For stepm > 1 the results are less biased than in previous versions. 
            */
 double hessij( double x[], double delti[], int thetai,int thetaj)          s1=s[mw[mi][i]][i];
 {          s2=s[mw[mi+1][i]][i];
   int i;          bbh=(double)bh[mi][i]/(double)stepm; 
   int l=1, l1, lmax=20;          /* bias is positive if real duration
   double k1,k2,k3,k4,res,fx;           * is higher than the multiple of stepm and negative otherwise.
   double p2[NPARMAX+1];           */
   int k;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
   fx=func(x);            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   for (k=1; k<=2; k++) {               to the likelihood is the probability to die between last step unit time and current 
     for (i=1;i<=npar;i++) p2[i]=x[i];               step unit time, which is also the differences between probability to die before dh 
     p2[thetai]=x[thetai]+delti[thetai]/k;               and probability to die before dh-stepm . 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;               In version up to 0.92 likelihood was computed
     k1=func(p2)-fx;          as if date of death was unknown. Death was treated as any other
            health state: the date of the interview describes the actual state
     p2[thetai]=x[thetai]+delti[thetai]/k;          and not the date of a change in health state. The former idea was
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          to consider that at each interview the state was recorded
     k2=func(p2)-fx;          (healthy, disable or death) and IMaCh was corrected; but when we
            introduced the exact date of death then we should have modified
     p2[thetai]=x[thetai]-delti[thetai]/k;          the contribution of an exact death to the likelihood. This new
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          contribution is smaller and very dependent of the step unit
     k3=func(p2)-fx;          stepm. It is no more the probability to die between last interview
            and month of death but the probability to survive from last
     p2[thetai]=x[thetai]-delti[thetai]/k;          interview up to one month before death multiplied by the
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          probability to die within a month. Thanks to Chris
     k4=func(p2)-fx;          Jackson for correcting this bug.  Former versions increased
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          mortality artificially. The bad side is that we add another loop
 #ifdef DEBUG          which slows down the processing. The difference can be up to 10%
     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);          lower mortality.
 #endif            */
   }            lli=log(out[s1][s2] - savm[s1][s2]);
   return res;          }else{
 }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
 /************** Inverse of matrix **************/          } 
 void ludcmp(double **a, int n, int *indx, double *d)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 {          /*if(lli ==000.0)*/
   int i,imax,j,k;          /*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); */
   double big,dum,sum,temp;          ipmx +=1;
   double *vv;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   vv=vector(1,n);        } /* end of wave */
   *d=1.0;      } /* end of individual */
   for (i=1;i<=n;i++) {    }  else if(mle==2){
     big=0.0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (j=1;j<=n;j++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if ((temp=fabs(a[i][j])) > big) big=temp;        for(mi=1; mi<= wav[i]-1; mi++){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          for (ii=1;ii<=nlstate+ndeath;ii++)
     vv[i]=1.0/big;            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1;j<=n;j++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1;i<j;i++) {            }
       sum=a[i][j];          for(d=0; d<=dh[mi][i]; d++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            newm=savm;
       a[i][j]=sum;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
     big=0.0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (i=j;i<=n;i++) {            }
       sum=a[i][j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (k=1;k<j;k++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         sum -= a[i][k]*a[k][j];            savm=oldm;
       a[i][j]=sum;            oldm=newm;
       if ( (dum=vv[i]*fabs(sum)) >= big) {          } /* end mult */
         big=dum;        
         imax=i;          /*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.
     }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     if (j != imax) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
       for (k=1;k<=n;k++) {           * the nearest (and in case of equal distance, to the lowest) interval but now
         dum=a[imax][k];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         a[imax][k]=a[j][k];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         a[j][k]=dum;           * probability in order to take into account the bias as a fraction of the way
       }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       *d = -(*d);           * -stepm/2 to stepm/2 .
       vv[imax]=vv[j];           * 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. 
     indx[j]=imax;           */
     if (a[j][j] == 0.0) a[j][j]=TINY;          s1=s[mw[mi][i]][i];
     if (j != n) {          s2=s[mw[mi+1][i]][i];
       dum=1.0/(a[j][j]);          bbh=(double)bh[mi][i]/(double)stepm; 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          /* bias is positive if real duration
     }           * is higher than the multiple of stepm and negative otherwise.
   }           */
   free_vector(vv,1,n);  /* Doesn't work */          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 ;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 }          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 void lubksb(double **a, int n, int *indx, double b[])          /*if(lli ==000.0)*/
 {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   int i,ii=0,ip,j;          ipmx +=1;
   double sum;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (i=1;i<=n;i++) {        } /* end of wave */
     ip=indx[i];      } /* end of individual */
     sum=b[ip];    }  else if(mle==3){  /* exponential inter-extrapolation */
     b[ip]=b[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if (ii)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        for(mi=1; mi<= wav[i]-1; mi++){
     else if (sum) ii=i;          for (ii=1;ii<=nlstate+ndeath;ii++)
     b[i]=sum;            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=n;i>=1;i--) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     sum=b[i];            }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          for(d=0; d<dh[mi][i]; d++){
     b[i]=sum/a[i][i];            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /************ Frequencies ********************/            }
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {  /* Some frequencies */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            oldm=newm;
   double ***freq; /* Frequencies */          } /* end mult */
   double *pp;        
   double pos;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   FILE *ficresp;          /* But now since version 0.9 we anticipate for bias and large stepm.
   char fileresp[FILENAMELENGTH];           * 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 
   pp=vector(1,nlstate);           * the nearest (and in case of equal distance, to the lowest) interval but now
  probs= ma3x(1,130 ,1,8, 1,8);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   strcpy(fileresp,"p");           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   strcat(fileresp,fileres);           * probability in order to take into account the bias as a fraction of the way
   if((ficresp=fopen(fileresp,"w"))==NULL) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     printf("Problem with prevalence resultfile: %s\n", fileresp);           * -stepm/2 to stepm/2 .
     exit(0);           * 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. 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           */
   j1=0;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   j=cptcoveff;          bbh=(double)bh[mi][i]/(double)stepm; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   for(k1=1; k1<=j;k1++){           */
    for(i1=1; i1<=ncodemax[k1];i1++){          /* 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 */
        j1++;          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 */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
          scanf("%d", i);*/          /*if(lli ==000.0)*/
         for (i=-1; i<=nlstate+ndeath; i++)            /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          for (jk=-1; jk<=nlstate+ndeath; jk++)            ipmx +=1;
            for(m=agemin; m <= agemax+3; m++)          sw += weight[i];
              freq[i][jk][m]=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                } /* end of wave */
        for (i=1; i<=imx; i++) {      } /* end of individual */
          bool=1;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
          if  (cptcovn>0) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
            for (z1=1; z1<=cptcoveff; z1++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        for(mi=1; mi<= wav[i]-1; mi++){
                bool=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
          }            for (j=1;j<=nlstate+ndeath;j++){
           if (bool==1) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
            for(m=fprev1; m<=lprev1; m++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              if(agev[m][i]==0) agev[m][i]=agemax+1;            }
              if(agev[m][i]==1) agev[m][i]=agemax+2;          for(d=0; d<dh[mi][i]; d++){
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            newm=savm;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
            }            for (kk=1; kk<=cptcovage;kk++) {
          }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        }            }
         if  (cptcovn>0) {          
          fprintf(ficresp, "\n#********** Variable ");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
        fprintf(ficresp, "**********\n#");            savm=oldm;
         }            oldm=newm;
        for(i=1; i<=nlstate;i++)          } /* end mult */
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        
        fprintf(ficresp, "\n");          s1=s[mw[mi][i]][i];
                  s2=s[mw[mi+1][i]][i];
   for(i=(int)agemin; i <= (int)agemax+3; i++){          if( s2 > nlstate){ 
     if(i==(int)agemax+3)            lli=log(out[s1][s2] - savm[s1][s2]);
       printf("Total");          }else{
     else            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       printf("Age %d", i);          }
     for(jk=1; jk <=nlstate ; jk++){          ipmx +=1;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          sw += weight[i];
         pp[jk] += freq[jk][m][i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     for(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
       for(m=-1, pos=0; m <=0 ; m++)      } /* end of individual */
         pos += freq[jk][m][i];    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       if(pp[jk]>=1.e-10)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       else        for(mi=1; mi<= wav[i]-1; mi++){
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      for(jk=1; jk <=nlstate ; jk++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            }
         pp[jk] += freq[jk][m][i];          for(d=0; d<dh[mi][i]; d++){
      }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(jk=1,pos=0; jk <=nlstate ; jk++)            for (kk=1; kk<=cptcovage;kk++) {
       pos += pp[jk];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     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);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            savm=oldm;
       if( i <= (int) agemax){            oldm=newm;
         if(pos>=1.e-5){          } /* end mult */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        
           probs[i][jk][j1]= pp[jk]/pos;          s1=s[mw[mi][i]][i];
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          s2=s[mw[mi+1][i]][i];
         }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       else          ipmx +=1;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     for(jk=-1; jk <=nlstate+ndeath; jk++)        } /* end of wave */
       for(m=-1; m <=nlstate+ndeath; m++)      } /* end of individual */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    } /* End of if */
     if(i <= (int) agemax)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       fprintf(ficresp,"\n");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     printf("\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }    /*exit(0); */
     }    return -l;
  }  }
    
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /*********** Maximum Likelihood Estimation ***************/
   free_vector(pp,1,nlstate);  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 }  /* End of Freq */  {
     int i,j, iter;
 /************ Prevalence ********************/    double **xi;
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)    double fret;
 {  /* Some frequencies */    char filerespow[FILENAMELENGTH];
      xi=matrix(1,npar,1,npar);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    for (i=1;i<=npar;i++)
   double ***freq; /* Frequencies */      for (j=1;j<=npar;j++)
   double *pp;        xi[i][j]=(i==j ? 1.0 : 0.0);
   double pos;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
   pp=vector(1,nlstate);    strcat(filerespow,fileres);
   probs= ma3x(1,130 ,1,8, 1,8);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", filerespow);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   j1=0;    }
      fprintf(ficrespow,"# Powell\n# iter -2*LL");
   j=cptcoveff;    for (i=1;i<=nlstate;i++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for(j=1;j<=nlstate+ndeath;j++)
          if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
  for(k1=1; k1<=j;k1++){    fprintf(ficrespow,"\n");
     for(i1=1; i1<=ncodemax[k1];i1++){    powell(p,xi,npar,ftol,&iter,&fret,func);
       j1++;  
      fclose(ficrespow);
       for (i=-1; i<=nlstate+ndeath; i++)      printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         for (jk=-1; jk<=nlstate+ndeath; jk++)      fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           for(m=agemin; m <= agemax+3; m++)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           freq[i][jk][m]=0;  
        }
       for (i=1; i<=imx; i++) {  
         bool=1;  /**** Computes Hessian and covariance matrix ***/
         if  (cptcovn>0) {  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           for (z1=1; z1<=cptcoveff; z1++)  {
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double  **a,**y,*x,pd;
               bool=0;    double **hess;
               }    int i, j,jk;
         if (bool==1) {    int *indx;
           for(m=fprev1; m<=lprev1; m++){  
             if(agev[m][i]==0) agev[m][i]=agemax+1;    double hessii(double p[], double delta, int theta, double delti[]);
             if(agev[m][i]==1) agev[m][i]=agemax+2;    double hessij(double p[], double delti[], int i, int j);
             freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    void lubksb(double **a, int npar, int *indx, double b[]) ;
             freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    void ludcmp(double **a, int npar, int *indx, double *d) ;
           }  
         }    hess=matrix(1,npar,1,npar);
       }  
        for(i=(int)agemin; i <= (int)agemax+3; i++){    printf("\nCalculation of the hessian matrix. Wait...\n");
         for(jk=1; jk <=nlstate ; jk++){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    for (i=1;i<=npar;i++){
             pp[jk] += freq[jk][m][i];      printf("%d",i);fflush(stdout);
         }      fprintf(ficlog,"%d",i);fflush(ficlog);
         for(jk=1; jk <=nlstate ; jk++){      hess[i][i]=hessii(p,ftolhess,i,delti);
           for(m=-1, pos=0; m <=0 ; m++)      /*printf(" %f ",p[i]);*/
             pos += freq[jk][m][i];      /*printf(" %lf ",hess[i][i]);*/
         }    }
            
          for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=npar;i++) {
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      for (j=1;j<=npar;j++)  {
              pp[jk] += freq[jk][m][i];        if (j>i) { 
          }          printf(".%d%d",i,j);fflush(stdout);
                    fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          hess[i][j]=hessij(p,delti,i,j);
           hess[j][i]=hess[i][j];    
          for(jk=1; jk <=nlstate ; jk++){                    /*printf(" %lf ",hess[i][j]);*/
            if( i <= (int) agemax){        }
              if(pos>=1.e-5){      }
                probs[i][jk][j1]= pp[jk]/pos;    }
              }    printf("\n");
            }    fprintf(ficlog,"\n");
          }  
              printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
          }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     }    
   }    a=matrix(1,npar,1,npar);
      y=matrix(1,npar,1,npar);
      x=vector(1,npar);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    indx=ivector(1,npar);
   free_vector(pp,1,nlstate);    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 }  /* End of Freq */    ludcmp(a,npar,indx,&pd);
 /************* Waves Concatenation ***************/  
     for (j=1;j<=npar;j++) {
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      for (i=1;i<=npar;i++) x[i]=0;
 {      x[j]=1;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      lubksb(a,npar,indx,x);
      Death is a valid wave (if date is known).      for (i=1;i<=npar;i++){ 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        matcov[i][j]=x[i];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      }
      and mw[mi+1][i]. dh depends on stepm.    }
      */  
     printf("\n#Hessian matrix#\n");
   int i, mi, m;    fprintf(ficlog,"\n#Hessian matrix#\n");
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    for (i=1;i<=npar;i++) { 
      double sum=0., jmean=0.;*/      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
   int j, k=0,jk, ju, jl;        fprintf(ficlog,"%.3e ",hess[i][j]);
   double sum=0.;      }
   jmin=1e+5;      printf("\n");
   jmax=-1;      fprintf(ficlog,"\n");
   jmean=0.;    }
   for(i=1; i<=imx; i++){  
     mi=0;    /* Recompute Inverse */
     m=firstpass;    for (i=1;i<=npar;i++)
     while(s[m][i] <= nlstate){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       if(s[m][i]>=1)    ludcmp(a,npar,indx,&pd);
         mw[++mi][i]=m;  
       if(m >=lastpass)    /*  printf("\n#Hessian matrix recomputed#\n");
         break;  
       else    for (j=1;j<=npar;j++) {
         m++;      for (i=1;i<=npar;i++) x[i]=0;
     }/* end while */      x[j]=1;
     if (s[m][i] > nlstate){      lubksb(a,npar,indx,x);
       mi++;     /* Death is another wave */      for (i=1;i<=npar;i++){ 
       /* if(mi==0)  never been interviewed correctly before death */        y[i][j]=x[i];
          /* Only death is a correct wave */        printf("%.3e ",y[i][j]);
       mw[mi][i]=m;        fprintf(ficlog,"%.3e ",y[i][j]);
     }      }
       printf("\n");
     wav[i]=mi;      fprintf(ficlog,"\n");
     if(mi==0)    }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    */
   }  
     free_matrix(a,1,npar,1,npar);
   for(i=1; i<=imx; i++){    free_matrix(y,1,npar,1,npar);
     for(mi=1; mi<wav[i];mi++){    free_vector(x,1,npar);
       if (stepm <=0)    free_ivector(indx,1,npar);
         dh[mi][i]=1;    free_matrix(hess,1,npar,1,npar);
       else{  
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {  }
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */  /*************** hessian matrix ****************/
           k=k+1;  double hessii( double x[], double delta, int theta, double delti[])
           if (j >= jmax) jmax=j;  {
           if (j <= jmin) jmin=j;    int i;
           sum=sum+j;    int l=1, lmax=20;
           /* if (j<10) printf("j=%d num=%d ",j,i); */    double k1,k2;
           }    double p2[NPARMAX+1];
         }    double res;
         else{    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    double fx;
           k=k+1;    int k=0,kmax=10;
           if (j >= jmax) jmax=j;    double l1;
           else if (j <= jmin)jmin=j;  
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    fx=func(x);
           sum=sum+j;    for (i=1;i<=npar;i++) p2[i]=x[i];
         }    for(l=0 ; l <=lmax; l++){
         jk= j/stepm;      l1=pow(10,l);
         jl= j -jk*stepm;      delts=delt;
         ju= j -(jk+1)*stepm;      for(k=1 ; k <kmax; k=k+1){
         if(jl <= -ju)        delt = delta*(l1*k);
           dh[mi][i]=jk;        p2[theta]=x[theta] +delt;
         else        k1=func(p2)-fx;
           dh[mi][i]=jk+1;        p2[theta]=x[theta]-delt;
         if(dh[mi][i]==0)        k2=func(p2)-fx;
           dh[mi][i]=1; /* At least one step */        /*res= (k1-2.0*fx+k2)/delt/delt; */
       }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     }        
   }  #ifdef DEBUG
   jmean=sum/k;        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);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        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
 /*********** Tricode ****************************/        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 void tricode(int *Tvar, int **nbcode, int imx)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 {          k=kmax;
   int Ndum[20],ij=1, k, j, i;        }
   int cptcode=0;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   cptcoveff=0;          k=kmax; l=lmax*10.;
          }
   for (k=0; k<19; k++) Ndum[k]=0;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   for (k=1; k<=7; k++) ncodemax[k]=0;          delts=delt;
         }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      }
     for (i=1; i<=imx; i++) {    }
       ij=(int)(covar[Tvar[j]][i]);    delti[theta]=delts;
       Ndum[ij]++;    return res; 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    
       if (ij > cptcode) cptcode=ij;  }
     }  
   double hessij( double x[], double delti[], int thetai,int thetaj)
     for (i=0; i<=cptcode; i++) {  {
       if(Ndum[i]!=0) ncodemax[j]++;    int i;
     }    int l=1, l1, lmax=20;
     ij=1;    double k1,k2,k3,k4,res,fx;
     double p2[NPARMAX+1];
     int k;
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {    fx=func(x);
         if (Ndum[k] != 0) {    for (k=1; k<=2; k++) {
           nbcode[Tvar[j]][ij]=k;      for (i=1;i<=npar;i++) p2[i]=x[i];
           ij++;      p2[thetai]=x[thetai]+delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         if (ij > ncodemax[j]) break;      k1=func(p2)-fx;
       }      
     }      p2[thetai]=x[thetai]+delti[thetai]/k;
   }        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
  for (k=0; k<19; k++) Ndum[k]=0;    
       p2[thetai]=x[thetai]-delti[thetai]/k;
  for (i=1; i<=ncovmodel-2; i++) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       ij=Tvar[i];      k3=func(p2)-fx;
       Ndum[ij]++;    
     }      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
  ij=1;      k4=func(p2)-fx;
  for (i=1; i<=10; i++) {      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    if((Ndum[i]!=0) && (i<=ncov)){  #ifdef DEBUG
      Tvaraff[ij]=i;      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);
      ij++;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
    }  #endif
  }    }
      return res;
     cptcoveff=ij-1;  }
 }  
   /************** Inverse of matrix **************/
 /*********** Health Expectancies ****************/  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    int i,imax,j,k; 
 {    double big,dum,sum,temp; 
   /* Health expectancies */    double *vv; 
   int i, j, nhstepm, hstepm, h;   
   double age, agelim,hf;    vv=vector(1,n); 
   double ***p3mat;    *d=1.0; 
      for (i=1;i<=n;i++) { 
   fprintf(ficreseij,"# Health expectancies\n");      big=0.0; 
   fprintf(ficreseij,"# Age");      for (j=1;j<=n;j++) 
   for(i=1; i<=nlstate;i++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
     for(j=1; j<=nlstate;j++)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       fprintf(ficreseij," %1d-%1d",i,j);      vv[i]=1.0/big; 
   fprintf(ficreseij,"\n");    } 
     for (j=1;j<=n;j++) { 
   hstepm=1*YEARM; /*  Every j years of age (in month) */      for (i=1;i<j;i++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   agelim=AGESUP;        a[i][j]=sum; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      } 
     /* nhstepm age range expressed in number of stepm */      big=0.0; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);      for (i=j;i<=n;i++) { 
     /* Typically if 20 years = 20*12/6=40 stepm */        sum=a[i][j]; 
     if (stepm >= YEARM) hstepm=1;        for (k=1;k<j;k++) 
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          sum -= a[i][k]*a[k][j]; 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        a[i][j]=sum; 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        if ( (dum=vv[i]*fabs(sum)) >= big) { 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          big=dum; 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            imax=i; 
         } 
       } 
     for(i=1; i<=nlstate;i++)      if (j != imax) { 
       for(j=1; j<=nlstate;j++)        for (k=1;k<=n;k++) { 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          dum=a[imax][k]; 
           eij[i][j][(int)age] +=p3mat[i][j][h];          a[imax][k]=a[j][k]; 
         }          a[j][k]=dum; 
            } 
     hf=1;        *d = -(*d); 
     if (stepm >= YEARM) hf=stepm/YEARM;        vv[imax]=vv[j]; 
     fprintf(ficreseij,"%.0f",age );      } 
     for(i=1; i<=nlstate;i++)      indx[j]=imax; 
       for(j=1; j<=nlstate;j++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);      if (j != n) { 
       }        dum=1.0/(a[j][j]); 
     fprintf(ficreseij,"\n");        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } 
   }    } 
 }    free_vector(vv,1,n);  /* Doesn't work */
   ;
 /************ Variance ******************/  } 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  
 {  void lubksb(double **a, int n, int *indx, double b[]) 
   /* Variance of health expectancies */  { 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    int i,ii=0,ip,j; 
   double **newm;    double sum; 
   double **dnewm,**doldm;   
   int i, j, nhstepm, hstepm, h;    for (i=1;i<=n;i++) { 
   int k, cptcode;      ip=indx[i]; 
   double *xp;      sum=b[ip]; 
   double **gp, **gm;      b[ip]=b[i]; 
   double ***gradg, ***trgradg;      if (ii) 
   double ***p3mat;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double age,agelim;      else if (sum) ii=i; 
   int theta;      b[i]=sum; 
     } 
    fprintf(ficresvij,"# Covariances of life expectancies\n");    for (i=n;i>=1;i--) { 
   fprintf(ficresvij,"# Age");      sum=b[i]; 
   for(i=1; i<=nlstate;i++)      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     for(j=1; j<=nlstate;j++)      b[i]=sum/a[i][i]; 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    } 
   fprintf(ficresvij,"\n");  } 
   
   xp=vector(1,npar);  /************ Frequencies ********************/
   dnewm=matrix(1,nlstate,1,npar);  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)
   doldm=matrix(1,nlstate,1,nlstate);  {  /* Some frequencies */
      
   hstepm=1*YEARM; /* Every year of age */    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    int first;
   agelim = AGESUP;    double ***freq; /* Frequencies */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double *pp, **prop;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     if (stepm >= YEARM) hstepm=1;    FILE *ficresp;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    char fileresp[FILENAMELENGTH];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    pp=vector(1,nlstate);
     gp=matrix(0,nhstepm,1,nlstate);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     gm=matrix(0,nhstepm,1,nlstate);    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
     for(theta=1; theta <=npar; theta++){    if((ficresp=fopen(fileresp,"w"))==NULL) {
       for(i=1; i<=npar; i++){ /* Computes gradient */      printf("Problem with prevalence resultfile: %s\n", fileresp);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       }      exit(0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
       if (popbased==1) {    
         for(i=1; i<=nlstate;i++)    j=cptcoveff;
           prlim[i][i]=probs[(int)age][i][ij];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       }  
          first=1;
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    for(k1=1; k1<=j;k1++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      for(i1=1; i1<=ncodemax[k1];i1++){
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        j1++;
         }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       }          scanf("%d", i);*/
            for (i=-1; i<=nlstate+ndeath; i++)  
       for(i=1; i<=npar; i++) /* Computes gradient */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            for(m=iagemin; m <= iagemax+3; m++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                freq[i][jk][m]=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for (i=1; i<=nlstate; i++)  
       if (popbased==1) {        for(m=iagemin; m <= iagemax+3; m++)
         for(i=1; i<=nlstate;i++)          prop[i][m]=0;
           prlim[i][i]=probs[(int)age][i][ij];        
       }        dateintsum=0;
         k2cpt=0;
       for(j=1; j<= nlstate; j++){        for (i=1; i<=imx; i++) {
         for(h=0; h<=nhstepm; h++){          bool=1;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          if  (cptcovn>0) {
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            for (z1=1; z1<=cptcoveff; z1++) 
         }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       }                bool=0;
           }
       for(j=1; j<= nlstate; j++)          if (bool==1){
         for(h=0; h<=nhstepm; h++){            for(m=firstpass; m<=lastpass; m++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              k2=anint[m][i]+(mint[m][i]/12.);
         }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     } /* End theta */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 if (m<lastpass) {
     for(h=0; h<=nhstepm; h++)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       for(j=1; j<=nlstate;j++)                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         for(theta=1; theta <=npar; theta++)                }
           trgradg[h][j][theta]=gradg[h][theta][j];                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     for(i=1;i<=nlstate;i++)                  dateintsum=dateintsum+k2;
       for(j=1;j<=nlstate;j++)                  k2cpt++;
         vareij[i][j][(int)age] =0.;                }
     for(h=0;h<=nhstepm;h++){                /*}*/
       for(k=0;k<=nhstepm;k++){            }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        }
         for(i=1;i<=nlstate;i++)         
           for(j=1;j<=nlstate;j++)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
             vareij[i][j][(int)age] += doldm[i][j];  
       }        if  (cptcovn>0) {
     }          fprintf(ficresp, "\n#********** Variable "); 
     h=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     if (stepm >= YEARM) h=stepm/YEARM;          fprintf(ficresp, "**********\n#");
     fprintf(ficresvij,"%.0f ",age );        }
     for(i=1; i<=nlstate;i++)        for(i=1; i<=nlstate;i++) 
       for(j=1; j<=nlstate;j++){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        fprintf(ficresp, "\n");
       }        
     fprintf(ficresvij,"\n");        for(i=iagemin; i <= iagemax+3; i++){
     free_matrix(gp,0,nhstepm,1,nlstate);          if(i==iagemax+3){
     free_matrix(gm,0,nhstepm,1,nlstate);            fprintf(ficlog,"Total");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          }else{
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            if(first==1){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              first=0;
   } /* End age */              printf("See log file for details...\n");
              }
   free_vector(xp,1,npar);            fprintf(ficlog,"Age %d", i);
   free_matrix(doldm,1,nlstate,1,npar);          }
   free_matrix(dnewm,1,nlstate,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 }              pp[jk] += freq[jk][m][i]; 
           }
 /************ Variance of prevlim ******************/          for(jk=1; jk <=nlstate ; jk++){
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)            for(m=-1, pos=0; m <=0 ; m++)
 {              pos += freq[jk][m][i];
   /* Variance of prevalence limit */            if(pp[jk]>=1.e-10){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/              if(first==1){
   double **newm;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   double **dnewm,**doldm;              }
   int i, j, nhstepm, hstepm;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   int k, cptcode;            }else{
   double *xp;              if(first==1)
   double *gp, *gm;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double **gradg, **trgradg;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double age,agelim;            }
   int theta;          }
      
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficresvpl,"# Age");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   for(i=1; i<=nlstate;i++)              pp[jk] += freq[jk][m][i];
       fprintf(ficresvpl," %1d-%1d",i,i);          }       
   fprintf(ficresvpl,"\n");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
   xp=vector(1,npar);            posprop += prop[jk][i];
   dnewm=matrix(1,nlstate,1,npar);          }
   doldm=matrix(1,nlstate,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
              if(pos>=1.e-5){
   hstepm=1*YEARM; /* Every year of age */              if(first==1)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   agelim = AGESUP;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }else{
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              if(first==1)
     if (stepm >= YEARM) hstepm=1;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     gradg=matrix(1,npar,1,nlstate);            }
     gp=vector(1,nlstate);            if( i <= iagemax){
     gm=vector(1,nlstate);              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     for(theta=1; theta <=npar; theta++){                /*probs[i][jk][j1]= pp[jk]/pos;*/
       for(i=1; i<=npar; i++){ /* Computes gradient */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              }
       }              else
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       for(i=1;i<=nlstate;i++)            }
         gp[i] = prlim[i][i];          }
              
       for(i=1; i<=npar; i++) /* Computes gradient */          for(jk=-1; jk <=nlstate+ndeath; jk++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            for(m=-1; m <=nlstate+ndeath; m++)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              if(freq[jk][m][i] !=0 ) {
       for(i=1;i<=nlstate;i++)              if(first==1)
         gm[i] = prlim[i][i];                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       for(i=1;i<=nlstate;i++)              }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          if(i <= iagemax)
     } /* End theta */            fprintf(ficresp,"\n");
           if(first==1)
     trgradg =matrix(1,nlstate,1,npar);            printf("Others in log...\n");
           fprintf(ficlog,"\n");
     for(j=1; j<=nlstate;j++)        }
       for(theta=1; theta <=npar; theta++)      }
         trgradg[j][theta]=gradg[theta][j];    }
     dateintmean=dateintsum/k2cpt; 
     for(i=1;i<=nlstate;i++)   
       varpl[i][(int)age] =0.;    fclose(ficresp);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    free_vector(pp,1,nlstate);
     for(i=1;i<=nlstate;i++)    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    /* End of Freq */
   }
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  /************ Prevalence ********************/
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  void prevalence(double ***probs, 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)
     fprintf(ficresvpl,"\n");  {  
     free_vector(gp,1,nlstate);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     free_vector(gm,1,nlstate);       in each health status at the date of interview (if between dateprev1 and dateprev2).
     free_matrix(gradg,1,npar,1,nlstate);       We still use firstpass and lastpass as another selection.
     free_matrix(trgradg,1,nlstate,1,npar);    */
   } /* End age */   
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   free_vector(xp,1,npar);    double ***freq; /* Frequencies */
   free_matrix(doldm,1,nlstate,1,npar);    double *pp, **prop;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double pos,posprop; 
     double  y2; /* in fractional years */
 }    int iagemin, iagemax;
   
 /************ Variance of one-step probabilities  ******************/    iagemin= (int) agemin;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    iagemax= (int) agemax;
 {    /*pp=vector(1,nlstate);*/
   int i, j;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   int k=0, cptcode;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   double **dnewm,**doldm;    j1=0;
   double *xp;    
   double *gp, *gm;    j=cptcoveff;
   double **gradg, **trgradg;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   double age,agelim, cov[NCOVMAX];    
   int theta;    for(k1=1; k1<=j;k1++){
   char fileresprob[FILENAMELENGTH];      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
   strcpy(fileresprob,"prob");        
   strcat(fileresprob,fileres);        for (i=1; i<=nlstate; i++)  
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          for(m=iagemin; m <= iagemax+3; m++)
     printf("Problem with resultfile: %s\n", fileresprob);            prop[i][m]=0.0;
   }       
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        for (i=1; i<=imx; i++) { /* Each individual */
            bool=1;
           if  (cptcovn>0) {
   xp=vector(1,npar);            for (z1=1; z1<=cptcoveff; z1++) 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));                bool=0;
            } 
   cov[1]=1;          if (bool==1) { 
   for (age=bage; age<=fage; age ++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     cov[2]=age;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     gradg=matrix(1,npar,1,9);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     trgradg=matrix(1,9,1,npar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                    if (s[m][i]>0 && s[m][i]<=nlstate) { 
     for(theta=1; theta <=npar; theta++){                  /*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]]);*/
       for(i=1; i<=npar; i++)                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                  prop[s[m][i]][iagemax+3] += weight[i]; 
                      } 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              }
                } /* end selection of waves */
       k=0;          }
       for(i=1; i<= (nlstate+ndeath); i++){        }
         for(j=1; j<=(nlstate+ndeath);j++){        for(i=iagemin; i <= iagemax+3; i++){  
            k=k+1;          
           gp[k]=pmmij[i][j];          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         }            posprop += prop[jk][i]; 
       }          } 
   
       for(i=1; i<=npar; i++)          for(jk=1; jk <=nlstate ; jk++){     
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            if( i <=  iagemax){ 
                  if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              } 
       k=0;            } 
       for(i=1; i<=(nlstate+ndeath); i++){          }/* end jk */ 
         for(j=1; j<=(nlstate+ndeath);j++){        }/* end i */ 
           k=k+1;      } /* end i1 */
           gm[k]=pmmij[i][j];    } /* end k1 */
         }    
       }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
          /*free_vector(pp,1,nlstate);*/
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    }  /* End of prevalence */
     }  
   /************* Waves Concatenation ***************/
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
       for(theta=1; theta <=npar; theta++)  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       trgradg[j][theta]=gradg[theta][j];  {
      /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);       Death is a valid wave (if date is known).
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);       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]
      pmij(pmmij,cov,ncovmodel,x,nlstate);       and mw[mi+1][i]. dh depends on stepm.
        */
      k=0;  
      for(i=1; i<=(nlstate+ndeath); i++){    int i, mi, m;
        for(j=1; j<=(nlstate+ndeath);j++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
          k=k+1;       double sum=0., jmean=0.;*/
          gm[k]=pmmij[i][j];    int first;
         }    int j, k=0,jk, ju, jl;
      }    double sum=0.;
          first=0;
      /*printf("\n%d ",(int)age);    jmin=1e+5;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    jmax=-1;
            jmean=0.;
     for(i=1; i<=imx; i++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      mi=0;
      }*/      m=firstpass;
       while(s[m][i] <= nlstate){
   fprintf(ficresprob,"\n%d ",(int)age);        if(s[m][i]>=1)
           mw[++mi][i]=m;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        if(m >=lastpass)
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          break;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        else
   }          m++;
       }/* end while */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      if (s[m][i] > nlstate){
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        mi++;     /* Death is another wave */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        /* if(mi==0)  never been interviewed correctly before death */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);           /* Only death is a correct wave */
 }        mw[mi][i]=m;
  free_vector(xp,1,npar);      }
 fclose(ficresprob);  
  exit(0);      wav[i]=mi;
 }      if(mi==0){
         if(first==0){
 /***********************************************/          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
 /**************** Main Program *****************/          first=1;
 /***********************************************/        }
         if(first==1){
 /*int main(int argc, char *argv[])*/          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
 int main()        }
 {      } /* end mi==0 */
     } /* End individuals */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  
   double agedeb, agefin,hf;    for(i=1; i<=imx; i++){
   double agemin=1.e20, agemax=-1.e20;      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
   double fret;          dh[mi][i]=1;
   double **xi,tmp,delta;        else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   double dum; /* Dummy variable */            if (agedc[i] < 2*AGESUP) {
   double ***p3mat;            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   int *indx;            if(j==0) j=1;  /* Survives at least one month after exam */
   char line[MAXLINE], linepar[MAXLINE];            k=k+1;
   char title[MAXLINE];            if (j >= jmax) jmax=j;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];            if (j <= jmin) jmin=j;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];            sum=sum+j;
   char filerest[FILENAMELENGTH];            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   char fileregp[FILENAMELENGTH];            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            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]);
   int firstobs=1, lastobs=10;            }
   int sdeb, sfin; /* Status at beginning and end */          }
   int c,  h , cpt,l;          else{
   int ju,jl, mi;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            k=k+1;
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast;            if (j >= jmax) jmax=j;
   int hstepm, nhstepm;            else if (j <= jmin)jmin=j;
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   double bage, fage, age, agelim, agebase;            /*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]);*/
   double ftolpl=FTOL;            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]);
   double **prlim;            sum=sum+j;
   double *severity;          }
   double ***param; /* Matrix of parameters */          jk= j/stepm;
   double  *p;          jl= j -jk*stepm;
   double **matcov; /* Matrix of covariance */          ju= j -(jk+1)*stepm;
   double ***delti3; /* Scale */          if(mle <=1){ 
   double *delti; /* Scale */            if(jl==0){
   double ***eij, ***vareij;              dh[mi][i]=jk;
   double **varpl; /* Variances of prevalence limits by age */              bh[mi][i]=0;
   double *epj, vepp;            }else{ /* We want a negative bias in order to only have interpolation ie
   double kk1;                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";              bh[mi][i]=ju;
   char *alph[]={"a","a","b","c","d","e"}, str[4];            }
           }else{
             if(jl <= -ju){
   char z[1]="c", occ;              dh[mi][i]=jk;
 #include <sys/time.h>              bh[mi][i]=jl;       /* bias is positive if real duration
 #include <time.h>                                   * is higher than the multiple of stepm and negative otherwise.
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                                   */
   /* long total_usecs;            }
   struct timeval start_time, end_time;            else{
                dh[mi][i]=jk+1;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */              bh[mi][i]=ju;
             }
             if(dh[mi][i]==0){
   printf("\nIMACH, Version 0.64b");              dh[mi][i]=1; /* At least one step */
   printf("\nEnter the parameter file name: ");              bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
 #ifdef windows            }
   scanf("%s",pathtot);          }
   getcwd(pathcd, size);        } /* end if mle */
   /*cygwin_split_path(pathtot,path,optionfile);      } /* end wave */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    }
   /* cutv(path,optionfile,pathtot,'\\');*/    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 split(pathtot, path,optionfile);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   chdir(path);   }
   replace(pathc,path);  
 #endif  /*********** Tricode ****************************/
 #ifdef unix  void tricode(int *Tvar, int **nbcode, int imx)
   scanf("%s",optionfile);  {
 #endif    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
 /*-------- arguments in the command line --------*/    int cptcode=0;
     cptcoveff=0; 
   strcpy(fileres,"r");   
   strcat(fileres, optionfile);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
   /*---------arguments file --------*/  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     printf("Problem with optionfile %s\n",optionfile);                                 modality*/ 
     goto end;        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);*/
   strcpy(filereso,"o");        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   strcat(filereso,fileres);                                         Tvar[j]. If V=sex and male is 0 and 
   if((ficparo=fopen(filereso,"w"))==NULL) {                                         female is 1, then  cptcode=1.*/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      }
   }  
       for (i=0; i<=cptcode; i++) {
   /* Reads comments: lines beginning with '#' */        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 */
   while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      ij=1; 
     puts(line);      for (i=1; i<=ncodemax[j]; i++) {
     fputs(line,ficparo);        for (k=0; k<= maxncov; k++) {
   }          if (Ndum[k] != 0) {
   ungetc(c,ficpar);            nbcode[Tvar[j]][ij]=k; 
             /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   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);            
   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);            ij++;
   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);          }
 while((c=getc(ficpar))=='#' && c!= EOF){          if (ij > ncodemax[j]) break; 
     ungetc(c,ficpar);        }  
     fgets(line, MAXLINE, ficpar);      } 
     puts(line);    }  
     fputs(line,ficparo);  
   }   for (k=0; k< maxncov; k++) Ndum[k]=0;
   ungetc(c,ficpar);  
     for (i=1; i<=ncovmodel-2; i++) { 
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
  while((c=getc(ficpar))=='#' && c!= EOF){     ij=Tvar[i];
     ungetc(c,ficpar);     Ndum[ij]++;
     fgets(line, MAXLINE, ficpar);   }
     puts(line);  
     fputs(line,ficparo);   ij=1;
   }   for (i=1; i<= maxncov; i++) {
   ungetc(c,ficpar);     if((Ndum[i]!=0) && (i<=ncovcol)){
         Tvaraff[ij]=i; /*For printing */
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);       ij++;
       }
   covar=matrix(0,NCOVMAX,1,n);   }
   cptcovn=0;   
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;   cptcoveff=ij-1; /*Number of simple covariates*/
   }
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  /*********** Health Expectancies ****************/
    
   /* Read guess parameters */  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 )
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  {
     ungetc(c,ficpar);    /* Health expectancies */
     fgets(line, MAXLINE, ficpar);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     puts(line);    double age, agelim, hf;
     fputs(line,ficparo);    double ***p3mat,***varhe;
   }    double **dnewm,**doldm;
   ungetc(c,ficpar);    double *xp;
      double **gp, **gm;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double ***gradg, ***trgradg;
     for(i=1; i <=nlstate; i++)    int theta;
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       fprintf(ficparo,"%1d%1d",i1,j1);    xp=vector(1,npar);
       printf("%1d%1d",i,j);    dnewm=matrix(1,nlstate*nlstate,1,npar);
       for(k=1; k<=ncovmodel;k++){    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         fscanf(ficpar," %lf",&param[i][j][k]);    
         printf(" %lf",param[i][j][k]);    fprintf(ficreseij,"# Health expectancies\n");
         fprintf(ficparo," %lf",param[i][j][k]);    fprintf(ficreseij,"# Age");
       }    for(i=1; i<=nlstate;i++)
       fscanf(ficpar,"\n");      for(j=1; j<=nlstate;j++)
       printf("\n");        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       fprintf(ficparo,"\n");    fprintf(ficreseij,"\n");
     }  
      if(estepm < stepm){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   p=param[1][1];    else  hstepm=estepm;   
      /* We compute the life expectancy from trapezoids spaced every estepm months
   /* Reads comments: lines beginning with '#' */     * This is mainly to measure the difference between two models: for example
   while((c=getc(ficpar))=='#' && c!= EOF){     * if stepm=24 months pijx are given only every 2 years and by summing them
     ungetc(c,ficpar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
     fgets(line, MAXLINE, ficpar);     * progression in between and thus overestimating or underestimating according
     puts(line);     * to the curvature of the survival function. If, for the same date, we 
     fputs(line,ficparo);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   }     * to compare the new estimate of Life expectancy with the same linear 
   ungetc(c,ficpar);     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    /* For example we decided to compute the life expectancy with the smallest unit */
   for(i=1; i <=nlstate; i++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     for(j=1; j <=nlstate+ndeath-1; j++){       nhstepm is the number of hstepm from age to agelim 
       fscanf(ficpar,"%1d%1d",&i1,&j1);       nstepm is the number of stepm from age to agelin. 
       printf("%1d%1d",i,j);       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficparo,"%1d%1d",i1,j1);       and note for a fixed period like estepm months */
       for(k=1; k<=ncovmodel;k++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fscanf(ficpar,"%le",&delti3[i][j][k]);       survival function given by stepm (the optimization length). Unfortunately it
         printf(" %le",delti3[i][j][k]);       means that if the survival funtion is printed only each two years of age and if
         fprintf(ficparo," %le",delti3[i][j][k]);       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.
       fscanf(ficpar,"\n");    */
       printf("\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficparo,"\n");  
     }    agelim=AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   delti=delti3[1][1];      /* nhstepm age range expressed in number of stepm */
        nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   /* Reads comments: lines beginning with '#' */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   while((c=getc(ficpar))=='#' && c!= EOF){      /* if (stepm >= YEARM) hstepm=1;*/
     ungetc(c,ficpar);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fgets(line, MAXLINE, ficpar);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     puts(line);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     fputs(line,ficparo);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   ungetc(c,ficpar);  
        /* Computed by stepm unit matrices, product of hstepm matrices, stored
   matcov=matrix(1,npar,1,npar);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   for(i=1; i <=npar; i++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     fscanf(ficpar,"%s",&str);   
     printf("%s",str);  
     fprintf(ficparo,"%s",str);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);      /* Computing Variances of health expectancies */
       printf(" %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);       for(theta=1; theta <=npar; theta++){
     }        for(i=1; i<=npar; i++){ 
     fscanf(ficpar,"\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     printf("\n");        }
     fprintf(ficparo,"\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }    
   for(i=1; i <=npar; i++)        cptj=0;
     for(j=i+1;j<=npar;j++)        for(j=1; j<= nlstate; j++){
       matcov[i][j]=matcov[j][i];          for(i=1; i<=nlstate; i++){
                cptj=cptj+1;
   printf("\n");            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
     /*-------- data file ----------*/          }
     if((ficres =fopen(fileres,"w"))==NULL) {        }
       printf("Problem with resultfile: %s\n", fileres);goto end;       
     }       
     fprintf(ficres,"#%s\n",version);        for(i=1; i<=npar; i++) 
              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     if((fic=fopen(datafile,"r"))==NULL)    {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       printf("Problem with datafile: %s\n", datafile);goto end;        
     }        cptj=0;
         for(j=1; j<= nlstate; j++){
     n= lastobs;          for(i=1;i<=nlstate;i++){
     severity = vector(1,maxwav);            cptj=cptj+1;
     outcome=imatrix(1,maxwav+1,1,n);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     num=ivector(1,n);  
     moisnais=vector(1,n);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     annais=vector(1,n);            }
     moisdc=vector(1,n);          }
     andc=vector(1,n);        }
     agedc=vector(1,n);        for(j=1; j<= nlstate*nlstate; j++)
     cod=ivector(1,n);          for(h=0; h<=nhstepm-1; h++){
     weight=vector(1,n);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     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);  /* End theta */
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     ncodemax=ivector(1,8);  
        for(h=0; h<=nhstepm-1; h++)
     i=1;        for(j=1; j<=nlstate*nlstate;j++)
     while (fgets(line, MAXLINE, fic) != NULL)    {          for(theta=1; theta <=npar; theta++)
       if ((i >= firstobs) && (i <=lastobs)) {            trgradg[h][j][theta]=gradg[h][theta][j];
               
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);       for(i=1;i<=nlstate*nlstate;i++)
           strcpy(line,stra);        for(j=1;j<=nlstate*nlstate;j++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          varhe[i][j][(int)age] =0.;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }       printf("%d|",(int)age);fflush(stdout);
               fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);       for(h=0;h<=nhstepm-1;h++){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1;i<=nlstate*nlstate;i++)
             for(j=1;j<=nlstate*nlstate;j++)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         for (j=ncov;j>=1;j--){        }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      }
         }      /* Computing expectancies */
         num[i]=atol(stra);      for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate;j++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           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;}*/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
         i=i+1;  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       }  
     }          }
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/      fprintf(ficreseij,"%3.0f",age );
   imx=i-1; /* Number of individuals */      cptj=0;
       for(i=1; i<=nlstate;i++)
   /* for (i=1; i<=imx; i++){        for(j=1; j<=nlstate;j++){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          cptj++;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        }
     }      fprintf(ficreseij,"\n");
     for (i=1; i<=imx; i++) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/     
       free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   /* Calculation of the number of parameter from char model*/      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   Tvar=ivector(1,15);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   Tprod=ivector(1,15);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   Tvaraff=ivector(1,15);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   Tvard=imatrix(1,15,1,2);    }
   Tage=ivector(1,15);          printf("\n");
        fprintf(ficlog,"\n");
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;    free_vector(xp,1,npar);
     j=nbocc(model,'+');    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     j1=nbocc(model,'*');    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     cptcovn=j+1;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     cptcovprod=j1;  }
      
      /************ Variance ******************/
     strcpy(modelsav,model);  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)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  {
       printf("Error. Non available option model=%s ",model);    /* Variance of health expectancies */
       goto end;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     }    /* double **newm;*/
        double **dnewm,**doldm;
     for(i=(j+1); i>=1;i--){    double **dnewmp,**doldmp;
       cutv(stra,strb,modelsav,'+');    int i, j, nhstepm, hstepm, h, nstepm ;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    int k, cptcode;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    double *xp;
       /*scanf("%d",i);*/    double **gp, **gm;  /* for var eij */
       if (strchr(strb,'*')) {    double ***gradg, ***trgradg; /*for var eij */
         cutv(strd,strc,strb,'*');    double **gradgp, **trgradgp; /* for var p point j */
         if (strcmp(strc,"age")==0) {    double *gpp, *gmp; /* for var p point j */
           cptcovprod--;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           cutv(strb,stre,strd,'V');    double ***p3mat;
           Tvar[i]=atoi(stre);    double age,agelim, hf;
           cptcovage++;    double ***mobaverage;
             Tage[cptcovage]=i;    int theta;
             /*printf("stre=%s ", stre);*/    char digit[4];
         }    char digitp[25];
         else if (strcmp(strd,"age")==0) {  
           cptcovprod--;    char fileresprobmorprev[FILENAMELENGTH];
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);    if(popbased==1){
           cptcovage++;      if(mobilav!=0)
           Tage[cptcovage]=i;        strcpy(digitp,"-populbased-mobilav-");
         }      else strcpy(digitp,"-populbased-nomobil-");
         else {    }
           cutv(strb,stre,strc,'V');    else 
           Tvar[i]=ncov+k1;      strcpy(digitp,"-stablbased-");
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;    if (mobilav!=0) {
           Tvard[k1][1]=atoi(strc);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           Tvard[k1][2]=atoi(stre);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           Tvar[cptcovn+k2]=Tvard[k1][1];        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           for (k=1; k<=lastobs;k++)      }
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    }
           k1++;  
           k2=k2+2;    strcpy(fileresprobmorprev,"prmorprev"); 
         }    sprintf(digit,"%-d",ij);
       }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       else {    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
        /*  scanf("%d",i);*/    strcat(fileresprobmorprev,fileres);
       cutv(strd,strc,strb,'V');    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       Tvar[i]=atoi(strc);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       strcpy(modelsav,stra);      }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         scanf("%d",i);*/    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);
 }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      fprintf(ficresprobmorprev," p.%-d SE",j);
   printf("cptcovprod=%d ", cptcovprod);      for(i=1; i<=nlstate;i++)
   scanf("%d ",i);*/        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     fclose(fic);    }  
     fprintf(ficresprobmorprev,"\n");
     /*  if(mle==1){*/    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     if (weightopt != 1) { /* Maximisation without weights*/      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       for(i=1;i<=n;i++) weight[i]=1.0;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     }      exit(0);
     /*-calculation of age at interview from date of interview and age at death -*/    }
     agev=matrix(1,maxwav,1,imx);    else{
       fprintf(ficgp,"\n# Routine varevsij");
    for (i=1; i<=imx; i++)    }
      for(m=2; (m<= maxwav); m++)    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      printf("Problem with html file: %s\n", optionfilehtm);
          anint[m][i]=9999;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
          s[m][i]=-1;      exit(0);
        }    }
        else{
     for (i=1; i<=imx; i++)  {      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");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       for(m=1; (m<= maxwav); m++){    }
         if(s[m][i] >0){    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           if (s[m][i] == nlstate+1) {  
             if(agedc[i]>0)    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");
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(ficresvij,"# Age");
               agev[m][i]=agedc[i];    for(i=1; i<=nlstate;i++)
             else {      for(j=1; j<=nlstate;j++)
               if (andc[i]!=9999){        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    fprintf(ficresvij,"\n");
               agev[m][i]=-1;  
               }    xp=vector(1,npar);
             }    dnewm=matrix(1,nlstate,1,npar);
           }    doldm=matrix(1,nlstate,1,nlstate);
           else if(s[m][i] !=9){ /* Should no more exist */    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
             else if(agev[m][i] <agemin){    gpp=vector(nlstate+1,nlstate+ndeath);
               agemin=agev[m][i];    gmp=vector(nlstate+1,nlstate+ndeath);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             }    
             else if(agev[m][i] >agemax){    if(estepm < stepm){
               agemax=agev[m][i];      printf ("Problem %d lower than %d\n",estepm, stepm);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    }
             }    else  hstepm=estepm;   
             /*agev[m][i]=anint[m][i]-annais[i];*/    /* For example we decided to compute the life expectancy with the smallest unit */
             /*   agev[m][i] = age[i]+2*m;*/    /* 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 
           else { /* =9 */       nstepm is the number of stepm from age to agelin. 
             agev[m][i]=1;       Look at hpijx to understand the reason of that which relies in memory size
             s[m][i]=-1;       and note for a fixed period like k years */
           }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         }       survival function given by stepm (the optimization length). Unfortunately it
         else /*= 0 Unknown */       means that if the survival funtion is printed every two years of age and if
           agev[m][i]=1;       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<=imx; i++)  {    agelim = AGESUP;
       for(m=1; (m<= maxwav); m++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         if (s[m][i] > (nlstate+ndeath)) {      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           printf("Error: Wrong value in nlstate or ndeath\n");        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           goto end;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       }      gp=matrix(0,nhstepm,1,nlstate);
     }      gm=matrix(0,nhstepm,1,nlstate);
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
       for(theta=1; theta <=npar; theta++){
     free_vector(severity,1,maxwav);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     free_imatrix(outcome,1,maxwav+1,1,n);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     free_vector(moisnais,1,n);        }
     free_vector(annais,1,n);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     free_matrix(mint,1,maxwav,1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_matrix(anint,1,maxwav,1,n);  
     free_vector(moisdc,1,n);        if (popbased==1) {
     free_vector(andc,1,n);          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
                  prlim[i][i]=probs[(int)age][i][ij];
     wav=ivector(1,imx);          }else{ /* mobilav */ 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            for(i=1; i<=nlstate;i++)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              prlim[i][i]=mobaverage[(int)age][i][ij];
              }
     /* Concatenates waves */        }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
       Tcode=ivector(1,100);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       ncodemax[1]=1;          }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        }
              /* This for computing probability of death (h=1 means
    codtab=imatrix(1,100,1,10);           computed over hstepm matrices product = hstepm*stepm months) 
    h=0;           as a weighted average of prlim.
    m=pow(2,cptcoveff);        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
    for(k=1;k<=cptcoveff; k++){          for(i=1,gpp[j]=0.; i<= nlstate; i++)
      for(i=1; i <=(m/pow(2,k));i++){            gpp[j] += prlim[i][i]*p3mat[i][j][1];
        for(j=1; j <= ncodemax[k]; j++){        }    
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        /* end probability of death */
            h++;  
            if (h>m) h=1;codtab[h][k]=j;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
          }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
        }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    }   
         if (popbased==1) {
           if(mobilav ==0){
    /*for(i=1; i <=m ;i++){            for(i=1; i<=nlstate;i++)
      for(k=1; k <=cptcovn; k++){              prlim[i][i]=probs[(int)age][i][ij];
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          }else{ /* mobilav */ 
      }            for(i=1; i<=nlstate;i++)
      printf("\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
    }          }
    scanf("%d",i);*/        }
      
    /* Calculates basic frequencies. Computes observed prevalence at single age        for(j=1; j<= nlstate; j++){
        and prints on file fileres'p'. */          for(h=0; h<=nhstepm; h++){
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     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 */        /* This for computing probability of death (h=1 means
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           computed over hstepm matrices product = hstepm*stepm months) 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */           as a weighted average of prlim.
              */
     /* For Powell, parameters are in a vector p[] starting at p[1]        for(j=nlstate+1;j<=nlstate+ndeath;j++){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
     if(mle==1){        /* end probability of death */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }        for(j=1; j<= nlstate; j++) /* vareij */
              for(h=0; h<=nhstepm; h++){
     /*--------- results files --------------*/            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     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);          }
      
    jk=1;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
    fprintf(ficres,"# Parameters\n");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
    printf("# Parameters\n");        }
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){      } /* End theta */
        if (k != i)  
          {      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);      for(h=0; h<=nhstepm; h++) /* veij */
            for(j=1; j <=ncovmodel; j++){        for(j=1; j<=nlstate;j++)
              printf("%f ",p[jk]);          for(theta=1; theta <=npar; theta++)
              fprintf(ficres,"%f ",p[jk]);            trgradg[h][j][theta]=gradg[h][theta][j];
              jk++;  
            }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
            printf("\n");        for(theta=1; theta <=npar; theta++)
            fprintf(ficres,"\n");          trgradgp[j][theta]=gradgp[theta][j];
          }    
      }  
    }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  if(mle==1){      for(i=1;i<=nlstate;i++)
     /* Computing hessian and covariance matrix */        for(j=1;j<=nlstate;j++)
     ftolhess=ftol; /* Usually correct */          vareij[i][j][(int)age] =0.;
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }      for(h=0;h<=nhstepm;h++){
     fprintf(ficres,"# Scales\n");        for(k=0;k<=nhstepm;k++){
     printf("# Scales\n");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
      for(i=1,jk=1; i <=nlstate; i++){          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       for(j=1; j <=nlstate+ndeath; j++){          for(i=1;i<=nlstate;i++)
         if (j!=i) {            for(j=1;j<=nlstate;j++)
           fprintf(ficres,"%1d%1d",i,j);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           printf("%1d%1d",i,j);        }
           for(k=1; k<=ncovmodel;k++){      }
             printf(" %.5e",delti[jk]);    
             fprintf(ficres," %.5e",delti[jk]);      /* pptj */
             jk++;      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);
           printf("\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           fprintf(ficres,"\n");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         }          varppt[j][i]=doldmp[j][i];
       }      /* end ppptj */
       }      /*  x centered again */
          hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     k=1;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     fprintf(ficres,"# Covariance\n");   
     printf("# Covariance\n");      if (popbased==1) {
     for(i=1;i<=npar;i++){        if(mobilav ==0){
       /*  if (k>nlstate) k=1;          for(i=1; i<=nlstate;i++)
       i1=(i-1)/(ncovmodel*nlstate)+1;            prlim[i][i]=probs[(int)age][i][ij];
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        }else{ /* mobilav */ 
       printf("%s%d%d",alph[k],i1,tab[i]);*/          for(i=1; i<=nlstate;i++)
       fprintf(ficres,"%3d",i);            prlim[i][i]=mobaverage[(int)age][i][ij];
       printf("%3d",i);        }
       for(j=1; j<=i;j++){      }
         fprintf(ficres," %.5e",matcov[i][j]);               
         printf(" %.5e",matcov[i][j]);      /* This for computing probability of death (h=1 means
       }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       fprintf(ficres,"\n");         as a weighted average of prlim.
       printf("\n");      */
       k++;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
              gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     while((c=getc(ficpar))=='#' && c!= EOF){      }    
       ungetc(c,ficpar);      /* end probability of death */
       fgets(line, MAXLINE, ficpar);  
       puts(line);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       fputs(line,ficparo);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     ungetc(c,ficpar);        for(i=1; i<=nlstate;i++){
            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        }
          } 
     if (fage <= 2) {      fprintf(ficresprobmorprev,"\n");
       bage = agemin;  
       fage = agemax;      fprintf(ficresvij,"%.0f ",age );
     }      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        }
       fprintf(ficresvij,"\n");
          free_matrix(gp,0,nhstepm,1,nlstate);
 /*------------ gnuplot -------------*/      free_matrix(gm,0,nhstepm,1,nlstate);
 chdir(pathcd);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   if((ficgp=fopen("graph.plt","w"))==NULL) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     printf("Problem with file graph.gp");goto end;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    } /* End age */
 #ifdef windows    free_vector(gpp,nlstate+1,nlstate+ndeath);
   fprintf(ficgp,"cd \"%s\" \n",pathc);    free_vector(gmp,nlstate+1,nlstate+ndeath);
 #endif    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
 m=pow(2,cptcoveff);    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");
  /* 1eme*/    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   for (cpt=1; cpt<= nlstate ; cpt ++) {    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
    for (k1=1; k1<= m ; k1 ++) {  /*   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); */
 #ifdef windows  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     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);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
 #endif    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
 #ifdef unix    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
 #endif    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
 for (i=1; i<= nlstate ; i ++) {  */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    free_vector(xp,1,npar);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    free_matrix(doldm,1,nlstate,1,nlstate);
     for (i=1; i<= nlstate ; i ++) {    free_matrix(dnewm,1,nlstate,1,npar);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
 }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      for (i=1; i<= nlstate ; i ++) {    fclose(ficresprobmorprev);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fclose(ficgp);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fclose(fichtm);
 }    }  /* end varevsij */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix  /************ Variance of prevlim ******************/
 fprintf(ficgp,"\nset ter gif small size 400,300");  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)
 #endif  {
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /* Variance of prevalence limit */
    }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   }    double **newm;
   /*2 eme*/    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   for (k1=1; k1<= m ; k1 ++) {    int k, cptcode;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    double *xp;
        double *gp, *gm;
     for (i=1; i<= nlstate+1 ; i ++) {    double **gradg, **trgradg;
       k=2*i;    double age,agelim;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    int theta;
       for (j=1; j<= nlstate+1 ; j ++) {     
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficresvpl,"# Age");
 }      for(i=1; i<=nlstate;i++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        fprintf(ficresvpl," %1d-%1d",i,i);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    fprintf(ficresvpl,"\n");
     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 ++) {    xp=vector(1,npar);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    dnewm=matrix(1,nlstate,1,npar);
         else fprintf(ficgp," \%%*lf (\%%*lf)");    doldm=matrix(1,nlstate,1,nlstate);
 }      
       fprintf(ficgp,"\" t\"\" w l 0,");    hstepm=1*YEARM; /* Every year of age */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       for (j=1; j<= nlstate+1 ; j ++) {    agelim = AGESUP;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 }        if (stepm >= YEARM) hstepm=1;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       else fprintf(ficgp,"\" t\"\" w l 0,");      gradg=matrix(1,npar,1,nlstate);
     }      gp=vector(1,nlstate);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      gm=vector(1,nlstate);
   }  
        for(theta=1; theta <=npar; theta++){
   /*3eme*/        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   for (k1=1; k1<= m ; k1 ++) {        }
     for (cpt=1; cpt<= nlstate ; cpt ++) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       k=2+nlstate*(cpt-1);        for(i=1;i<=nlstate;i++)
       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);          gp[i] = prlim[i][i];
       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+i,cpt,i+1);        for(i=1; i<=npar; i++) /* Computes gradient */
       }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }        for(i=1;i<=nlstate;i++)
   }          gm[i] = prlim[i][i];
    
   /* CV preval stat */        for(i=1;i<=nlstate;i++)
   for (k1=1; k1<= m ; k1 ++) {          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     for (cpt=1; cpt<nlstate ; cpt ++) {      } /* End theta */
       k=3;  
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      trgradg =matrix(1,nlstate,1,npar);
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);      for(j=1; j<=nlstate;j++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        for(theta=1; theta <=npar; theta++)
                trgradg[j][theta]=gradg[theta][j];
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      for(i=1;i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++) {        varpl[i][(int)age] =0.;
         l=3+(nlstate+ndeath)*cpt;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
         fprintf(ficgp,"+$%d",l+i+1);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       }      for(i=1;i<=nlstate;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }      fprintf(ficresvpl,"%.0f ",age );
   }        for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   /* proba elementaires */      fprintf(ficresvpl,"\n");
    for(i=1,jk=1; i <=nlstate; i++){      free_vector(gp,1,nlstate);
     for(k=1; k <=(nlstate+ndeath); k++){      free_vector(gm,1,nlstate);
       if (k != i) {      free_matrix(gradg,1,npar,1,nlstate);
         for(j=1; j <=ncovmodel; j++){      free_matrix(trgradg,1,nlstate,1,npar);
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    } /* End age */
           /*fprintf(ficgp,"%s",alph[1]);*/  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    free_vector(xp,1,npar);
           jk++;    free_matrix(doldm,1,nlstate,1,npar);
           fprintf(ficgp,"\n");    free_matrix(dnewm,1,nlstate,1,nlstate);
         }  
       }  }
     }  
     }  /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   for(jk=1; jk <=m; jk++) {  {
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    int i, j=0,  i1, k1, l1, t, tj;
    i=1;    int k2, l2, j1,  z1;
    for(k2=1; k2<=nlstate; k2++) {    int k=0,l, cptcode;
      k3=i;    int first=1, first1;
      for(k=1; k<=(nlstate+ndeath); k++) {    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
        if (k != k2){    double **dnewm,**doldm;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    double *xp;
 ij=1;    double *gp, *gm;
         for(j=3; j <=ncovmodel; j++) {    double **gradg, **trgradg;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double **mu;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double age,agelim, cov[NCOVMAX];
             ij++;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           }    int theta;
           else    char fileresprob[FILENAMELENGTH];
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    char fileresprobcov[FILENAMELENGTH];
         }    char fileresprobcor[FILENAMELENGTH];
           fprintf(ficgp,")/(1");  
            double ***varpij;
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    strcpy(fileresprob,"prob"); 
 ij=1;    strcat(fileresprob,fileres);
           for(j=3; j <=ncovmodel; j++){    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      printf("Problem with resultfile: %s\n", fileresprob);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
             ij++;    }
           }    strcpy(fileresprobcov,"probcov"); 
           else    strcat(fileresprobcov,fileres);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
           }      printf("Problem with resultfile: %s\n", fileresprobcov);
           fprintf(ficgp,")");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
         }    }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    strcpy(fileresprobcor,"probcor"); 
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    strcat(fileresprobcor,fileres);
         i=i+ncovmodel;    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        }      printf("Problem with resultfile: %s\n", fileresprobcor);
      }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
    }    }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    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);
        printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   fclose(ficgp);    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);
 chdir(path);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
        
     free_ivector(wav,1,imx);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    fprintf(ficresprob,"# Age");
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     free_ivector(num,1,n);    fprintf(ficresprobcov,"# Age");
     free_vector(agedc,1,n);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    fprintf(ficresprobcov,"# Age");
     fclose(ficparo);  
     fclose(ficres);  
     /*  }*/    for(i=1; i<=nlstate;i++)
          for(j=1; j<=(nlstate+ndeath);j++){
    /*________fin mle=1_________*/        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
            fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
     /* No more information from the sample is required now */   /* fprintf(ficresprob,"\n");
   /* Reads comments: lines beginning with '#' */    fprintf(ficresprobcov,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresprobcor,"\n");
     ungetc(c,ficpar);   */
     fgets(line, MAXLINE, ficpar);   xp=vector(1,npar);
     puts(line);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     fputs(line,ficparo);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   ungetc(c,ficpar);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
 /*--------- index.htm --------*/      exit(0);
     }
   strcpy(optionfilehtm,optionfile);    else{
   strcat(optionfilehtm,".htm");      fprintf(ficgp,"\n# Routine varprob");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    }
     printf("Problem with %s \n",optionfilehtm);goto end;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   }      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">      exit(0);
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    }
 Total number of observations=%d <br>    else{
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
 <hr  size=\"2\" color=\"#EC5E5E\">      fprintf(fichtm,"\n");
 <li>Outputs files<br><br>\n  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>      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");
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      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");
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    cov[1]=1;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    tj=cptcoveff;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>    j1=0;
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
  fprintf(fichtm," <li>Graphs</li><p>");        j1++;
         if  (cptcovn>0) {
  m=cptcoveff;          fprintf(ficresprob, "\n#********** Variable "); 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
  j1=0;          fprintf(ficresprobcov, "\n#********** Variable "); 
  for(k1=1; k1<=m;k1++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    for(i1=1; i1<=ncodemax[k1];i1++){          fprintf(ficresprobcov, "**********\n#\n");
        j1++;          
        if (cptcovn > 0) {          fprintf(ficgp, "\n#********** Variable "); 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          for (cpt=1; cpt<=cptcoveff;cpt++)          fprintf(ficgp, "**********\n#\n");
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);          
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          
        }          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
        for(cpt=1; cpt<nlstate;cpt++){          
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          fprintf(ficresprobcor, "\n#********** Variable ");    
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        }          fprintf(ficresprobcor, "**********\n#");    
     for(cpt=1; cpt<=nlstate;cpt++) {        }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        
 interval) in state (%d): v%s%d%d.gif <br>        for (age=bage; age<=fage; age ++){ 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            cov[2]=age;
      }          for (k=1; k<=cptcovn;k++) {
      for(cpt=1; cpt<=nlstate;cpt++) {            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          }
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      }          for (k=1; k<=cptcovprod;k++)
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 health expectancies in states (1) and (2): e%s%d.gif<br>          
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
 fprintf(fichtm,"\n</body>");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    }          gp=vector(1,(nlstate)*(nlstate+ndeath));
  }          gm=vector(1,(nlstate)*(nlstate+ndeath));
 fclose(fichtm);      
           for(theta=1; theta <=npar; theta++){
   /*--------------- Prevalence limit --------------*/            for(i=1; i<=npar; i++)
                xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   strcpy(filerespl,"pl");            
   strcat(filerespl,fileres);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            k=0;
   }            for(i=1; i<= (nlstate); i++){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);              for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(ficrespl,"#Prevalence limit\n");                k=k+1;
   fprintf(ficrespl,"#Age ");                gp[k]=pmmij[i][j];
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              }
   fprintf(ficrespl,"\n");            }
              
   prlim=matrix(1,nlstate,1,nlstate);            for(i=1; i<=npar; i++)
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            k=0;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            for(i=1; i<=(nlstate); i++){
   k=0;              for(j=1; j<=(nlstate+ndeath);j++){
   agebase=agemin;                k=k+1;
   agelim=agemax;                gm[k]=pmmij[i][j];
   ftolpl=1.e-10;              }
   i1=cptcoveff;            }
   if (cptcovn < 1){i1=1;}       
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   for(cptcov=1;cptcov<=i1;cptcov++){              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     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]);*/          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
         fprintf(ficrespl,"\n#******");            for(theta=1; theta <=npar; theta++)
         for(j=1;j<=cptcoveff;j++)              trgradg[j][theta]=gradg[theta][j];
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          
         fprintf(ficrespl,"******\n");          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);
         for (age=agebase; age<=agelim; age++){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           fprintf(ficrespl,"%.0f",age );          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           for(i=1; i<=nlstate;i++)          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");          pmij(pmmij,cov,ncovmodel,x,nlstate);
         }          
       }          k=0;
     }          for(i=1; i<=(nlstate); i++){
   fclose(ficrespl);            for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
   /*------------- h Pij x at various ages ------------*/              mu[k][(int) age]=pmmij[i][j];
              }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   }              varpij[i][j][(int)age] = doldm[i][j];
   printf("Computing pij: result on file '%s' \n", filerespij);  
            /*printf("\n%d ",(int)age);
   stepsize=(int) (stepm+YEARM-1)/YEARM;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   /*if (stepm<=24) stepsize=2;*/            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]));
   agelim=AGESUP;            }*/
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          fprintf(ficresprob,"\n%d ",(int)age);
            fprintf(ficresprobcov,"\n%d ",(int)age);
   k=0;          fprintf(ficresprobcor,"\n%d ",(int)age);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       k=k+1;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
         fprintf(ficrespij,"\n#****** ");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         for(j=1;j<=cptcoveff;j++)            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
         fprintf(ficrespij,"******\n");          }
                  i=0;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          for (k=1; k<=(nlstate);k++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            for (l=1; l<=(nlstate+ndeath);l++){ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              i=i++;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
           oldm=oldms;savm=savms;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                for (j=1; j<=i;j++){
           fprintf(ficrespij,"# Age");                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
           for(i=1; i<=nlstate;i++)                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
             for(j=1; j<=nlstate+ndeath;j++)              }
               fprintf(ficrespij," %1d-%1d",i,j);            }
           fprintf(ficrespij,"\n");          }/* end of loop for state */
           for (h=0; h<=nhstepm; h++){        } /* end of loop for age */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)        /* Confidence intervalle of pij  */
               for(j=1; j<=nlstate+ndeath;j++)        /*
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          fprintf(ficgp,"\nset noparametric;unset label");
             fprintf(ficrespij,"\n");          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");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          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(ficrespij,"\n");          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);
   }        */
   
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
   fclose(ficrespij);        for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   /*---------- Forecasting ------------------*/            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
   strcpy(fileresf,"f");            for (k1=1; k1<=(nlstate);k1++){
   strcat(fileresf,fileres);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   if((ficresf=fopen(fileresf,"w"))==NULL) {                if(l1==k1) continue;
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;                i=(k1-1)*(nlstate+ndeath)+l1;
   }                if(i<=j) continue;
   printf("Computing forecasting: result on file '%s' \n", fileresf);                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
  free_matrix(agev,1,maxwav,1,imx);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   /* Mobile average */                    mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                    c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
   if (mobilav==1) {                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)                    /* Eigen vectors */
       for (i=1; i<=nlstate;i++)                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                    /*v21=sqrt(1.-v11*v11); *//* error */
           mobaverage[(int)agedeb][i][cptcod]=0.;                    v21=(lc1-v1)/cv12*v11;
                        v12=-v21;
     for (agedeb=bage+4; agedeb<=fage; agedeb++){                    v22=v11;
       for (i=1; i<=nlstate;i++){                    tnalp=v21/v11;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                    if(first1==1){
           for (cpt=0;cpt<=4;cpt++){                      first1=0;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                      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);
           }                    }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                    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;
   stepsize=(int) (stepm+YEARM-1)/YEARM;                      fprintf(ficgp,"\nset parametric;unset label");
   if (stepm<=12) stepsize=1;                      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");
   agelim=AGESUP;                      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);
   hstepm=stepsize*YEARM; /* Every year of age */                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */                      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);
    k=0;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   for(cptcov=1;cptcov<=i1;cptcov++){                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                      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",\
       k=k+1;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       fprintf(ficresf,"\n#****** ");                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       for(j=1;j<=cptcoveff;j++) {                    }else{
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                      first=0;
       }                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
       fprintf(ficresf,"******\n");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                      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),\
       for (agedeb=fage; agedeb>=bage; agedeb--){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);                    }/* if first */
        if (mobilav==1) {                  } /* age mod 5 */
         for(j=1; j<=nlstate;j++)                } /* end loop age */
           fprintf(ficresf," %.5f ",mobaverage[(int)agedeb][j][cptcod]);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
         }                first=1;
         else {              } /*l12 */
           for(j=1; j<=nlstate;j++)            } /* k12 */
           fprintf(ficresf," %.5f ",probs[(int)agedeb][j][cptcod]);          } /*l1 */
         }          }/* k1 */
       for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");      } /* loop covariates */
       }    }
       for (cpt=1; cpt<=nforecast;cpt++)      free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
            free_vector(xp,1,npar);
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fclose(ficresprob);
         nhstepm = nhstepm/hstepm;    fclose(ficresprobcov);
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/    fclose(ficresprobcor);
     fclose(ficgp);
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fclose(fichtm);
         oldm=oldms;savm=savms;  }
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
                  
         for (h=0; h<=nhstepm; h++){  /******************* Printing html file ***********/
          void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
          if (h*hstepm/YEARM*stepm==cpt)                    int lastpass, int stepm, int weightopt, char model[],\
             fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                              int popforecast, int estepm ,\
                              double jprev1, double mprev1,double anprev1, \
           for(j=1; j<=nlstate+ndeath;j++) {                    double jprev2, double mprev2,double anprev2){
             kk1=0.;    int jj1, k1, i1, cpt;
             for(i=1; i<=nlstate;i++) {            /*char optionfilehtm[FILENAMELENGTH];*/
               if (mobilav==1)    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
               kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];      printf("Problem with %s \n",optionfilehtm), exit(0);
               else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
             }        }
           if (h*hstepm/YEARM*stepm==cpt) fprintf(ficresf," %.5f ", kk1);  
           }     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
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   - 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>", \
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   free_imatrix(s,1,maxwav+1,1,n);  
   free_vector(weight,1,n);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   fclose(ficresf);  
   /*---------- Health expectancies and variances ------------*/   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   strcpy(filerest,"t");  
   strcat(filerest,fileres);   jj1=0;
   if((ficrest=fopen(filerest,"w"))==NULL) {   for(k1=1; k1<=m;k1++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;     for(i1=1; i1<=ncodemax[k1];i1++){
   }       jj1++;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
   strcpy(filerese,"e");           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   strcat(filerese,fileres);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   if((ficreseij=fopen(filerese,"w"))==NULL) {       }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);       /* 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>
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
  strcpy(fileresv,"v");       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>
   strcat(fileresv,fileres);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
   if((ficresvij=fopen(fileresv,"w"))==NULL) {         /* Stable prevalence in each health state */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);         for(cpt=1; cpt<nlstate;cpt++){
   }           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
   k=0;       for(cpt=1; cpt<=nlstate;cpt++) {
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       k=k+1;       }
       fprintf(ficrest,"\n#****** ");       fprintf(fichtm,"\n<br>- Total life expectancy by age and
       for(j=1;j<=cptcoveff;j++)  health expectancies in states (1) and (2): e%s%d.png<br>
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
       fprintf(ficrest,"******\n");     } /* end i1 */
    }/* End k1 */
       fprintf(ficreseij,"\n#****** ");   fprintf(fichtm,"</ul>");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
       fprintf(ficresvij,"\n#****** ");   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
       for(j=1;j<=cptcoveff;j++)   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
       fprintf(ficresvij,"******\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
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   - 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);
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    /*  if(popforecast==1) fprintf(fichtm,"\n */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
       oldm=oldms;savm=savms;  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  /*      <br>",fileres,fileres,fileres,fileres); */
        /*  else  */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       fprintf(ficrest,"\n");  
           m=cptcoveff;
       hf=1;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       if (stepm >= YEARM) hf=stepm/YEARM;  
       epj=vector(1,nlstate+1);   jj1=0;
       for(age=bage; age <=fage ;age++){   for(k1=1; k1<=m;k1++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     for(i1=1; i1<=ncodemax[k1];i1++){
         if (popbased==1) {       jj1++;
           for(i=1; i<=nlstate;i++)       if (cptcovn > 0) {
             prlim[i][i]=probs[(int)age][i][k];         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(ficrest," %.0f",age);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {       for(cpt=1; cpt<=nlstate;cpt++) {
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
           }  interval) in state (%d): v%s%d%d.png <br>
           epj[nlstate+1] +=epj[j];  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
         }       }
         for(i=1, vepp=0.;i <=nlstate;i++)     } /* end i1 */
           for(j=1;j <=nlstate;j++)   }/* End k1 */
             vepp += vareij[i][j][(int)age];   fprintf(fichtm,"</ul>");
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  fclose(fichtm);
         for(j=1;j <=nlstate;j++){  }
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  
         }  /******************* Gnuplot file **************/
         fprintf(ficrest,"\n");  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);
     }
  fclose(ficreseij);  
  fclose(ficresvij);    /*#ifdef windows */
   fclose(ficrest);      fprintf(ficgp,"cd \"%s\" \n",pathc);
   fclose(ficpar);      /*#endif */
   free_vector(epj,1,nlstate+1);  m=pow(2,cptcoveff);
   /*  scanf("%d ",i); */    
    /* 1eme*/
   /*------- Variance limit prevalence------*/      for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
 strcpy(fileresvpl,"vpl");       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   strcat(fileresvpl,fileres);       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);       for (i=1; i<= nlstate ; i ++) {
     exit(0);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   }         else fprintf(ficgp," \%%*lf (\%%*lf)");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);       }
        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);
  k=0;       for (i=1; i<= nlstate ; i ++) {
  for(cptcov=1;cptcov<=i1;cptcov++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
      k=k+1;       } 
      fprintf(ficresvpl,"\n#****** ");       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
      for(j=1;j<=cptcoveff;j++)       for (i=1; i<= nlstate ; i ++) {
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
      fprintf(ficresvpl,"******\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
             }  
      varpl=matrix(1,nlstate,(int) bage, (int) fage);       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      oldm=oldms;savm=savms;     }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    }
    }    /*2 eme*/
  }    
     for (k1=1; k1<= m ; k1 ++) { 
   fclose(ficresvpl);      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);
   /*---------- End : free ----------------*/      
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      for (i=1; i<= nlstate+1 ; i ++) {
          k=2*i;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        for (j=1; j<= nlstate+1 ; j ++) {
            if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
            else fprintf(ficgp," \%%*lf (\%%*lf)");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        }   
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        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 ++) {
   free_matrix(matcov,1,npar,1,npar);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   free_vector(delti,1,npar);          else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
   printf("End of Imach\n");        for (j=1; j<= nlstate+1 ; j ++) {
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
            else fprintf(ficgp," \%%*lf (\%%*lf)");
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        }   
   /*printf("Total time was %d uSec.\n", total_usecs);*/        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   /*------ End -----------*/        else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
  end:    
 #ifdef windows    /*3eme*/
  chdir(pathcd);    
 #endif    for (k1=1; k1<= m ; k1 ++) { 
        for (cpt=1; cpt<= nlstate ; cpt ++) {
  system("..\\gp37mgw\\wgnuplot graph.plt");        k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
 #ifdef windows        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
   while (z[0] != 'q') {        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     chdir(pathcd);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     scanf("%s",z);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     if (z[0] == 'c') system("./imach");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     else if (z[0] == 'e') {          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       chdir(path);          
       system(optionfilehtm);        */
     }        for (i=1; i< nlstate ; i ++) {
     else if (z[0] == 'q') exit(0);          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);
   }          
 #endif        } 
 }      }
     }
     
     /* 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(probs, 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(probs, 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);
   } /* End of popforecast */
   
   /***********************************************/
   /**************** 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; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     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'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
       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!=0){
       /* 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);
   
     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);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- 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(probs, 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.1.15  
changed lines
  Added in v.1.84


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