Diff for /imach/src/imach.c between versions 1.46 and 1.86

version 1.46, 2002/05/30 17:44:35 version 1.86, 2003/06/17 20:04:08
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.86  2003/06/17 20:04:08  brouard
      (Module): Change position of html and gnuplot routines and added
   This program computes Healthy Life Expectancies from    routine fileappend.
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.85  2003/06/17 13:12:43  brouard
   interviewed on their health status or degree of disability (in the    * imach.c (Repository): Check when date of death was earlier that
   case of a health survey which is our main interest) -2- at least a    current date of interview. It may happen when the death was just
   second wave of interviews ("longitudinal") which measure each change    prior to the death. In this case, dh was negative and likelihood
   (if any) in individual health status.  Health expectancies are    was wrong (infinity). We still send an "Error" but patch by
   computed from the time spent in each health state according to a    assuming that the date of death was just one stepm after the
   model. More health states you consider, more time is necessary to reach the    interview.
   Maximum Likelihood of the parameters involved in the model.  The    (Repository): Because some people have very long ID (first column)
   simplest model is the multinomial logistic model where pij is the    we changed int to long in num[] and we added a new lvector for
   probability to be observed in state j at the second wave    memory allocation. But we also truncated to 8 characters (left
   conditional to be observed in state i at the first wave. Therefore    truncation)
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    (Repository): No more line truncation errors.
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.84  2003/06/13 21:44:43  brouard
   where the markup *Covariates have to be included here again* invites    * imach.c (Repository): Replace "freqsummary" at a correct
   you to do it.  More covariates you add, slower the    place. It differs from routine "prevalence" which may be called
   convergence.    many times. Probs is memory consuming and must be used with
     parcimony.
   The advantage of this computer programme, compared to a simple    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.83  2003/06/10 13:39:11  lievre
   intermediate interview, the information is lost, but taken into    *** empty log message ***
   account using an interpolation or extrapolation.    
     Revision 1.82  2003/06/05 15:57:20  brouard
   hPijx is the probability to be observed in state i at age x+h    Add log in  imach.c and  fullversion number is now printed.
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate  */
   states. This elementary transition (by month or quarter trimester,  /*
   semester or year) is model as a multinomial logistic.  The hPx     Interpolated Markov Chain
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Short summary of the programme:
   hPijx.    
     This program computes Healthy Life Expectancies from
   Also this programme outputs the covariance matrix of the parameters but also    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   of the life expectancies. It also computes the prevalence limits.    first survey ("cross") where individuals from different ages are
      interviewed on their health status or degree of disability (in the
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    case of a health survey which is our main interest) -2- at least a
            Institut national d'études démographiques, Paris.    second wave of interviews ("longitudinal") which measure each change
   This software have been partly granted by Euro-REVES, a concerted action    (if any) in individual health status.  Health expectancies are
   from the European Union.    computed from the time spent in each health state according to a
   It is copyrighted identically to a GNU software product, ie programme and    model. More health states you consider, more time is necessary to reach the
   software can be distributed freely for non commercial use. Latest version    Maximum Likelihood of the parameters involved in the model.  The
   can be accessed at http://euroreves.ined.fr/imach .    simplest model is the multinomial logistic model where pij is the
   **********************************************************************/    probability to be observed in state j at the second wave
      conditional to be observed in state i at the first wave. Therefore
 #include <math.h>    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #include <stdio.h>    'age' is age and 'sex' is a covariate. If you want to have a more
 #include <stdlib.h>    complex model than "constant and age", you should modify the program
 #include <unistd.h>    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 #define MAXLINE 256    convergence.
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    The advantage of this computer programme, compared to a simple
 #define FILENAMELENGTH 80    multinomial logistic model, is clear when the delay between waves is not
 /*#define DEBUG*/    identical for each individual. Also, if a individual missed an
 #define windows    intermediate interview, the information is lost, but taken into
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    account using an interpolation or extrapolation.  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     hPijx is the probability to be observed in state i at age x+h
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    conditional to the observed state i at age x. The delay 'h' can be
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 #define NINTERVMAX 8    semester or year) is modelled as a multinomial logistic.  The hPx
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    matrix is simply the matrix product of nh*stepm elementary matrices
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    and the contribution of each individual to the likelihood is simply
 #define NCOVMAX 8 /* Maximum number of covariates */    hPijx.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Also this programme outputs the covariance matrix of the parameters but also
 #define AGESUP 130    of the life expectancies. It also computes the stable prevalence. 
 #define AGEBASE 40    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 int erreur; /* Error number */    This software have been partly granted by Euro-REVES, a concerted action
 int nvar;    from the European Union.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    It is copyrighted identically to a GNU software product, ie programme and
 int npar=NPARMAX;    software can be distributed freely for non commercial use. Latest version
 int nlstate=2; /* Number of live states */    can be accessed at http://euroreves.ined.fr/imach .
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int popbased=0;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
 int *wav; /* Number of waves for this individuual 0 is possible */    **********************************************************************/
 int maxwav; /* Maxim number of waves */  /*
 int jmin, jmax; /* min, max spacing between 2 waves */    main
 int mle, weightopt;    read parameterfile
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    read datafile
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    concatwav
 double jmean; /* Mean space between 2 waves */    freqsummary
 double **oldm, **newm, **savm; /* Working pointers to matrices */    if (mle >= 1)
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */      mlikeli
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    print results files
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    if mle==1 
 FILE *ficreseij;       computes hessian
   char filerese[FILENAMELENGTH];    read end of parameter file: agemin, agemax, bage, fage, estepm
  FILE  *ficresvij;        begin-prev-date,...
   char fileresv[FILENAMELENGTH];    open gnuplot file
  FILE  *ficresvpl;    open html file
   char fileresvpl[FILENAMELENGTH];    stable prevalence
      for age prevalim()
 #define NR_END 1    h Pij x
 #define FREE_ARG char*    variance of p varprob
 #define FTOL 1.0e-10    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 #define NRANSI    Variance-covariance of DFLE
 #define ITMAX 200    prevalence()
      movingaverage()
 #define TOL 2.0e-4    varevsij() 
     if popbased==1 varevsij(,popbased)
 #define CGOLD 0.3819660    total life expectancies
 #define ZEPS 1.0e-10    Variance of stable prevalence
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);   end
   */
 #define GOLD 1.618034  
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  
    
 static double maxarg1,maxarg2;  #include <math.h>
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #include <stdio.h>
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #include <stdlib.h>
    #include <unistd.h>
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)  #include <sys/time.h>
   #include <time.h>
 static double sqrarg;  #include "timeval.h"
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 int imx;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 int stepm;  #define FILENAMELENGTH 132
 /* Stepm, step in month: minimum step interpolation*/  /*#define DEBUG*/
   /*#define windows*/
 int estepm;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 int m,nb;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;  #define NINTERVMAX 8
 double dateintmean=0;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 double *weight;  #define NCOVMAX 8 /* Maximum number of covariates */
 int **s; /* Status */  #define MAXN 20000
 double *agedc, **covar, idx;  #define YEARM 12. /* Number of months per year */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define AGESUP 130
   #define AGEBASE 40
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #ifdef unix
 double ftolhess; /* Tolerance for computing hessian */  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 /**************** split *************************/  #else
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define DIRSEPARATOR '\\'
 {  #define ODIRSEPARATOR '/'
    char *s;                             /* pointer */  #endif
    int  l1, l2;                         /* length counters */  
   /* $Id$ */
    l1 = strlen( path );                 /* length of path */  /* $State$ */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows  char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
    s = strrchr( path, '\\' );           /* find last / */  char fullversion[]="$Revision$ $Date$"; 
 #else  int erreur; /* Error number */
    s = strrchr( path, '/' );            /* find last / */  int nvar;
 #endif  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    if ( s == NULL ) {                   /* no directory, so use current */  int npar=NPARMAX;
 #if     defined(__bsd__)                /* get current working directory */  int nlstate=2; /* Number of live states */
       extern char       *getwd( );  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       if ( getwd( dirc ) == NULL ) {  int popbased=0;
 #else  
       extern char       *getcwd( );  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int jmin, jmax; /* min, max spacing between 2 waves */
 #endif  int mle, weightopt;
          return( GLOCK_ERROR_GETCWD );  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       strcpy( name, path );             /* we've got it */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
    } else {                             /* strip direcotry from path */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       s++;                              /* after this, the filename */  double jmean; /* Mean space between 2 waves */
       l2 = strlen( s );                 /* length of filename */  double **oldm, **newm, **savm; /* Working pointers to matrices */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       strcpy( name, s );                /* save file name */  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  FILE *ficlog, *ficrespow;
       dirc[l1-l2] = 0;                  /* add zero */  int globpr; /* Global variable for printing or not */
    }  double fretone; /* Only one call to likelihood */
    l1 = strlen( dirc );                 /* length of directory */  long ipmx; /* Number of contributions */
 #ifdef windows  double sw; /* Sum of weights */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 #else  FILE *ficresilk;
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #endif  FILE *ficresprobmorprev;
    s = strrchr( name, '.' );            /* find last / */  FILE *fichtm; /* Html File */
    s++;  FILE *ficreseij;
    strcpy(ext,s);                       /* save extension */  char filerese[FILENAMELENGTH];
    l1= strlen( name);  FILE  *ficresvij;
    l2= strlen( s)+1;  char fileresv[FILENAMELENGTH];
    strncpy( finame, name, l1-l2);  FILE  *ficresvpl;
    finame[l1-l2]= 0;  char fileresvpl[FILENAMELENGTH];
    return( 0 );                         /* we're done */  char title[MAXLINE];
 }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
 /******************************************/  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 void replace(char *s, char*t)  char filerest[FILENAMELENGTH];
 {  char fileregp[FILENAMELENGTH];
   int i;  char popfile[FILENAMELENGTH];
   int lg=20;  
   i=0;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  #define NR_END 1
     (s[i] = t[i]);  #define FREE_ARG char*
     if (t[i]== '\\') s[i]='/';  #define FTOL 1.0e-10
   }  
 }  #define NRANSI 
   #define ITMAX 200 
 int nbocc(char *s, char occ)  
 {  #define TOL 2.0e-4 
   int i,j=0;  
   int lg=20;  #define CGOLD 0.3819660 
   i=0;  #define ZEPS 1.0e-10 
   lg=strlen(s);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  #define GOLD 1.618034 
   }  #define GLIMIT 100.0 
   return j;  #define TINY 1.0e-20 
 }  
   static double maxarg1,maxarg2;
 void cutv(char *u,char *v, char*t, char occ)  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   int i,lg,j,p=0;    
   i=0;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   for(j=0; j<=strlen(t)-1; j++) {  #define rint(a) floor(a+0.5)
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   lg=strlen(t);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  int imx; 
   }  int stepm;
      u[p]='\0';  /* Stepm, step in month: minimum step interpolation*/
   
    for(j=0; j<= lg; j++) {  int estepm;
     if (j>=(p+1))(v[j-p-1] = t[j]);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   }  
 }  int m,nb;
   long *num;
 /********************** nrerror ********************/  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 void nrerror(char error_text[])  double **pmmij, ***probs;
 {  double dateintmean=0;
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  double *weight;
   exit(1);  int **s; /* Status */
 }  double *agedc, **covar, idx;
 /*********************** vector *******************/  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 double *vector(int nl, int nh)  
 {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double *v;  double ftolhess; /* Tolerance for computing hessian */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  /**************** split *************************/
   return v-nl+NR_END;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 }  {
     char  *ss;                            /* pointer */
 /************************ free vector ******************/    int   l1, l2;                         /* length counters */
 void free_vector(double*v, int nl, int nh)  
 {    l1 = strlen(path );                   /* length of path */
   free((FREE_ARG)(v+nl-NR_END));    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
 /************************ivector *******************************/      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 int *ivector(long nl,long nh)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 {      /* get current working directory */
   int *v;      /*    extern  char* getcwd ( char *buf , int len);*/
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   if (!v) nrerror("allocation failure in ivector");        return( GLOCK_ERROR_GETCWD );
   return v-nl+NR_END;      }
 }      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 /******************free ivector **************************/      ss++;                               /* after this, the filename */
 void free_ivector(int *v, long nl, long nh)      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   free((FREE_ARG)(v+nl-NR_END));      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 /******************* imatrix *******************************/    }
 int **imatrix(long nrl, long nrh, long ncl, long nch)    l1 = strlen( dirc );                  /* length of directory */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    /*#ifdef windows
 {    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #else
   int **m;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
    #endif
   /* allocate pointers to rows */    */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    ss = strrchr( name, '.' );            /* find last / */
   if (!m) nrerror("allocation failure 1 in matrix()");    ss++;
   m += NR_END;    strcpy(ext,ss);                       /* save extension */
   m -= nrl;    l1= strlen( name);
      l2= strlen(ss)+1;
      strncpy( finame, name, l1-l2);
   /* allocate rows and set pointers to them */    finame[l1-l2]= 0;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    return( 0 );                          /* we're done */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  }
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  
    /******************************************/
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    void replace(char *s, char*t)
   /* return pointer to array of pointers to rows */  {
   return m;    int i;
 }    int lg=20;
     i=0;
 /****************** free_imatrix *************************/    lg=strlen(t);
 void free_imatrix(m,nrl,nrh,ncl,nch)    for(i=0; i<= lg; i++) {
       int **m;      (s[i] = t[i]);
       long nch,ncl,nrh,nrl;      if (t[i]== '\\') s[i]='/';
      /* free an int matrix allocated by imatrix() */    }
 {  }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /******************* matrix *******************************/    int lg=20;
 double **matrix(long nrl, long nrh, long ncl, long nch)    i=0;
 {    lg=strlen(s);
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    for(i=0; i<= lg; i++) {
   double **m;    if  (s[i] == occ ) j++;
     }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    return j;
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   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)));    /* cuts string t into u and v where u is ended by char occ excluding it
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   m[nrl] += NR_END;       gives u="abcedf" and v="ghi2j" */
   m[nrl] -= ncl;    int i,lg,j,p=0;
     i=0;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    for(j=0; j<=strlen(t)-1; j++) {
   return m;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 }    }
   
 /*************************free matrix ************************/    lg=strlen(t);
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    for(j=0; j<p; j++) {
 {      (u[j] = t[j]);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    }
   free((FREE_ARG)(m+nrl-NR_END));       u[p]='\0';
 }  
      for(j=0; j<= lg; j++) {
 /******************* ma3x *******************************/      if (j>=(p+1))(v[j-p-1] = t[j]);
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    }
 {  }
   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*)));  void nrerror(char error_text[])
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    fprintf(stderr,"ERREUR ...\n");
   m -= nrl;    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /*********************** vector *******************/
   m[nrl] += NR_END;  double *vector(int nl, int nh)
   m[nrl] -= ncl;  {
     double *v;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    return v-nl+NR_END;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  }
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  /************************ free vector ******************/
   for (j=ncl+1; j<=nch; j++)  void free_vector(double*v, int nl, int nh)
     m[nrl][j]=m[nrl][j-1]+nlay;  {
      free((FREE_ARG)(v+nl-NR_END));
   for (i=nrl+1; i<=nrh; i++) {  }
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  /************************ivector *******************************/
       m[i][j]=m[i][j-1]+nlay;  int *ivector(long nl,long nh)
   }  {
   return m;    int *v;
 }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
 /*************************free ma3x ************************/    return v-nl+NR_END;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  }
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  /******************free ivector **************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  void free_ivector(int *v, long nl, long nh)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /***************** f1dim *************************/  
 extern int ncom;  /************************lvector *******************************/
 extern double *pcom,*xicom;  long *lvector(long nl,long nh)
 extern double (*nrfunc)(double []);  {
      long *v;
 double f1dim(double x)    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 {    if (!v) nrerror("allocation failure in ivector");
   int j;    return v-nl+NR_END;
   double f;  }
   double *xt;  
    /******************free lvector **************************/
   xt=vector(1,ncom);  void free_lvector(long *v, long nl, long nh)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  {
   f=(*nrfunc)(xt);    free((FREE_ARG)(v+nl-NR_END));
   free_vector(xt,1,ncom);  }
   return f;  
 }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 /*****************brent *************************/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  { 
 {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   int iter;    int **m; 
   double a,b,d,etemp;    
   double fu,fv,fw,fx;    /* allocate pointers to rows */ 
   double ftemp;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double p,q,r,tol1,tol2,u,v,w,x,xm;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double e=0.0;    m += NR_END; 
      m -= nrl; 
   a=(ax < cx ? ax : cx);    
   b=(ax > cx ? ax : cx);    
   x=w=v=bx;    /* allocate rows and set pointers to them */ 
   fw=fv=fx=(*f)(x);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   for (iter=1;iter<=ITMAX;iter++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     xm=0.5*(a+b);    m[nrl] += NR_END; 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    m[nrl] -= ncl; 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    
     printf(".");fflush(stdout);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 #ifdef DEBUG    
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    /* return pointer to array of pointers to rows */ 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    return m; 
 #endif  } 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /****************** free_imatrix *************************/
       return fx;  void free_imatrix(m,nrl,nrh,ncl,nch)
     }        int **m;
     ftemp=fu;        long nch,ncl,nrh,nrl; 
     if (fabs(e) > tol1) {       /* free an int matrix allocated by imatrix() */ 
       r=(x-w)*(fx-fv);  { 
       q=(x-v)*(fx-fw);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       p=(x-v)*q-(x-w)*r;    free((FREE_ARG) (m+nrl-NR_END)); 
       q=2.0*(q-r);  } 
       if (q > 0.0) p = -p;  
       q=fabs(q);  /******************* matrix *******************************/
       etemp=e;  double **matrix(long nrl, long nrh, long ncl, long nch)
       e=d;  {
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    double **m;
       else {  
         d=p/q;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         u=x+d;    if (!m) nrerror("allocation failure 1 in matrix()");
         if (u-a < tol2 || b-u < tol2)    m += NR_END;
           d=SIGN(tol1,xm-x);    m -= nrl;
       }  
     } else {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    m[nrl] -= ncl;
     fu=(*f)(u);  
     if (fu <= fx) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       if (u >= x) a=x; else b=x;    return m;
       SHFT(v,w,x,u)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
         SHFT(fv,fw,fx,fu)     */
         } else {  }
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /*************************free matrix ************************/
             v=w;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
             w=u;  {
             fv=fw;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
             fw=fu;    free((FREE_ARG)(m+nrl-NR_END));
           } else if (fu <= fv || v == x || v == w) {  }
             v=u;  
             fv=fu;  /******************* ma3x *******************************/
           }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         }  {
   }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   nrerror("Too many iterations in brent");    double ***m;
   *xmin=x;  
   return fx;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /****************** mnbrak ***********************/    m -= nrl;
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
             double (*func)(double))    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 {    m[nrl] += NR_END;
   double ulim,u,r,q, dum;    m[nrl] -= ncl;
   double fu;  
      for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   if (*fb > *fa) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     SHFT(dum,*ax,*bx,dum)    m[nrl][ncl] += NR_END;
       SHFT(dum,*fb,*fa,dum)    m[nrl][ncl] -= nll;
       }    for (j=ncl+1; j<=nch; j++) 
   *cx=(*bx)+GOLD*(*bx-*ax);      m[nrl][j]=m[nrl][j-1]+nlay;
   *fc=(*func)(*cx);    
   while (*fb > *fc) {    for (i=nrl+1; i<=nrh; i++) {
     r=(*bx-*ax)*(*fb-*fc);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     q=(*bx-*cx)*(*fb-*fa);      for (j=ncl+1; j<=nch; j++) 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        m[i][j]=m[i][j-1]+nlay;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    }
     ulim=(*bx)+GLIMIT*(*cx-*bx);    return m; 
     if ((*bx-u)*(u-*cx) > 0.0) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       fu=(*func)(u);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     } else if ((*cx-u)*(u-ulim) > 0.0) {    */
       fu=(*func)(u);  }
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /*************************free ma3x ************************/
           SHFT(*fb,*fc,fu,(*func)(u))  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) {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       u=ulim;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       fu=(*func)(u);    free((FREE_ARG)(m+nrl-NR_END));
     } else {  }
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  /***************** f1dim *************************/
     }  extern int ncom; 
     SHFT(*ax,*bx,*cx,u)  extern double *pcom,*xicom;
       SHFT(*fa,*fb,*fc,fu)  extern double (*nrfunc)(double []); 
       }   
 }  double f1dim(double x) 
   { 
 /*************** linmin ************************/    int j; 
     double f;
 int ncom;    double *xt; 
 double *pcom,*xicom;   
 double (*nrfunc)(double []);    xt=vector(1,ncom); 
      for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    f=(*nrfunc)(xt); 
 {    free_vector(xt,1,ncom); 
   double brent(double ax, double bx, double cx,    return f; 
                double (*f)(double), double tol, double *xmin);  } 
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /*****************brent *************************/
               double *fc, double (*func)(double));  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   int j;  { 
   double xx,xmin,bx,ax;    int iter; 
   double fx,fb,fa;    double a,b,d,etemp;
      double fu,fv,fw,fx;
   ncom=n;    double ftemp;
   pcom=vector(1,n);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   xicom=vector(1,n);    double e=0.0; 
   nrfunc=func;   
   for (j=1;j<=n;j++) {    a=(ax < cx ? ax : cx); 
     pcom[j]=p[j];    b=(ax > cx ? ax : cx); 
     xicom[j]=xi[j];    x=w=v=bx; 
   }    fw=fv=fx=(*f)(x); 
   ax=0.0;    for (iter=1;iter<=ITMAX;iter++) { 
   xx=1.0;      xm=0.5*(a+b); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 #ifdef DEBUG      printf(".");fflush(stdout);
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      fprintf(ficlog,".");fflush(ficlog);
 #endif  #ifdef DEBUG
   for (j=1;j<=n;j++) {      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     xi[j] *= xmin;      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);
     p[j] += xi[j];      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   }  #endif
   free_vector(xicom,1,n);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   free_vector(pcom,1,n);        *xmin=x; 
 }        return fx; 
       } 
 /*************** powell ************************/      ftemp=fu;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      if (fabs(e) > tol1) { 
             double (*func)(double []))        r=(x-w)*(fx-fv); 
 {        q=(x-v)*(fx-fw); 
   void linmin(double p[], double xi[], int n, double *fret,        p=(x-v)*q-(x-w)*r; 
               double (*func)(double []));        q=2.0*(q-r); 
   int i,ibig,j;        if (q > 0.0) p = -p; 
   double del,t,*pt,*ptt,*xit;        q=fabs(q); 
   double fp,fptt;        etemp=e; 
   double *xits;        e=d; 
   pt=vector(1,n);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   ptt=vector(1,n);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   xit=vector(1,n);        else { 
   xits=vector(1,n);          d=p/q; 
   *fret=(*func)(p);          u=x+d; 
   for (j=1;j<=n;j++) pt[j]=p[j];          if (u-a < tol2 || b-u < tol2) 
   for (*iter=1;;++(*iter)) {            d=SIGN(tol1,xm-x); 
     fp=(*fret);        } 
     ibig=0;      } else { 
     del=0.0;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      } 
     for (i=1;i<=n;i++)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       printf(" %d %.12f",i, p[i]);      fu=(*f)(u); 
     printf("\n");      if (fu <= fx) { 
     for (i=1;i<=n;i++) {        if (u >= x) a=x; else b=x; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        SHFT(v,w,x,u) 
       fptt=(*fret);          SHFT(fv,fw,fx,fu) 
 #ifdef DEBUG          } else { 
       printf("fret=%lf \n",*fret);            if (u < x) a=u; else b=u; 
 #endif            if (fu <= fw || w == x) { 
       printf("%d",i);fflush(stdout);              v=w; 
       linmin(p,xit,n,fret,func);              w=u; 
       if (fabs(fptt-(*fret)) > del) {              fv=fw; 
         del=fabs(fptt-(*fret));              fw=fu; 
         ibig=i;            } else if (fu <= fv || v == x || v == w) { 
       }              v=u; 
 #ifdef DEBUG              fv=fu; 
       printf("%d %.12e",i,(*fret));            } 
       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"); 
       }    *xmin=x; 
       for(j=1;j<=n;j++)    return fx; 
         printf(" p=%.12e",p[j]);  } 
       printf("\n");  
 #endif  /****************** mnbrak ***********************/
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 #ifdef DEBUG              double (*func)(double)) 
       int k[2],l;  { 
       k[0]=1;    double ulim,u,r,q, dum;
       k[1]=-1;    double fu; 
       printf("Max: %.12e",(*func)(p));   
       for (j=1;j<=n;j++)    *fa=(*func)(*ax); 
         printf(" %.12e",p[j]);    *fb=(*func)(*bx); 
       printf("\n");    if (*fb > *fa) { 
       for(l=0;l<=1;l++) {      SHFT(dum,*ax,*bx,dum) 
         for (j=1;j<=n;j++) {        SHFT(dum,*fb,*fa,dum) 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        } 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    *cx=(*bx)+GOLD*(*bx-*ax); 
         }    *fc=(*func)(*cx); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    while (*fb > *fc) { 
       }      r=(*bx-*ax)*(*fb-*fc); 
 #endif      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       free_vector(xit,1,n);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       free_vector(xits,1,n);      if ((*bx-u)*(u-*cx) > 0.0) { 
       free_vector(ptt,1,n);        fu=(*func)(u); 
       free_vector(pt,1,n);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       return;        fu=(*func)(u); 
     }        if (fu < *fc) { 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for (j=1;j<=n;j++) {            SHFT(*fb,*fc,fu,(*func)(u)) 
       ptt[j]=2.0*p[j]-pt[j];            } 
       xit[j]=p[j]-pt[j];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       pt[j]=p[j];        u=ulim; 
     }        fu=(*func)(u); 
     fptt=(*func)(ptt);      } else { 
     if (fptt < fp) {        u=(*cx)+GOLD*(*cx-*bx); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        fu=(*func)(u); 
       if (t < 0.0) {      } 
         linmin(p,xit,n,fret,func);      SHFT(*ax,*bx,*cx,u) 
         for (j=1;j<=n;j++) {        SHFT(*fa,*fb,*fc,fu) 
           xi[j][ibig]=xi[j][n];        } 
           xi[j][n]=xit[j];  } 
         }  
 #ifdef DEBUG  /*************** linmin ************************/
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)  int ncom; 
           printf(" %.12e",xit[j]);  double *pcom,*xicom;
         printf("\n");  double (*nrfunc)(double []); 
 #endif   
       }  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); 
     double f1dim(double x); 
 /**** Prevalence limit ****************/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    int j; 
 {    double xx,xmin,bx,ax; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    double fx,fb,fa;
      matrix by transitions matrix until convergence is reached */   
     ncom=n; 
   int i, ii,j,k;    pcom=vector(1,n); 
   double min, max, maxmin, maxmax,sumnew=0.;    xicom=vector(1,n); 
   double **matprod2();    nrfunc=func; 
   double **out, cov[NCOVMAX], **pmij();    for (j=1;j<=n;j++) { 
   double **newm;      pcom[j]=p[j]; 
   double agefin, delaymax=50 ; /* Max number of years to converge */      xicom[j]=xi[j]; 
     } 
   for (ii=1;ii<=nlstate+ndeath;ii++)    ax=0.0; 
     for (j=1;j<=nlstate+ndeath;j++){    xx=1.0; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
    cov[1]=1.;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
      fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #endif
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    for (j=1;j<=n;j++) { 
     newm=savm;      xi[j] *= xmin; 
     /* Covariates have to be included here again */      p[j] += xi[j]; 
      cov[2]=agefin;    } 
      free_vector(xicom,1,n); 
       for (k=1; k<=cptcovn;k++) {    free_vector(pcom,1,n); 
         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]]);*/  
       }  /*************** powell ************************/
       for (k=1; k<=cptcovage;k++) 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; 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    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 \n",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,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)            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, k2, dateintsum=0,k2cpt=0;          /*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,AGESUP,1,NCOVMAX, 1,NCOVMAX);           * 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 */
       dateintsum=0;      } /* end of individual */
       k2cpt=0;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1; i<=imx; i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         bool=1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if  (cptcovn>0) {        for(mi=1; mi<= wav[i]-1; mi++){
           for (z1=1; z1<=cptcoveff; z1++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            for (j=1;j<=nlstate+ndeath;j++){
               bool=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (bool==1) {            }
           for(m=firstpass; m<=lastpass; m++){          for(d=0; d<dh[mi][i]; d++){
             k2=anint[m][i]+(mint[m][i]/12.);            newm=savm;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               if(agev[m][i]==0) agev[m][i]=agemax+1;            for (kk=1; kk<=cptcovage;kk++) {
               if(agev[m][i]==1) agev[m][i]=agemax+2;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               if (m<lastpass) {            }
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                          savm=oldm;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            oldm=newm;
                 dateintsum=dateintsum+k2;          } /* end mult */
                 k2cpt++;        
               }          s1=s[mw[mi][i]][i];
             }          s2=s[mw[mi+1][i]][i];
           }          if( s2 > nlstate){ 
         }            lli=log(out[s1][s2] - savm[s1][s2]);
       }          }else{
                    lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          }
           ipmx +=1;
       if  (cptcovn>0) {          sw += weight[i];
         fprintf(ficresp, "\n#********** Variable ");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /*      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]); */
         fprintf(ficresp, "**********\n#");        } /* end of wave */
       }      } /* end of individual */
       for(i=1; i<=nlstate;i++)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficresp, "\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              for(mi=1; mi<= wav[i]-1; mi++){
       for(i=(int)agemin; i <= (int)agemax+3; i++){          for (ii=1;ii<=nlstate+ndeath;ii++)
         if(i==(int)agemax+3)            for (j=1;j<=nlstate+ndeath;j++){
           printf("Total");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           printf("Age %d", i);            }
         for(jk=1; jk <=nlstate ; jk++){          for(d=0; d<dh[mi][i]; d++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            newm=savm;
             pp[jk] += freq[jk][m][i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
         for(jk=1; jk <=nlstate ; jk++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for(m=-1, pos=0; m <=0 ; m++)            }
             pos += freq[jk][m][i];          
           if(pp[jk]>=1.e-10)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           else            savm=oldm;
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            oldm=newm;
         }          } /* end mult */
         
         for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          s2=s[mw[mi+1][i]][i];
             pp[jk] += freq[jk][m][i];          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          ipmx +=1;
           sw += weight[i];
         for(jk=1,pos=0; jk <=nlstate ; jk++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           pos += pp[jk];          /*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 */
           if(pos>=1.e-5)      } /* end of individual */
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    } /* End of if */
           else    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           if( i <= (int) agemax){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
             if(pos>=1.e-5){    return -l;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  }
               probs[i][jk][j1]= pp[jk]/pos;  
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  /*************** log-likelihood *************/
             }  double funcone( double *x)
             else  {
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    int i, ii, j, k, mi, d, kk;
           }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         }    double **out;
            double lli; /* Individual log likelihood */
         for(jk=-1; jk <=nlstate+ndeath; jk++)    int s1, s2;
           for(m=-1; m <=nlstate+ndeath; m++)    double bbh, survp;
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    /*extern weight */
         if(i <= (int) agemax)    /* We are differentiating ll according to initial status */
           fprintf(ficresp,"\n");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         printf("\n");    /*for(i=1;i<imx;i++) 
       }      printf(" %d\n",s[4][i]);
     }    */
   }    cov[1]=1.;
   dateintmean=dateintsum/k2cpt;  
      for(k=1; k<=nlstate; k++) ll[k]=0.;
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_vector(pp,1,nlstate);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
   /* End of Freq */        for (ii=1;ii<=nlstate+ndeath;ii++)
 }          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ Prevalence ********************/            savm[ii][j]=(ii==j ? 1.0 : 0.0);
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)          }
 {  /* Some frequencies */        for(d=0; d<dh[mi][i]; d++){
            newm=savm;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***freq; /* Frequencies */          for (kk=1; kk<=cptcovage;kk++) {
   double *pp;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double pos, k2;          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   pp=vector(1,nlstate);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          savm=oldm;
            oldm=newm;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        } /* end mult */
   j1=0;        
          s1=s[mw[mi][i]][i];
   j=cptcoveff;        s2=s[mw[mi+1][i]][i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        bbh=(double)bh[mi][i]/(double)stepm; 
          /* bias is positive if real duration
   for(k1=1; k1<=j;k1++){         * is higher than the multiple of stepm and negative otherwise.
     for(i1=1; i1<=ncodemax[k1];i1++){         */
       j1++;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
                lli=log(out[s1][s2] - savm[s1][s2]);
       for (i=-1; i<=nlstate+ndeath; i++)          } else if (mle==1){
         for (jk=-1; jk<=nlstate+ndeath; jk++)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           for(m=agemin; m <= agemax+3; m++)        } else if(mle==2){
             freq[i][jk][m]=0;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
              } else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1; i<=imx; i++) {          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         bool=1;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         if  (cptcovn>0) {          lli=log(out[s1][s2]); /* Original formula */
           for (z1=1; z1<=cptcoveff; z1++)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          lli=log(out[s1][s2]); /* Original formula */
               bool=0;        } /* End of if */
         }        ipmx +=1;
         if (bool==1) {        sw += weight[i];
           for(m=firstpass; m<=lastpass; m++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             k2=anint[m][i]+(mint[m][i]/12.);  /*       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]); */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        if(globpr){
               if(agev[m][i]==0) agev[m][i]=agemax+1;          fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
               if(agev[m][i]==1) agev[m][i]=agemax+2;   %10.6f %10.6f %10.6f ", \
               if (m<lastpass) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                 if (calagedate>0)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          for(k=1,l=0.; k<=nlstate; k++) 
                 else            fprintf(ficresilk," %10.6f",ll[k]);
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          fprintf(ficresilk,"\n");
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];        }
               }      } /* end of wave */
             }    } /* end of individual */
           }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       for(i=(int)agemin; i <= (int)agemax+3; i++){    return -l;
         for(jk=1; jk <=nlstate ; jk++){  }
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
             pp[jk] += freq[jk][m][i];  
         }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpr, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         for(jk=1; jk <=nlstate ; jk++){  {
           for(m=-1, pos=0; m <=0 ; m++)    /* This routine should help understanding what is done with the selection of individuals/waves and
             pos += freq[jk][m][i];       to check the exact contribution to the likelihood.
         }       Plotting could be done.
             */
         for(jk=1; jk <=nlstate ; jk++){    int k;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    if(globpr !=0){ /* Just counts and sums no printings */
             pp[jk] += freq[jk][m][i];      strcpy(fileresilk,"ilk"); 
         }      strcat(fileresilk,fileres);
              if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        printf("Problem with resultfile: %s\n", fileresilk);
                fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         for(jk=1; jk <=nlstate ; jk++){          }
           if( i <= (int) agemax){      fprintf(ficresilk, "#individual(line's record) s1 s2 wave# effective_wave# number_of_product_matrix pij weight 2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state\n");
             if(pos>=1.e-5){      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight out sav ");
               probs[i][jk][j1]= pp[jk]/pos;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
             }      for(k=1; k<=nlstate; k++) 
           }        fprintf(ficresilk," ll[%d]",k);
         }      fprintf(ficresilk,"\n");
            }
       }  
     }    *fretone=(*funcone)(p);
   }    if(globpr !=0){
       fclose(ficresilk);
        if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        printf("Problem with html file: %s\n", optionfilehtm);
   free_vector(pp,1,nlstate);        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
          exit(0);
 }  /* End of Freq */      }
       else{
 /************* Waves Concatenation ***************/        fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",fileresilk);
         fclose(fichtm);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      }
 {    }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    return;
      Death is a valid wave (if date is known).  }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  /*********** Maximum Likelihood Estimation ***************/
      and mw[mi+1][i]. dh depends on stepm.  
      */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
   int i, mi, m;    int i,j, iter;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    double **xi;
      double sum=0., jmean=0.;*/    double fret;
     double fretone; /* Only one call to likelihood */
   int j, k=0,jk, ju, jl;    char filerespow[FILENAMELENGTH];
   double sum=0.;    xi=matrix(1,npar,1,npar);
   jmin=1e+5;    for (i=1;i<=npar;i++)
   jmax=-1;      for (j=1;j<=npar;j++)
   jmean=0.;        xi[i][j]=(i==j ? 1.0 : 0.0);
   for(i=1; i<=imx; i++){    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     mi=0;    strcpy(filerespow,"pow"); 
     m=firstpass;    strcat(filerespow,fileres);
     while(s[m][i] <= nlstate){    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       if(s[m][i]>=1)      printf("Problem with resultfile: %s\n", filerespow);
         mw[++mi][i]=m;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       if(m >=lastpass)    }
         break;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       else    for (i=1;i<=nlstate;i++)
         m++;      for(j=1;j<=nlstate+ndeath;j++)
     }/* end while */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     if (s[m][i] > nlstate){    fprintf(ficrespow,"\n");
       mi++;     /* Death is another wave */  
       /* if(mi==0)  never been interviewed correctly before death */    powell(p,xi,npar,ftol,&iter,&fret,func);
          /* Only death is a correct wave */  
       mw[mi][i]=m;    fclose(ficrespow);
     }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     wav[i]=mi;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     if(mi==0)  
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  }
   }  
   /**** Computes Hessian and covariance matrix ***/
   for(i=1; i<=imx; i++){  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for(mi=1; mi<wav[i];mi++){  {
       if (stepm <=0)    double  **a,**y,*x,pd;
         dh[mi][i]=1;    double **hess;
       else{    int i, j,jk;
         if (s[mw[mi+1][i]][i] > nlstate) {    int *indx;
           if (agedc[i] < 2*AGESUP) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    double hessii(double p[], double delta, int theta, double delti[]);
           if(j==0) j=1;  /* Survives at least one month after exam */    double hessij(double p[], double delti[], int i, int j);
           k=k+1;    void lubksb(double **a, int npar, int *indx, double b[]) ;
           if (j >= jmax) jmax=j;    void ludcmp(double **a, int npar, int *indx, double *d) ;
           if (j <= jmin) jmin=j;  
           sum=sum+j;    hess=matrix(1,npar,1,npar);
           /*if (j<0) printf("j=%d num=%d \n",j,i); */  
           }    printf("\nCalculation of the hessian matrix. Wait...\n");
         }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         else{    for (i=1;i<=npar;i++){
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      printf("%d",i);fflush(stdout);
           k=k+1;      fprintf(ficlog,"%d",i);fflush(ficlog);
           if (j >= jmax) jmax=j;      hess[i][i]=hessii(p,ftolhess,i,delti);
           else if (j <= jmin)jmin=j;      /*printf(" %f ",p[i]);*/
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      /*printf(" %lf ",hess[i][i]);*/
           sum=sum+j;    }
         }    
         jk= j/stepm;    for (i=1;i<=npar;i++) {
         jl= j -jk*stepm;      for (j=1;j<=npar;j++)  {
         ju= j -(jk+1)*stepm;        if (j>i) { 
         if(jl <= -ju)          printf(".%d%d",i,j);fflush(stdout);
           dh[mi][i]=jk;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         else          hess[i][j]=hessij(p,delti,i,j);
           dh[mi][i]=jk+1;          hess[j][i]=hess[i][j];    
         if(dh[mi][i]==0)          /*printf(" %lf ",hess[i][j]);*/
           dh[mi][i]=1; /* At least one step */        }
       }      }
     }    }
   }    printf("\n");
   jmean=sum/k;    fprintf(ficlog,"\n");
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  
  }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 /*********** Tricode ****************************/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 void tricode(int *Tvar, int **nbcode, int imx)    
 {    a=matrix(1,npar,1,npar);
   int Ndum[20],ij=1, k, j, i;    y=matrix(1,npar,1,npar);
   int cptcode=0;    x=vector(1,npar);
   cptcoveff=0;    indx=ivector(1,npar);
      for (i=1;i<=npar;i++)
   for (k=0; k<19; k++) Ndum[k]=0;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   for (k=1; k<=7; k++) ncodemax[k]=0;    ludcmp(a,npar,indx,&pd);
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    for (j=1;j<=npar;j++) {
     for (i=1; i<=imx; i++) {      for (i=1;i<=npar;i++) x[i]=0;
       ij=(int)(covar[Tvar[j]][i]);      x[j]=1;
       Ndum[ij]++;      lubksb(a,npar,indx,x);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      for (i=1;i<=npar;i++){ 
       if (ij > cptcode) cptcode=ij;        matcov[i][j]=x[i];
     }      }
     }
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;    printf("\n#Hessian matrix#\n");
     }    fprintf(ficlog,"\n#Hessian matrix#\n");
     ij=1;    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
     for (i=1; i<=ncodemax[j]; i++) {        fprintf(ficlog,"%.3e ",hess[i][j]);
       for (k=0; k<=19; k++) {      }
         if (Ndum[k] != 0) {      printf("\n");
           nbcode[Tvar[j]][ij]=k;      fprintf(ficlog,"\n");
              }
           ij++;  
         }    /* Recompute Inverse */
         if (ij > ncodemax[j]) break;    for (i=1;i<=npar;i++)
       }        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     }    ludcmp(a,npar,indx,&pd);
   }    
     /*  printf("\n#Hessian matrix recomputed#\n");
  for (k=0; k<19; k++) Ndum[k]=0;  
     for (j=1;j<=npar;j++) {
  for (i=1; i<=ncovmodel-2; i++) {      for (i=1;i<=npar;i++) x[i]=0;
       ij=Tvar[i];      x[j]=1;
       Ndum[ij]++;      lubksb(a,npar,indx,x);
     }      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
  ij=1;        printf("%.3e ",y[i][j]);
  for (i=1; i<=10; i++) {        fprintf(ficlog,"%.3e ",y[i][j]);
    if((Ndum[i]!=0) && (i<=ncovcol)){      }
      Tvaraff[ij]=i;      printf("\n");
      ij++;      fprintf(ficlog,"\n");
    }    }
  }    */
    
     cptcoveff=ij-1;    free_matrix(a,1,npar,1,npar);
 }    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
 /*********** Health Expectancies ****************/    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )  
   
 {  }
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  /*************** hessian matrix ****************/
   double age, agelim, hf;  double hessii( double x[], double delta, int theta, double delti[])
   double ***p3mat,***varhe;  {
   double **dnewm,**doldm;    int i;
   double *xp;    int l=1, lmax=20;
   double **gp, **gm;    double k1,k2;
   double ***gradg, ***trgradg;    double p2[NPARMAX+1];
   int theta;    double res;
     double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    double fx;
   xp=vector(1,npar);    int k=0,kmax=10;
   dnewm=matrix(1,nlstate*2,1,npar);    double l1;
   doldm=matrix(1,nlstate*2,1,nlstate*2);  
      fx=func(x);
   fprintf(ficreseij,"# Health expectancies\n");    for (i=1;i<=npar;i++) p2[i]=x[i];
   fprintf(ficreseij,"# Age");    for(l=0 ; l <=lmax; l++){
   for(i=1; i<=nlstate;i++)      l1=pow(10,l);
     for(j=1; j<=nlstate;j++)      delts=delt;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);      for(k=1 ; k <kmax; k=k+1){
   fprintf(ficreseij,"\n");        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
   if(estepm < stepm){        k1=func(p2)-fx;
     printf ("Problem %d lower than %d\n",estepm, stepm);        p2[theta]=x[theta]-delt;
   }        k2=func(p2)-fx;
   else  hstepm=estepm;          /*res= (k1-2.0*fx+k2)/delt/delt; */
   /* We compute the life expectancy from trapezoids spaced every estepm months        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
    * This is mainly to measure the difference between two models: for example        
    * if stepm=24 months pijx are given only every 2 years and by summing them  #ifdef DEBUG
    * we are calculating an estimate of the Life Expectancy assuming a linear        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);
    * progression inbetween and thus overestimating or underestimating according        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);
    * to the curvature of the survival function. If, for the same date, we  #endif
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
    * to compare the new estimate of Life expectancy with the same linear        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
    * hypothesis. A more precise result, taking into account a more precise          k=kmax;
    * curvature will be obtained if estepm is as small as stepm. */        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   /* For example we decided to compute the life expectancy with the smallest unit */          k=kmax; l=lmax*10.;
   /* 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 if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
      nstepm is the number of stepm from age to agelin.          delts=delt;
      Look at hpijx to understand the reason of that which relies in memory size        }
      and note for a fixed period like estepm months */      }
   /* 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    delti[theta]=delts;
      means that if the survival funtion is printed only each two years of age and if    return res; 
      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 */  double hessij( double x[], double delti[], int thetai,int thetaj)
   {
   agelim=AGESUP;    int i;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int l=1, l1, lmax=20;
     /* nhstepm age range expressed in number of stepm */    double k1,k2,k3,k4,res,fx;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    double p2[NPARMAX+1];
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    int k;
     /* if (stepm >= YEARM) hstepm=1;*/  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    fx=func(x);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (k=1; k<=2; k++) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      for (i=1;i<=npar;i++) p2[i]=x[i];
     gp=matrix(0,nhstepm,1,nlstate*2);      p2[thetai]=x[thetai]+delti[thetai]/k;
     gm=matrix(0,nhstepm,1,nlstate*2);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      p2[thetai]=x[thetai]+delti[thetai]/k;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k2=func(p2)-fx;
     
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     /* Computing Variances of health expectancies */      k3=func(p2)-fx;
     
      for(theta=1; theta <=npar; theta++){      p2[thetai]=x[thetai]-delti[thetai]/k;
       for(i=1; i<=npar; i++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      k4=func(p2)-fx;
       }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    #ifdef DEBUG
        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);
       cptj=0;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       for(j=1; j<= nlstate; j++){  #endif
         for(i=1; i<=nlstate; i++){    }
           cptj=cptj+1;    return res;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){  }
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  /************** Inverse of matrix **************/
         }  void ludcmp(double **a, int n, int *indx, double *d) 
       }  { 
          int i,imax,j,k; 
          double big,dum,sum,temp; 
       for(i=1; i<=npar; i++)    double *vv; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);   
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      vv=vector(1,n); 
          *d=1.0; 
       cptj=0;    for (i=1;i<=n;i++) { 
       for(j=1; j<= nlstate; j++){      big=0.0; 
         for(i=1;i<=nlstate;i++){      for (j=1;j<=n;j++) 
           cptj=cptj+1;        if ((temp=fabs(a[i][j])) > big) big=temp; 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      vv[i]=1.0/big; 
           }    } 
         }    for (j=1;j<=n;j++) { 
       }      for (i=1;i<j;i++) { 
       for(j=1; j<= nlstate*2; j++)        sum=a[i][j]; 
         for(h=0; h<=nhstepm-1; h++){        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        a[i][j]=sum; 
         }      } 
      }      big=0.0; 
          for (i=j;i<=n;i++) { 
 /* End theta */        sum=a[i][j]; 
         for (k=1;k<j;k++) 
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
      for(h=0; h<=nhstepm-1; h++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       for(j=1; j<=nlstate*2;j++)          big=dum; 
         for(theta=1; theta <=npar; theta++)          imax=i; 
           trgradg[h][j][theta]=gradg[h][theta][j];        } 
            } 
       if (j != imax) { 
      for(i=1;i<=nlstate*2;i++)        for (k=1;k<=n;k++) { 
       for(j=1;j<=nlstate*2;j++)          dum=a[imax][k]; 
         varhe[i][j][(int)age] =0.;          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
      printf("%d|",(int)age);fflush(stdout);        } 
      for(h=0;h<=nhstepm-1;h++){        *d = -(*d); 
       for(k=0;k<=nhstepm-1;k++){        vv[imax]=vv[j]; 
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);      } 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);      indx[j]=imax; 
         for(i=1;i<=nlstate*2;i++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
           for(j=1;j<=nlstate*2;j++)      if (j != n) { 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;        dum=1.0/(a[j][j]); 
       }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     }      } 
     } 
          free_vector(vv,1,n);  /* Doesn't work */
     /* Computing expectancies */  ;
     for(i=1; i<=nlstate;i++)  } 
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  void lubksb(double **a, int n, int *indx, double b[]) 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  { 
              int i,ii=0,ip,j; 
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    double sum; 
    
         }    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
     fprintf(ficreseij,"%3.0f",age );      sum=b[ip]; 
     cptj=0;      b[ip]=b[i]; 
     for(i=1; i<=nlstate;i++)      if (ii) 
       for(j=1; j<=nlstate;j++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         cptj++;      else if (sum) ii=i; 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      b[i]=sum; 
       }    } 
     fprintf(ficreseij,"\n");    for (i=n;i>=1;i--) { 
          sum=b[i]; 
     free_matrix(gm,0,nhstepm,1,nlstate*2);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     free_matrix(gp,0,nhstepm,1,nlstate*2);      b[i]=sum/a[i][i]; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    } 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);  } 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }  /************ Frequencies ********************/
   free_vector(xp,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)
   free_matrix(dnewm,1,nlstate*2,1,npar);  {  /* Some frequencies */
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
 }    int first;
     double ***freq; /* Frequencies */
 /************ Variance ******************/    double *pp, **prop;
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    double pos,posprop, k2, dateintsum=0,k2cpt=0;
 {    FILE *ficresp;
   /* Variance of health expectancies */    char fileresp[FILENAMELENGTH];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    
   double **newm;    pp=vector(1,nlstate);
   double **dnewm,**doldm;    prop=matrix(1,nlstate,iagemin,iagemax+3);
   int i, j, nhstepm, hstepm, h, nstepm ;    strcpy(fileresp,"p");
   int k, cptcode;    strcat(fileresp,fileres);
   double *xp;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   double **gp, **gm;      printf("Problem with prevalence resultfile: %s\n", fileresp);
   double ***gradg, ***trgradg;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   double ***p3mat;      exit(0);
   double age,agelim, hf;    }
   int theta;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=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");    
   fprintf(ficresvij,"# Age");    j=cptcoveff;
   for(i=1; i<=nlstate;i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    first=1;
   fprintf(ficresvij,"\n");  
     for(k1=1; k1<=j;k1++){
   xp=vector(1,npar);      for(i1=1; i1<=ncodemax[k1];i1++){
   dnewm=matrix(1,nlstate,1,npar);        j1++;
   doldm=matrix(1,nlstate,1,nlstate);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
            scanf("%d", i);*/
   if(estepm < stepm){        for (i=-1; i<=nlstate+ndeath; i++)  
     printf ("Problem %d lower than %d\n",estepm, stepm);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   }            for(m=iagemin; m <= iagemax+3; m++)
   else  hstepm=estepm;                freq[i][jk][m]=0;
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (i=1; i<=nlstate; i++)  
      nhstepm is the number of hstepm from age to agelim        for(m=iagemin; m <= iagemax+3; m++)
      nstepm is the number of stepm from age to agelin.          prop[i][m]=0;
      Look at hpijx to understand the reason of that which relies in memory size        
      and note for a fixed period like k years */        dateintsum=0;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        k2cpt=0;
      survival function given by stepm (the optimization length). Unfortunately it        for (i=1; i<=imx; i++) {
      means that if the survival funtion is printed only each two years of age and if          bool=1;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          if  (cptcovn>0) {
      results. So we changed our mind and took the option of the best precision.            for (z1=1; z1<=cptcoveff; z1++) 
   */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */                bool=0;
   agelim = AGESUP;          }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          if (bool==1){
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            for(m=firstpass; m<=lastpass; m++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */              k2=anint[m][i]+(mint[m][i]/12.);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     gp=matrix(0,nhstepm,1,nlstate);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     gm=matrix(0,nhstepm,1,nlstate);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 if (m<lastpass) {
     for(theta=1; theta <=npar; theta++){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       for(i=1; i<=npar; i++){ /* Computes gradient */                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                }
       }                
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                  dateintsum=dateintsum+k2;
                   k2cpt++;
       if (popbased==1) {                }
         for(i=1; i<=nlstate;i++)                /*}*/
           prlim[i][i]=probs[(int)age][i][ij];            }
       }          }
          }
       for(j=1; j<= nlstate; j++){         
         for(h=0; h<=nhstepm; h++){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        if  (cptcovn>0) {
         }          fprintf(ficresp, "\n#********** Variable "); 
       }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficresp, "**********\n#");
       for(i=1; i<=npar; i++) /* Computes gradient */        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for(i=1; i<=nlstate;i++) 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        fprintf(ficresp, "\n");
          
       if (popbased==1) {        for(i=iagemin; i <= iagemax+3; i++){
         for(i=1; i<=nlstate;i++)          if(i==iagemax+3){
           prlim[i][i]=probs[(int)age][i][ij];            fprintf(ficlog,"Total");
       }          }else{
             if(first==1){
       for(j=1; j<= nlstate; j++){              first=0;
         for(h=0; h<=nhstepm; h++){              printf("See log file for details...\n");
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            fprintf(ficlog,"Age %d", i);
         }          }
       }          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       for(j=1; j<= nlstate; j++)              pp[jk] += freq[jk][m][i]; 
         for(h=0; h<=nhstepm; h++){          }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=-1, pos=0; m <=0 ; m++)
     } /* End theta */              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     for(h=0; h<=nhstepm; h++)              }
       for(j=1; j<=nlstate;j++)              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for(theta=1; theta <=npar; theta++)            }else{
           trgradg[h][j][theta]=gradg[h][theta][j];              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for(i=1;i<=nlstate;i++)            }
       for(j=1;j<=nlstate;j++)          }
         vareij[i][j][(int)age] =0.;  
           for(jk=1; jk <=nlstate ; jk++){
     for(h=0;h<=nhstepm;h++){            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for(k=0;k<=nhstepm;k++){              pp[jk] += freq[jk][m][i];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          }       
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         for(i=1;i<=nlstate;i++)            pos += pp[jk];
           for(j=1;j<=nlstate;j++)            posprop += prop[jk][i];
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          }
       }          for(jk=1; jk <=nlstate ; jk++){
     }            if(pos>=1.e-5){
               if(first==1)
     fprintf(ficresvij,"%.0f ",age );                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       for(j=1; j<=nlstate;j++){            }else{
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);              if(first==1)
       }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     fprintf(ficresvij,"\n");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     free_matrix(gp,0,nhstepm,1,nlstate);            }
     free_matrix(gm,0,nhstepm,1,nlstate);            if( i <= iagemax){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);              if(pos>=1.e-5){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                /*probs[i][jk][j1]= pp[jk]/pos;*/
   } /* End age */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                }
   free_vector(xp,1,npar);              else
   free_matrix(doldm,1,nlstate,1,npar);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   free_matrix(dnewm,1,nlstate,1,nlstate);            }
           }
 }          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
 /************ Variance of prevlim ******************/            for(m=-1; m <=nlstate+ndeath; m++)
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)              if(freq[jk][m][i] !=0 ) {
 {              if(first==1)
   /* Variance of prevalence limit */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   double **newm;              }
   double **dnewm,**doldm;          if(i <= iagemax)
   int i, j, nhstepm, hstepm;            fprintf(ficresp,"\n");
   int k, cptcode;          if(first==1)
   double *xp;            printf("Others in log...\n");
   double *gp, *gm;          fprintf(ficlog,"\n");
   double **gradg, **trgradg;        }
   double age,agelim;      }
   int theta;    }
        dateintmean=dateintsum/k2cpt; 
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");   
   fprintf(ficresvpl,"# Age");    fclose(ficresp);
   for(i=1; i<=nlstate;i++)    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
       fprintf(ficresvpl," %1d-%1d",i,i);    free_vector(pp,1,nlstate);
   fprintf(ficresvpl,"\n");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
   xp=vector(1,npar);  }
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);  /************ Prevalence ********************/
    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)
   hstepm=1*YEARM; /* Every year of age */  {  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   agelim = AGESUP;       in each health status at the date of interview (if between dateprev1 and dateprev2).
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       We still use firstpass and lastpass as another selection.
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    */
     if (stepm >= YEARM) hstepm=1;   
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     gradg=matrix(1,npar,1,nlstate);    double ***freq; /* Frequencies */
     gp=vector(1,nlstate);    double *pp, **prop;
     gm=vector(1,nlstate);    double pos,posprop; 
     double  y2; /* in fractional years */
     for(theta=1; theta <=npar; theta++){    int iagemin, iagemax;
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    iagemin= (int) agemin;
       }    iagemax= (int) agemax;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /*pp=vector(1,nlstate);*/
       for(i=1;i<=nlstate;i++)    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         gp[i] = prlim[i][i];    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
        j1=0;
       for(i=1; i<=npar; i++) /* Computes gradient */    
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    j=cptcoveff;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(i=1;i<=nlstate;i++)    
         gm[i] = prlim[i][i];    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
       for(i=1;i<=nlstate;i++)        j1++;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        
     } /* End theta */        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
     trgradg =matrix(1,nlstate,1,npar);            prop[i][m]=0.0;
        
     for(j=1; j<=nlstate;j++)        for (i=1; i<=imx; i++) { /* Each individual */
       for(theta=1; theta <=npar; theta++)          bool=1;
         trgradg[j][theta]=gradg[theta][j];          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
     for(i=1;i<=nlstate;i++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       varpl[i][(int)age] =0.;                bool=0;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          } 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          if (bool==1) { 
     for(i=1;i<=nlstate;i++)            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     fprintf(ficresvpl,"%.0f ",age );                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     for(i=1; i<=nlstate;i++)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));                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); 
     fprintf(ficresvpl,"\n");                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     free_vector(gp,1,nlstate);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     free_vector(gm,1,nlstate);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     free_matrix(gradg,1,npar,1,nlstate);                  prop[s[m][i]][iagemax+3] += weight[i]; 
     free_matrix(trgradg,1,nlstate,1,npar);                } 
   } /* End age */              }
             } /* end selection of waves */
   free_vector(xp,1,npar);          }
   free_matrix(doldm,1,nlstate,1,npar);        }
   free_matrix(dnewm,1,nlstate,1,nlstate);        for(i=iagemin; i <= iagemax+3; i++){  
           
 }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
 /************ Variance of one-step probabilities  ******************/          } 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)  
 {          for(jk=1; jk <=nlstate ; jk++){     
   int i, j, i1, k1, j1, z1;            if( i <=  iagemax){ 
   int k=0,l, cptcode;              if(posprop>=1.e-5){ 
   double **dnewm,**doldm;                probs[i][jk][j1]= prop[jk][i]/posprop;
   double *xp;              } 
   double *gp, *gm;            } 
   double **gradg, **trgradg;          }/* end jk */ 
   double age,agelim, cov[NCOVMAX];        }/* end i */ 
   int theta;      } /* end i1 */
   char fileresprob[FILENAMELENGTH];    } /* end k1 */
   char fileresprobcov[FILENAMELENGTH];    
   char fileresprobcor[FILENAMELENGTH];    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
   strcpy(fileresprob,"prob");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   strcat(fileresprob,fileres);  }  /* End of prevalence */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);  /************* Waves Concatenation ***************/
   }  
   strcpy(fileresprobcov,"probcov");  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)
   strcat(fileresprobcov,fileres);  {
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     printf("Problem with resultfile: %s\n", fileresprobcov);       Death is a valid wave (if date is known).
   }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   strcpy(fileresprobcor,"probcor");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   strcat(fileresprobcor,fileres);       and mw[mi+1][i]. dh depends on stepm.
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {       */
     printf("Problem with resultfile: %s\n", fileresprobcor);  
   }    int i, mi, m;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);       double sum=0., jmean=0.;*/
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    int first;
      int j, k=0,jk, ju, jl;
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    double sum=0.;
   fprintf(ficresprob,"# Age");    first=0;
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    jmin=1e+5;
   fprintf(ficresprobcov,"# Age");    jmax=-1;
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    jmean=0.;
   fprintf(ficresprobcov,"# Age");    for(i=1; i<=imx; i++){
   for(i=1; i<=nlstate;i++)      mi=0;
     for(j=1; j<=(nlstate+ndeath);j++){      m=firstpass;
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      while(s[m][i] <= nlstate){
       fprintf(ficresprobcov," p%1d-%1d ",i,j);        if(s[m][i]>=1)
       fprintf(ficresprobcor," p%1d-%1d ",i,j);          mw[++mi][i]=m;
     }          if(m >=lastpass)
   fprintf(ficresprob,"\n");          break;
   fprintf(ficresprobcov,"\n");        else
   fprintf(ficresprobcor,"\n");          m++;
   xp=vector(1,npar);      }/* end while */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      if (s[m][i] > nlstate){
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        mi++;     /* Death is another wave */
          /* if(mi==0)  never been interviewed correctly before death */
   cov[1]=1;           /* Only death is a correct wave */
   j=cptcoveff;        mw[mi][i]=m;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      }
   j1=0;  
   for(k1=1; k1<=1;k1++){      wav[i]=mi;
     for(i1=1; i1<=ncodemax[k1];i1++){      if(mi==0){
     j1++;        if(first==0){
           printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     if  (cptcovn>0) {          first=1;
       fprintf(ficresprob, "\n#********** Variable ");        }
       fprintf(ficresprobcov, "\n#********** Variable ");        if(first==1){
       fprintf(ficresprobcor, "\n#********** Variable ");          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        }
       fprintf(ficresprob, "**********\n#");      } /* end mi==0 */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    } /* End individuals */
       fprintf(ficresprobcov, "**********\n#");  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for(i=1; i<=imx; i++){
       fprintf(ficresprobcor, "**********\n#");      for(mi=1; mi<wav[i];mi++){
     }        if (stepm <=0)
              dh[mi][i]=1;
       for (age=bage; age<=fage; age ++){        else{
         cov[2]=age;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         for (k=1; k<=cptcovn;k++) {            if (agedc[i] < 2*AGESUP) {
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         }              if(j==0) j=1;  /* Survives at least one month after exam */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];              else if(j<0){
         for (k=1; k<=cptcovprod;k++)                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld 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]);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];                j=1; /* Careful Patch */
                        printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
         gradg=matrix(1,npar,1,9);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         trgradg=matrix(1,9,1,npar);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              }
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              k=k+1;
                  if (j >= jmax) jmax=j;
         for(theta=1; theta <=npar; theta++){              if (j <= jmin) jmin=j;
           for(i=1; i<=npar; i++)              sum=sum+j;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                        /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            }
                    }
           k=0;          else{
           for(i=1; i<= (nlstate+ndeath); i++){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             for(j=1; j<=(nlstate+ndeath);j++){            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
               k=k+1;            k=k+1;
               gp[k]=pmmij[i][j];            if (j >= jmax) jmax=j;
             }            else if (j <= jmin)jmin=j;
           }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                      /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
           for(i=1; i<=npar; i++)            if(j<0){
             xp[i] = x[i] - (i==theta ?delti[theta]:0);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld 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]);
                  fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld 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]);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            }
           k=0;            sum=sum+j;
           for(i=1; i<=(nlstate+ndeath); i++){          }
             for(j=1; j<=(nlstate+ndeath);j++){          jk= j/stepm;
               k=k+1;          jl= j -jk*stepm;
               gm[k]=pmmij[i][j];          ju= j -(jk+1)*stepm;
             }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           }            if(jl==0){
                    dh[mi][i]=jk;
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)              bh[mi][i]=0;
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              }else{ /* We want a negative bias in order to only have interpolation ie
         }                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)              bh[mi][i]=ju;
           for(theta=1; theta <=npar; theta++)            }
             trgradg[j][theta]=gradg[theta][j];          }else{
                    if(jl <= -ju){
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);              dh[mi][i]=jk;
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);              bh[mi][i]=jl;       /* bias is positive if real duration
                                           * is higher than the multiple of stepm and negative otherwise.
         pmij(pmmij,cov,ncovmodel,x,nlstate);                                   */
                    }
         k=0;            else{
         for(i=1; i<=(nlstate+ndeath); i++){              dh[mi][i]=jk+1;
           for(j=1; j<=(nlstate+ndeath);j++){              bh[mi][i]=ju;
             k=k+1;            }
             gm[k]=pmmij[i][j];            if(dh[mi][i]==0){
           }              dh[mi][i]=1; /* At least one step */
         }              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);*/
         /*printf("\n%d ",(int)age);            }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          } /* end if mle */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        }
      }*/      } /* end wave */
     }
         fprintf(ficresprob,"\n%d ",(int)age);    jmean=sum/k;
         fprintf(ficresprobcov,"\n%d ",(int)age);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         fprintf(ficresprobcor,"\n%d ",(int)age);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    }
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)  
           fprintf(ficresprob,"%12.3e (%12.3e) ",gm[i],sqrt(doldm[i][j]));  /*********** Tricode ****************************/
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  void tricode(int *Tvar, int **nbcode, int imx)
           fprintf(ficresprobcov,"%12.3e ",gm[i]);  {
           fprintf(ficresprobcor,"%12.3e ",gm[i]);    
         }    int Ndum[20],ij=1, k, j, i, maxncov=19;
         i=0;    int cptcode=0;
         for (k=1; k<=(nlstate);k++){    cptcoveff=0; 
           for (l=1; l<=(nlstate+ndeath);l++){   
             i=i++;    for (k=0; k<maxncov; k++) Ndum[k]=0;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    for (k=1; k<=7; k++) ncodemax[k]=0;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);  
             for (j=1; j<=i;j++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
               fprintf(ficresprobcov," %12.3e",doldm[i][j]);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
               fprintf(ficresprobcor," %12.3e",doldm[i][j]/sqrt(doldm[i][i])/sqrt(doldm[j][j]));                                 modality*/ 
             }        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);*/
       }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     }                                         Tvar[j]. If V=sex and male is 0 and 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));                                         female is 1, then  cptcode=1.*/
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (i=0; i<=cptcode; i++) {
   }        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
   free_vector(xp,1,npar);      }
   fclose(ficresprob);  
   fclose(ficresprobcov);      ij=1; 
   fclose(ficresprobcor);      for (i=1; i<=ncodemax[j]; i++) {
 }        for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
             nbcode[Tvar[j]][ij]=k; 
 /******************* Printing html file ***********/            /* 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; */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \            
                   int lastpass, int stepm, int weightopt, char model[],\            ij++;
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \          }
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\          if (ij > ncodemax[j]) break; 
                   char version[], int popforecast, int estepm ,\        }  
                   double jprev1, double mprev1,double anprev1, \      } 
                   double jprev2, double mprev2,double anprev2){    }  
   int jj1, k1, i1, cpt;  
   FILE *fichtm;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   /*char optionfilehtm[FILENAMELENGTH];*/  
    for (i=1; i<=ncovmodel-2; i++) { 
   strcpy(optionfilehtm,optionfile);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   strcat(optionfilehtm,".htm");     ij=Tvar[i];
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {     Ndum[ij]++;
     printf("Problem with %s \n",optionfilehtm), exit(0);   }
   }  
    ij=1;
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n   for (i=1; i<= maxncov; i++) {
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n     if((Ndum[i]!=0) && (i<=ncovcol)){
 \n       Tvaraff[ij]=i; /*For printing */
 Total number of observations=%d <br>\n       ij++;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n     }
 <hr  size=\"2\" color=\"#EC5E5E\">   }
  <ul><li>Parameter files<br>\n   
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n   cptcoveff=ij-1; /*Number of simple covariates*/
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);  }
   
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n  /*********** Health Expectancies ****************/
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n  
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n  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 )
  - 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>", \    /* Health expectancies */
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n    double ***p3mat,***varhe;
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    double **dnewm,**doldm;
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    double *xp;
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    double **gp, **gm;
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    double ***gradg, ***trgradg;
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    int theta;
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n  
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
  if(popforecast==1) fprintf(fichtm,"\n    dnewm=matrix(1,nlstate*nlstate,1,npar);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    
         <br>",fileres,fileres,fileres,fileres);    fprintf(ficreseij,"# Health expectancies\n");
  else    fprintf(ficreseij,"# Age");
    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(fichtm," <li>Graphs</li><p>");      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
  m=cptcoveff;    fprintf(ficreseij,"\n");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
     if(estepm < stepm){
  jj1=0;      printf ("Problem %d lower than %d\n",estepm, stepm);
  for(k1=1; k1<=m;k1++){    }
    for(i1=1; i1<=ncodemax[k1];i1++){    else  hstepm=estepm;   
      jj1++;    /* We compute the life expectancy from trapezoids spaced every estepm months
      if (cptcovn > 0) {     * This is mainly to measure the difference between two models: for example
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");     * if stepm=24 months pijx are given only every 2 years and by summing them
        for (cpt=1; cpt<=cptcoveff;cpt++)     * we are calculating an estimate of the Life Expectancy assuming a linear 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);     * progression in between and thus overestimating or underestimating according
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");     * to the curvature of the survival function. If, for the same date, we 
      }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      /* Pij */     * to compare the new estimate of Life expectancy with the same linear 
      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>     * hypothesis. A more precise result, taking into account a more precise
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);         * curvature will be obtained if estepm is as small as stepm. */
      /* Quasi-incidences */  
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    /* For example we decided to compute the life expectancy with the smallest unit */
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        /* Stable prevalence in each health state */       nhstepm is the number of hstepm from age to agelim 
        for(cpt=1; cpt<nlstate;cpt++){       nstepm is the number of stepm from age to agelin. 
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>       Look at hpijx to understand the reason of that which relies in memory size
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);       and note for a fixed period like estepm months */
        }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     for(cpt=1; cpt<=nlstate;cpt++) {       survival function given by stepm (the optimization length). Unfortunately it
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident       means that if the survival funtion is printed only each two years of age and if
 interval) in state (%d): v%s%d%d.png <br>       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);         results. So we changed our mind and took the option of the best precision.
      }    */
      for(cpt=1; cpt<=nlstate;cpt++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>  
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    agelim=AGESUP;
      }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      /* nhstepm age range expressed in number of stepm */
 health expectancies in states (1) and (2): e%s%d.png<br>      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 fprintf(fichtm,"\n</body>");      /* if (stepm >= YEARM) hstepm=1;*/
    }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 fclose(fichtm);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       gm=matrix(0,nhstepm,1,nlstate*nlstate);
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   int ng;   
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".gp");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);      /* Computing Variances of health expectancies */
   }  
        for(theta=1; theta <=npar; theta++){
 #ifdef windows        for(i=1; i<=npar; i++){ 
     fprintf(ficgp,"cd \"%s\" \n",pathc);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #endif        }
 m=pow(2,cptcoveff);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      
  /* 1eme*/        cptj=0;
   for (cpt=1; cpt<= nlstate ; cpt ++) {        for(j=1; j<= nlstate; j++){
    for (k1=1; k1<= m ; k1 ++) {          for(i=1; i<=nlstate; i++){
             cptj=cptj+1;
 #ifdef windows            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);            }
 #endif          }
 #ifdef unix        }
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);       
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);       
 #endif        for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
 for (i=1; i<= nlstate ; i ++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        
   else fprintf(ficgp," \%%*lf (\%%*lf)");        cptj=0;
 }        for(j=1; j<= nlstate; j++){
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          for(i=1;i<=nlstate;i++){
     for (i=1; i<= nlstate ; i ++) {            cptj=cptj+1;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            }
      for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<= nlstate*nlstate; j++)
 }            for(h=0; h<=nhstepm-1; h++){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 #ifdef unix          }
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");       } 
 #endif     
    }  /* End theta */
   }  
   /*2 eme*/       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   
   for (k1=1; k1<= m ; k1 ++) {       for(h=0; h<=nhstepm-1; h++)
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);        for(j=1; j<=nlstate*nlstate;j++)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);          for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
     for (i=1; i<= nlstate+1 ; i ++) {       
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);       for(i=1;i<=nlstate*nlstate;i++)
       for (j=1; j<= nlstate+1 ; j ++) {        for(j=1;j<=nlstate*nlstate;j++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          varhe[i][j][(int)age] =0.;
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }         printf("%d|",(int)age);fflush(stdout);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);       for(h=0;h<=nhstepm-1;h++){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        for(k=0;k<=nhstepm-1;k++){
       for (j=1; j<= nlstate+1 ; j ++) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         else fprintf(ficgp," \%%*lf (\%%*lf)");          for(i=1;i<=nlstate*nlstate;i++)
 }              for(j=1;j<=nlstate*nlstate;j++)
       fprintf(ficgp,"\" t\"\" w l 0,");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {      }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      /* Computing expectancies */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i=1; i<=nlstate;i++)
 }          for(j=1; j<=nlstate;j++)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       else fprintf(ficgp,"\" t\"\" w l 0,");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     }            
   }  /* 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]);*/
    
   /*3eme*/          }
   
   for (k1=1; k1<= m ; k1 ++) {      fprintf(ficreseij,"%3.0f",age );
     for (cpt=1; cpt<= nlstate ; cpt ++) {      cptj=0;
       k=2+nlstate*(2*cpt-2);      for(i=1; i<=nlstate;i++)
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for(j=1; j<=nlstate;j++){
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          cptj++;
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      fprintf(ficreseij,"\n");
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);     
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
 */      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       for (i=1; i< nlstate ; i ++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         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);    }
     printf("\n");
       }    fprintf(ficlog,"\n");
     }  
   }    free_vector(xp,1,npar);
      free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   /* CV preval stat */    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     for (k1=1; k1<= m ; k1 ++) {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     for (cpt=1; cpt<nlstate ; cpt ++) {  }
       k=3;  
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  /************ Variance ******************/
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
   {
       for (i=1; i< nlstate ; i ++)    /* Variance of health expectancies */
         fprintf(ficgp,"+$%d",k+i+1);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    /* double **newm;*/
          double **dnewm,**doldm;
       l=3+(nlstate+ndeath)*cpt;    double **dnewmp,**doldmp;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    int i, j, nhstepm, hstepm, h, nstepm ;
       for (i=1; i< nlstate ; i ++) {    int k, cptcode;
         l=3+(nlstate+ndeath)*cpt;    double *xp;
         fprintf(ficgp,"+$%d",l+i+1);    double **gp, **gm;  /* for var eij */
       }    double ***gradg, ***trgradg; /*for var eij */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      double **gradgp, **trgradgp; /* for var p point j */
     }    double *gpp, *gmp; /* for var p point j */
   }      double **varppt; /* for var p point j nlstate to nlstate+ndeath */
      double ***p3mat;
   /* proba elementaires */    double age,agelim, hf;
    for(i=1,jk=1; i <=nlstate; i++){    double ***mobaverage;
     for(k=1; k <=(nlstate+ndeath); k++){    int theta;
       if (k != i) {    char digit[4];
         for(j=1; j <=ncovmodel; j++){    char digitp[25];
          
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    char fileresprobmorprev[FILENAMELENGTH];
           jk++;  
           fprintf(ficgp,"\n");    if(popbased==1){
         }      if(mobilav!=0)
       }        strcpy(digitp,"-populbased-mobilav-");
     }      else strcpy(digitp,"-populbased-nomobil-");
    }    }
     else 
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/      strcpy(digitp,"-stablbased-");
      for(jk=1; jk <=m; jk++) {  
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    if (mobilav!=0) {
        if (ng==2)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
        else        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          fprintf(ficgp,"\nset title \"Probability\"\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        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;    strcpy(fileresprobmorprev,"prmorprev"); 
          for(k=1; k<=(nlstate+ndeath); k++) {    sprintf(digit,"%-d",ij);
            if (k != k2){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
              if(ng==2)    strcat(fileresprobmorprev,digit); /* Tvar to be done */
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
              else    strcat(fileresprobmorprev,fileres);
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
              ij=1;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
              for(j=3; j <=ncovmodel; j++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
                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]]]);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                  ij++;    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);
                else    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
              }      fprintf(ficresprobmorprev," p.%-d SE",j);
              fprintf(ficgp,")/(1");      for(i=1; i<=nlstate;i++)
                      fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
              for(k1=1; k1 <=nlstate; k1++){      }  
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    fprintf(ficresprobmorprev,"\n");
                ij=1;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
                for(j=3; j <=ncovmodel; j++){      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      exit(0);
                    ij++;    }
                  }    else{
                  else      fprintf(ficgp,"\n# Routine varevsij");
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    }
                }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
                fprintf(ficgp,")");      printf("Problem with html file: %s\n", optionfilehtm);
              }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      exit(0);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    }
              i=i+ncovmodel;    else{
            }      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
          }      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
        }    }
      }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    }  
    fclose(ficgp);    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");
 }  /* end gnuplot */    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
 /*************** Moving average **************/        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    fprintf(ficresvij,"\n");
   
   int i, cpt, cptcod;    xp=vector(1,npar);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    dnewm=matrix(1,nlstate,1,npar);
       for (i=1; i<=nlstate;i++)    doldm=matrix(1,nlstate,1,nlstate);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           mobaverage[(int)agedeb][i][cptcod]=0.;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       for (i=1; i<=nlstate;i++){    gpp=vector(nlstate+1,nlstate+ndeath);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    gmp=vector(nlstate+1,nlstate+ndeath);
           for (cpt=0;cpt<=4;cpt++){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    
           }    if(estepm < stepm){
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      printf ("Problem %d lower than %d\n",estepm, stepm);
         }    }
       }    else  hstepm=estepm;   
     }    /* For example we decided to compute the life expectancy with the smallest unit */
        /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 }       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
 /************** Forecasting ******************/       and note for a fixed period like k years */
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         survival function given by stepm (the optimization length). Unfortunately it
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       means that if the survival funtion is printed every two years of age and if
   int *popage;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;       results. So we changed our mind and took the option of the best precision.
   double *popeffectif,*popcount;    */
   double ***p3mat;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   char fileresf[FILENAMELENGTH];    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  agelim=AGESUP;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        gp=matrix(0,nhstepm,1,nlstate);
        gm=matrix(0,nhstepm,1,nlstate);
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {      for(theta=1; theta <=npar; theta++){
     printf("Problem with forecast resultfile: %s\n", fileresf);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   printf("Computing forecasting: result on file '%s' \n", fileresf);        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
   if (mobilav==1) {        if (popbased==1) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          if(mobilav ==0){
     movingaverage(agedeb, fage, ageminpar, mobaverage);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   stepsize=(int) (stepm+YEARM-1)/YEARM;            for(i=1; i<=nlstate;i++)
   if (stepm<=12) stepsize=1;              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
   agelim=AGESUP;        }
      
   hstepm=1;        for(j=1; j<= nlstate; j++){
   hstepm=hstepm/stepm;          for(h=0; h<=nhstepm; h++){
   yp1=modf(dateintmean,&yp);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   anprojmean=yp;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   yp2=modf((yp1*12),&yp);          }
   mprojmean=yp;        }
   yp1=modf((yp2*30.5),&yp);        /* This for computing probability of death (h=1 means
   jprojmean=yp;           computed over hstepm matrices product = hstepm*stepm months) 
   if(jprojmean==0) jprojmean=1;           as a weighted average of prlim.
   if(mprojmean==0) jprojmean=1;        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   for(cptcov=1;cptcov<=i2;cptcov++){        }    
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        /* end probability of death */
       k=k+1;  
       fprintf(ficresf,"\n#******");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       for(j=1;j<=cptcoveff;j++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fprintf(ficresf,"******\n");   
       fprintf(ficresf,"# StartingAge FinalAge");        if (popbased==1) {
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          if(mobilav ==0){
                  for(i=1; i<=nlstate;i++)
                    prlim[i][i]=probs[(int)age][i][ij];
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          }else{ /* mobilav */ 
         fprintf(ficresf,"\n");            for(i=1; i<=nlstate;i++)
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;        for(j=1; j<= nlstate; j++){
                    for(h=0; h<=nhstepm; h++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
           oldm=oldms;savm=savms;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
                }
           for (h=0; h<=nhstepm; h++){        /* This for computing probability of death (h=1 means
             if (h==(int) (calagedate+YEARM*cpt)) {           computed over hstepm matrices product = hstepm*stepm months) 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);           as a weighted average of prlim.
             }        */
             for(j=1; j<=nlstate+ndeath;j++) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
               kk1=0.;kk2=0;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
               for(i=1; i<=nlstate;i++) {                         gmp[j] += prlim[i][i]*p3mat[i][j][1];
                 if (mobilav==1)        }    
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        /* end probability of death */
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        for(j=1; j<= nlstate; j++) /* vareij */
                 }          for(h=0; h<=nhstepm; h++){
                            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
               }          }
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                                  gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
               }        }
             }  
           }      } /* End theta */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       }  
     }      for(h=0; h<=nhstepm; h++) /* veij */
   }        for(j=1; j<=nlstate;j++)
                  for(theta=1; theta <=npar; theta++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            trgradg[h][j][theta]=gradg[h][theta][j];
   
   fclose(ficresf);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
 }        for(theta=1; theta <=npar; theta++)
 /************** Forecasting ******************/          trgradgp[j][theta]=gradgp[theta][j];
 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;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   int *popage;      for(i=1;i<=nlstate;i++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        for(j=1;j<=nlstate;j++)
   double *popeffectif,*popcount;          vareij[i][j][(int)age] =0.;
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   agelim=AGESUP;          for(i=1;i<=nlstate;i++)
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            for(j=1;j<=nlstate;j++)
                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }
        }
      
   strcpy(filerespop,"pop");      /* pptj */
   strcat(filerespop,fileres);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     printf("Problem with forecast resultfile: %s\n", filerespop);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   printf("Computing forecasting: result on file '%s' \n", filerespop);          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   if (mobilav==1) {      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
     movingaverage(agedeb, fage, ageminpar, mobaverage);      if (popbased==1) {
   }        if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;            prlim[i][i]=probs[(int)age][i][ij];
   if (stepm<=12) stepsize=1;        }else{ /* mobilav */ 
            for(i=1; i<=nlstate;i++)
   agelim=AGESUP;            prlim[i][i]=mobaverage[(int)age][i][ij];
          }
   hstepm=1;      }
   hstepm=hstepm/stepm;               
        /* This for computing probability of death (h=1 means
   if (popforecast==1) {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     if((ficpop=fopen(popfile,"r"))==NULL) {         as a weighted average of prlim.
       printf("Problem with population file : %s\n",popfile);exit(0);      */
     }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     popage=ivector(0,AGESUP);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     popeffectif=vector(0,AGESUP);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     popcount=vector(0,AGESUP);      }    
          /* end probability of death */
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
          for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     imx=i;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        for(i=1; i<=nlstate;i++){
   }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
   for(cptcov=1;cptcov<=i2;cptcov++){      } 
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fprintf(ficresprobmorprev,"\n");
       k=k+1;  
       fprintf(ficrespop,"\n#******");      fprintf(ficresvij,"%.0f ",age );
       for(j=1;j<=cptcoveff;j++) {      for(i=1; i<=nlstate;i++)
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<=nlstate;j++){
       }          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       fprintf(ficrespop,"******\n");        }
       fprintf(ficrespop,"# Age");      fprintf(ficresvij,"\n");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      free_matrix(gp,0,nhstepm,1,nlstate);
       if (popforecast==1)  fprintf(ficrespop," [Population]");      free_matrix(gm,0,nhstepm,1,nlstate);
            free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       for (cpt=0; cpt<=0;cpt++) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            } /* End age */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    free_vector(gpp,nlstate+1,nlstate+ndeath);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_vector(gmp,nlstate+1,nlstate+ndeath);
           nhstepm = nhstepm/hstepm;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
              free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           oldm=oldms;savm=savms;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
          /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           for (h=0; h<=nhstepm; h++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
             if (h==(int) (calagedate+YEARM*cpt)) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
             }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
             for(j=1; j<=nlstate+ndeath;j++) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
               kk1=0.;kk2=0;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
               for(i=1; i<=nlstate;i++) {                  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);
                 if (mobilav==1)    /*  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);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  */
                 else {    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }    free_vector(xp,1,npar);
               }    free_matrix(doldm,1,nlstate,1,nlstate);
               if (h==(int)(calagedate+12*cpt)){    free_matrix(dnewm,1,nlstate,1,npar);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   /*fprintf(ficrespop," %.3f", kk1);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             }    fclose(ficresprobmorprev);
             for(i=1; i<=nlstate;i++){    fclose(ficgp);
               kk1=0.;    fclose(fichtm);
                 for(j=1; j<=nlstate;j++){  }  /* end varevsij */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  
                 }  /************ Variance of prevlim ******************/
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
             }  {
     /* Variance of prevalence limit */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    double **newm;
           }    double **dnewm,**doldm;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i, j, nhstepm, hstepm;
         }    int k, cptcode;
       }    double *xp;
      double *gp, *gm;
   /******/    double **gradg, **trgradg;
     double age,agelim;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    int theta;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);       
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficresvpl,"# Age");
           nhstepm = nhstepm/hstepm;    for(i=1; i<=nlstate;i++)
                  fprintf(ficresvpl," %1d-%1d",i,i);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresvpl,"\n");
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      xp=vector(1,npar);
           for (h=0; h<=nhstepm; h++){    dnewm=matrix(1,nlstate,1,npar);
             if (h==(int) (calagedate+YEARM*cpt)) {    doldm=matrix(1,nlstate,1,nlstate);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    
             }    hstepm=1*YEARM; /* Every year of age */
             for(j=1; j<=nlstate+ndeath;j++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
               kk1=0.;kk2=0;    agelim = AGESUP;
               for(i=1; i<=nlstate;i++) {                  for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
               }      if (stepm >= YEARM) hstepm=1;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
             }      gradg=matrix(1,npar,1,nlstate);
           }      gp=vector(1,nlstate);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gm=vector(1,nlstate);
         }  
       }      for(theta=1; theta <=npar; theta++){
    }        for(i=1; i<=npar; i++){ /* Computes gradient */
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
   if (popforecast==1) {          gp[i] = prlim[i][i];
     free_ivector(popage,0,AGESUP);      
     free_vector(popeffectif,0,AGESUP);        for(i=1; i<=npar; i++) /* Computes gradient */
     free_vector(popcount,0,AGESUP);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(i=1;i<=nlstate;i++)
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          gm[i] = prlim[i][i];
   fclose(ficrespop);  
 }        for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 /***********************************************/      } /* End theta */
 /**************** Main Program *****************/  
 /***********************************************/      trgradg =matrix(1,nlstate,1,npar);
   
 int main(int argc, char *argv[])      for(j=1; j<=nlstate;j++)
 {        for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  
   double agedeb, agefin,hf;      for(i=1;i<=nlstate;i++)
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   double fret;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   double **xi,tmp,delta;      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   double dum; /* Dummy variable */  
   double ***p3mat;      fprintf(ficresvpl,"%.0f ",age );
   int *indx;      for(i=1; i<=nlstate;i++)
   char line[MAXLINE], linepar[MAXLINE];        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   char title[MAXLINE];      fprintf(ficresvpl,"\n");
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      free_vector(gp,1,nlstate);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      free_vector(gm,1,nlstate);
        free_matrix(gradg,1,npar,1,nlstate);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];    free_vector(xp,1,npar);
   char popfile[FILENAMELENGTH];    free_matrix(doldm,1,nlstate,1,npar);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    free_matrix(dnewm,1,nlstate,1,nlstate);
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */  }
   int c,  h , cpt,l;  
   int ju,jl, mi;  /************ Variance of one-step probabilities  ******************/
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  {
   int mobilav=0,popforecast=0;    int i, j=0,  i1, k1, l1, t, tj;
   int hstepm, nhstepm;    int k2, l2, j1,  z1;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    int k=0,l, cptcode;
     int first=1, first1;
   double bage, fage, age, agelim, agebase;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double ftolpl=FTOL;    double **dnewm,**doldm;
   double **prlim;    double *xp;
   double *severity;    double *gp, *gm;
   double ***param; /* Matrix of parameters */    double **gradg, **trgradg;
   double  *p;    double **mu;
   double **matcov; /* Matrix of covariance */    double age,agelim, cov[NCOVMAX];
   double ***delti3; /* Scale */    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   double *delti; /* Scale */    int theta;
   double ***eij, ***vareij;    char fileresprob[FILENAMELENGTH];
   double **varpl; /* Variances of prevalence limits by age */    char fileresprobcov[FILENAMELENGTH];
   double *epj, vepp;    char fileresprobcor[FILENAMELENGTH];
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    double ***varpij;
    
     strcpy(fileresprob,"prob"); 
   char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";    strcat(fileresprob,fileres);
   char *alph[]={"a","a","b","c","d","e"}, str[4];    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   char z[1]="c", occ;    }
 #include <sys/time.h>    strcpy(fileresprobcov,"probcov"); 
 #include <time.h>    strcat(fileresprobcov,fileres);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcov);
   /* long total_usecs;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   struct timeval start_time, end_time;    }
      strcpy(fileresprobcor,"probcor"); 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    strcat(fileresprobcor,fileres);
   getcwd(pathcd, size);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
   printf("\n%s",version);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   if(argc <=1){    }
     printf("\nEnter the parameter file name: ");    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     scanf("%s",pathtot);    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);
   else{    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     strcpy(pathtot,argv[1]);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    
   /*cygwin_split_path(pathtot,path,optionfile);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    fprintf(ficresprob,"# Age");
   /* cutv(path,optionfile,pathtot,'\\');*/    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    fprintf(ficresprobcov,"# Age");
   chdir(path);  
   replace(pathc,path);  
     for(i=1; i<=nlstate;i++)
 /*-------- arguments in the command line --------*/      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   strcpy(fileres,"r");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   strcat(fileres, optionfilefiname);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   strcat(fileres,".txt");    /* Other files have txt extension */      }  
    /* fprintf(ficresprob,"\n");
   /*---------arguments file --------*/    fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {   */
     printf("Problem with optionfile %s\n",optionfile);   xp=vector(1,npar);
     goto end;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   strcpy(filereso,"o");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   strcat(filereso,fileres);    first=1;
   if((ficparo=fopen(filereso,"w"))==NULL) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    else{
     ungetc(c,ficpar);      fprintf(ficgp,"\n# Routine varprob");
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     fputs(line,ficparo);      printf("Problem with html file: %s\n", optionfilehtm);
   }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   ungetc(c,ficpar);      exit(0);
     }
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    else{
   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(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);      fprintf(fichtm,"\n");
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
     fgets(line, MAXLINE, ficpar);      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");
     puts(line);      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");
     fputs(line,ficparo);  
   }    }
   ungetc(c,ficpar);  
      cov[1]=1;
        tj=cptcoveff;
   covar=matrix(0,NCOVMAX,1,n);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   cptcovn=0;    j1=0;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
   ncovmodel=2+cptcovn;        j1++;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        if  (cptcovn>0) {
            fprintf(ficresprob, "\n#********** Variable "); 
   /* Read guess parameters */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* Reads comments: lines beginning with '#' */          fprintf(ficresprob, "**********\n#\n");
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobcov, "\n#********** Variable "); 
     ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcov, "**********\n#\n");
     puts(line);          
     fputs(line,ficparo);          fprintf(ficgp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   ungetc(c,ficpar);          fprintf(ficgp, "**********\n#\n");
            
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          
     for(i=1; i <=nlstate; i++)          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     for(j=1; j <=nlstate+ndeath-1; j++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       fprintf(ficparo,"%1d%1d",i1,j1);          
       printf("%1d%1d",i,j);          fprintf(ficresprobcor, "\n#********** Variable ");    
       for(k=1; k<=ncovmodel;k++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fscanf(ficpar," %lf",&param[i][j][k]);          fprintf(ficresprobcor, "**********\n#");    
         printf(" %lf",param[i][j][k]);        }
         fprintf(ficparo," %lf",param[i][j][k]);        
       }        for (age=bage; age<=fage; age ++){ 
       fscanf(ficpar,"\n");          cov[2]=age;
       printf("\n");          for (k=1; k<=cptcovn;k++) {
       fprintf(ficparo,"\n");            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     }          }
            for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          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]]];
   p=param[1][1];          
            gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   /* Reads comments: lines beginning with '#' */          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){          gp=vector(1,(nlstate)*(nlstate+ndeath));
     ungetc(c,ficpar);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     fgets(line, MAXLINE, ficpar);      
     puts(line);          for(theta=1; theta <=npar; theta++){
     fputs(line,ficparo);            for(i=1; i<=npar; i++)
   }              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   ungetc(c,ficpar);            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            k=0;
   for(i=1; i <=nlstate; i++){            for(i=1; i<= (nlstate); i++){
     for(j=1; j <=nlstate+ndeath-1; j++){              for(j=1; j<=(nlstate+ndeath);j++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);                k=k+1;
       printf("%1d%1d",i,j);                gp[k]=pmmij[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]);            for(i=1; i<=npar; i++)
         fprintf(ficparo," %le",delti3[i][j][k]);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       }      
       fscanf(ficpar,"\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       printf("\n");            k=0;
       fprintf(ficparo,"\n");            for(i=1; i<=(nlstate); i++){
     }              for(j=1; j<=(nlstate+ndeath);j++){
   }                k=k+1;
   delti=delti3[1][1];                gm[k]=pmmij[i][j];
                }
   /* Reads comments: lines beginning with '#' */            }
   while((c=getc(ficpar))=='#' && c!= EOF){       
     ungetc(c,ficpar);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     fgets(line, MAXLINE, ficpar);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     puts(line);          }
     fputs(line,ficparo);  
   }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   ungetc(c,ficpar);            for(theta=1; theta <=npar; theta++)
                trgradg[j][theta]=gradg[theta][j];
   matcov=matrix(1,npar,1,npar);          
   for(i=1; i <=npar; i++){          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     fscanf(ficpar,"%s",&str);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     printf("%s",str);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     fprintf(ficparo,"%s",str);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     for(j=1; j <=i; j++){          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       fscanf(ficpar," %le",&matcov[i][j]);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       printf(" %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);          pmij(pmmij,cov,ncovmodel,x,nlstate);
     }          
     fscanf(ficpar,"\n");          k=0;
     printf("\n");          for(i=1; i<=(nlstate); i++){
     fprintf(ficparo,"\n");            for(j=1; j<=(nlstate+ndeath);j++){
   }              k=k+1;
   for(i=1; i <=npar; i++)              mu[k][(int) age]=pmmij[i][j];
     for(j=i+1;j<=npar;j++)            }
       matcov[i][j]=matcov[j][i];          }
              for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   printf("\n");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
     /*-------- Rewriting paramater file ----------*/          /*printf("\n%d ",(int)age);
      strcpy(rfileres,"r");    /* "Rparameterfile */            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      strcat(rfileres,".");    /* */            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      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(ficresprob,"\n%d ",(int)age);
     }          fprintf(ficresprobcov,"\n%d ",(int)age);
     fprintf(ficres,"#%s\n",version);          fprintf(ficresprobcor,"\n%d ",(int)age);
      
     /*-------- data file ----------*/          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     if((fic=fopen(datafile,"r"))==NULL)    {            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       printf("Problem with datafile: %s\n", datafile);goto end;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     n= lastobs;          }
     severity = vector(1,maxwav);          i=0;
     outcome=imatrix(1,maxwav+1,1,n);          for (k=1; k<=(nlstate);k++){
     num=ivector(1,n);            for (l=1; l<=(nlstate+ndeath);l++){ 
     moisnais=vector(1,n);              i=i++;
     annais=vector(1,n);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     moisdc=vector(1,n);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     andc=vector(1,n);              for (j=1; j<=i;j++){
     agedc=vector(1,n);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     cod=ivector(1,n);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     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);          }/* end of loop for state */
     anint=matrix(1,maxwav,1,n);        } /* end of loop for age */
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);            /* Confidence intervalle of pij  */
     tab=ivector(1,NCOVMAX);        /*
     ncodemax=ivector(1,8);          fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     i=1;          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     while (fgets(line, MAXLINE, fic) != NULL)    {          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);
       if ((i >= firstobs) && (i <=lastobs)) {          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
                  fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
         for (j=maxwav;j>=1;j--){          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           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);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        first1=1;
         }        for (k2=1; k2<=(nlstate);k2++){
                  for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            if(l2==k2) continue;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                if(i<=j) continue;
         for (j=ncovcol;j>=1;j--){                for (age=bage; age<=fage; age ++){ 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                  if ((int)age %5==0){
         }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         num[i]=atol(stra);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                            cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                    mu1=mu[i][(int) age]/stepm*YEARM ;
           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;}*/                    mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
         i=i+1;                    /* Computing eigen value of matrix of covariance */
       }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     /* printf("ii=%d", ij);                    /* Eigen vectors */
        scanf("%d",i);*/                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   imx=i-1; /* Number of individuals */                    /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
   /* for (i=1; i<=imx; i++){                    v12=-v21;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                    v22=v11;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                    tnalp=v21/v11;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                    if(first1==1){
     }*/                      first1=0;
    /*  for (i=1; i<=imx; i++){                      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);
      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]));}*/                    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) */
   /* Calculation of the number of parameter from char model*/                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   Tvar=ivector(1,15);                    if(first==1){
   Tprod=ivector(1,15);                      first=0;
   Tvaraff=ivector(1,15);                      fprintf(ficgp,"\nset parametric;unset label");
   Tvard=imatrix(1,15,1,2);                      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);
   Tage=ivector(1,15);                            fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                          fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
   if (strlen(model) >1){                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
     j=0, j1=0, k1=1, k2=1;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     j=nbocc(model,'+');                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
     j1=nbocc(model,'*');                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     cptcovn=j+1;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     cptcovprod=j1;                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                  mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     strcpy(modelsav,model);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                    }else{
       printf("Error. Non available option model=%s ",model);                      first=0;
       goto end;                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
     }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                          fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     for(i=(j+1); i>=1;i--){                      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",\
       cutv(stra,strb,modelsav,'+');                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                    }/* if first */
       /*scanf("%d",i);*/                  } /* age mod 5 */
       if (strchr(strb,'*')) {                } /* end loop age */
         cutv(strd,strc,strb,'*');                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
         if (strcmp(strc,"age")==0) {                first=1;
           cptcovprod--;              } /*l12 */
           cutv(strb,stre,strd,'V');            } /* k12 */
           Tvar[i]=atoi(stre);          } /*l1 */
           cptcovage++;        }/* k1 */
             Tage[cptcovage]=i;      } /* loop covariates */
             /*printf("stre=%s ", stre);*/    }
         }    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         else if (strcmp(strd,"age")==0) {    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
           cptcovprod--;    free_vector(xp,1,npar);
           cutv(strb,stre,strc,'V');    fclose(ficresprob);
           Tvar[i]=atoi(stre);    fclose(ficresprobcov);
           cptcovage++;    fclose(ficresprobcor);
           Tage[cptcovage]=i;    fclose(ficgp);
         }    fclose(fichtm);
         else {  }
           cutv(strb,stre,strc,'V');  
           Tvar[i]=ncovcol+k1;  
           cutv(strb,strc,strd,'V');  /******************* Printing html file ***********/
           Tprod[k1]=i;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
           Tvard[k1][1]=atoi(strc);                    int lastpass, int stepm, int weightopt, char model[],\
           Tvard[k1][2]=atoi(stre);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
           Tvar[cptcovn+k2]=Tvard[k1][1];                    int popforecast, int estepm ,\
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                    double jprev1, double mprev1,double anprev1, \
           for (k=1; k<=lastobs;k++)                    double jprev2, double mprev2,double anprev2){
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    int jj1, k1, i1, cpt;
           k1++;    /*char optionfilehtm[FILENAMELENGTH];*/
           k2=k2+2;    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
         }      printf("Problem with %s \n",optionfilehtm), exit(0);
       }      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
       else {    }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
       cutv(strd,strc,strb,'V');   - 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 \
       Tvar[i]=atoi(strc);   - 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 \
       strcpy(modelsav,stra);     - Life expectancies by age and initial health status (estepm=%2d months): \
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
         scanf("%d",i);*/    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
     }  
 }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);   m=cptcoveff;
   printf("cptcovprod=%d ", cptcovprod);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   scanf("%d ",i);*/  
     fclose(fic);   jj1=0;
    for(k1=1; k1<=m;k1++){
     /*  if(mle==1){*/     for(i1=1; i1<=ncodemax[k1];i1++){
     if (weightopt != 1) { /* Maximisation without weights*/       jj1++;
       for(i=1;i<=n;i++) weight[i]=1.0;       if (cptcovn > 0) {
     }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     /*-calculation of age at interview from date of interview and age at death -*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
     agev=matrix(1,maxwav,1,imx);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     for (i=1; i<=imx; i++) {       }
       for(m=2; (m<= maxwav); m++) {       /* Pij */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){       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> \
          anint[m][i]=9999;  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
          s[m][i]=-1;       /* Quasi-incidences */
        }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> \
       }  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
     }         /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
     for (i=1; i<=imx; i++)  {           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       for(m=1; (m<= maxwav); m++){         }
         if(s[m][i] >0){       for(cpt=1; cpt<=nlstate;cpt++) {
           if (s[m][i] >= nlstate+1) {          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
             if(agedc[i]>0)  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
               if(moisdc[i]!=99 && andc[i]!=9999)       }
                 agev[m][i]=agedc[i];       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  health expectancies in states (1) and (2): e%s%d.png<br>\
            else {  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
               if (andc[i]!=9999){     } /* end i1 */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);   }/* End k1 */
               agev[m][i]=-1;   fprintf(fichtm,"</ul>");
               }  
             }  
           }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
           else if(s[m][i] !=9){ /* Should no more exist */   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
             if(mint[m][i]==99 || anint[m][i]==9999)   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
               agev[m][i]=1;   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
             else if(agev[m][i] <agemin){   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
               agemin=agev[m][i];   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/   - 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);
             }  
             else if(agev[m][i] >agemax){  /*  if(popforecast==1) fprintf(fichtm,"\n */
               agemax=agev[m][i];  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
             }  /*      <br>",fileres,fileres,fileres,fileres); */
             /*agev[m][i]=anint[m][i]-annais[i];*/  /*  else  */
             /*   agev[m][i] = age[i]+2*m;*/  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
           }  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           else { /* =9 */  
             agev[m][i]=1;   m=cptcoveff;
             s[m][i]=-1;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           }  
         }   jj1=0;
         else /*= 0 Unknown */   for(k1=1; k1<=m;k1++){
           agev[m][i]=1;     for(i1=1; i1<=ncodemax[k1];i1++){
       }       jj1++;
           if (cptcovn > 0) {
     }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     for (i=1; i<=imx; i++)  {         for (cpt=1; cpt<=cptcoveff;cpt++) 
       for(m=1; (m<= maxwav); m++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         if (s[m][i] > (nlstate+ndeath)) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           printf("Error: Wrong value in nlstate or ndeath\n");         }
           goto end;       for(cpt=1; cpt<=nlstate;cpt++) {
         }         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
       }  interval) in state (%d): v%s%d%d.png <br>\
     }  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);     } /* end i1 */
    }/* End k1 */
     free_vector(severity,1,maxwav);   fprintf(fichtm,"</ul>");
     free_imatrix(outcome,1,maxwav+1,1,n);  fclose(fichtm);
     free_vector(moisnais,1,n);  }
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);  /******************* Gnuplot file **************/
        free_matrix(anint,1,maxwav,1,n);*/  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
        if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     wav=ivector(1,imx);      printf("Problem with file %s",optionfilegnuplot);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    }
      
     /* Concatenates waves */    /*#ifdef windows */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   m=pow(2,cptcoveff);
       Tcode=ivector(1,100);    
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);   /* 1eme*/
       ncodemax[1]=1;    for (cpt=1; cpt<= nlstate ; cpt ++) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);     for (k1=1; k1<= m ; k1 ++) {
             fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
    codtab=imatrix(1,100,1,10);       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);
    h=0;  
    m=pow(2,cptcoveff);       for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
    for(k=1;k<=cptcoveff; k++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
      for(i=1; i <=(m/pow(2,k));i++){       }
        for(j=1; j <= ncodemax[k]; j++){       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){       for (i=1; i<= nlstate ; i ++) {
            h++;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;         else fprintf(ficgp," \%%*lf (\%%*lf)");
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/       } 
          }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        }       for (i=1; i<= nlstate ; i ++) {
      }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
    }         else fprintf(ficgp," \%%*lf (\%%*lf)");
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);       }  
       codtab[1][2]=1;codtab[2][2]=2; */       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
    /* 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);    /*2 eme*/
       }    
       printf("\n");    for (k1=1; k1<= m ; k1 ++) { 
       }      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       scanf("%d",i);*/      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
          
    /* Calculates basic frequencies. Computes observed prevalence at single age      for (i=1; i<= nlstate+1 ; i ++) {
        and prints on file fileres'p'. */        k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
            for (j=1; j<= nlstate+1 ; j ++) {
              if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          else fprintf(ficgp," \%%*lf (\%%*lf)");
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }   
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
              for (j=1; j<= nlstate+1 ; j ++) {
     /* For Powell, parameters are in a vector p[] starting at p[1]          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          else fprintf(ficgp," \%%*lf (\%%*lf)");
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        }   
         fprintf(ficgp,"\" t\"\" w l 0,");
     if(mle==1){        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        for (j=1; j<= nlstate+1 ; j ++) {
     }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
              else fprintf(ficgp," \%%*lf (\%%*lf)");
     /*--------- results files --------------*/        }   
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
          else fprintf(ficgp,"\" t\"\" w l 0,");
       }
    jk=1;    }
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    /*3eme*/
    for(i=1,jk=1; i <=nlstate; i++){    
      for(k=1; k <=(nlstate+ndeath); k++){    for (k1=1; k1<= m ; k1 ++) { 
        if (k != i)      for (cpt=1; cpt<= nlstate ; cpt ++) {
          {        k=2+nlstate*(2*cpt-2);
            printf("%d%d ",i,k);        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
            fprintf(ficres,"%1d%1d ",i,k);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
            for(j=1; j <=ncovmodel; j++){        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
              printf("%f ",p[jk]);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
              fprintf(ficres,"%f ",p[jk]);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
              jk++;          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
            }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
            printf("\n");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
            fprintf(ficres,"\n");          
          }        */
      }        for (i=1; i< nlstate ; i ++) {
    }          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
  if(mle==1){          
     /* Computing hessian and covariance matrix */        } 
     ftolhess=ftol; /* Usually correct */      }
     hesscov(matcov, p, npar, delti, ftolhess, func);    }
  }    
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    /* CV preval stable (period) */
     printf("# Scales (for hessian or gradient estimation)\n");    for (k1=1; k1<= m ; k1 ++) { 
      for(i=1,jk=1; i <=nlstate; i++){      for (cpt=1; cpt<=nlstate ; cpt ++) {
       for(j=1; j <=nlstate+ndeath; j++){        k=3;
         if (j!=i) {        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           fprintf(ficres,"%1d%1d",i,j);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
           printf("%1d%1d",i,j);        
           for(k=1; k<=ncovmodel;k++){        for (i=1; i< nlstate ; i ++)
             printf(" %.5e",delti[jk]);          fprintf(ficgp,"+$%d",k+i+1);
             fprintf(ficres," %.5e",delti[jk]);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
             jk++;        
           }        l=3+(nlstate+ndeath)*cpt;
           printf("\n");        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
           fprintf(ficres,"\n");        for (i=1; i< nlstate ; i ++) {
         }          l=3+(nlstate+ndeath)*cpt;
       }          fprintf(ficgp,"+$%d",l+i+1);
      }        }
            fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     k=1;      } 
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    }  
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    
     for(i=1;i<=npar;i++){    /* proba elementaires */
       /*  if (k>nlstate) k=1;    for(i=1,jk=1; i <=nlstate; i++){
       i1=(i-1)/(ncovmodel*nlstate)+1;      for(k=1; k <=(nlstate+ndeath); k++){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        if (k != i) {
       printf("%s%d%d",alph[k],i1,tab[i]);*/          for(j=1; j <=ncovmodel; j++){
       fprintf(ficres,"%3d",i);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       printf("%3d",i);            jk++; 
       for(j=1; j<=i;j++){            fprintf(ficgp,"\n");
         fprintf(ficres," %.5e",matcov[i][j]);          }
         printf(" %.5e",matcov[i][j]);        }
       }      }
       fprintf(ficres,"\n");     }
       printf("\n");  
       k++;     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); 
     while((c=getc(ficpar))=='#' && c!= EOF){         if (ng==2)
       ungetc(c,ficpar);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
       fgets(line, MAXLINE, ficpar);         else
       puts(line);           fprintf(ficgp,"\nset title \"Probability\"\n");
       fputs(line,ficparo);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     }         i=1;
     ungetc(c,ficpar);         for(k2=1; k2<=nlstate; k2++) {
     estepm=0;           k3=i;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);           for(k=1; k<=(nlstate+ndeath); k++) {
     if (estepm==0 || estepm < stepm) estepm=stepm;             if (k != k2){
     if (fage <= 2) {               if(ng==2)
       bage = ageminpar;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
       fage = agemaxpar;               else
     }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                   ij=1;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");               for(j=3; j <=ncovmodel; j++) {
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                     ij++;
     while((c=getc(ficpar))=='#' && c!= EOF){                 }
     ungetc(c,ficpar);                 else
     fgets(line, MAXLINE, ficpar);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     puts(line);               }
     fputs(line,ficparo);               fprintf(ficgp,")/(1");
   }               
   ungetc(c,ficpar);               for(k1=1; k1 <=nlstate; k1++){   
                   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                 ij=1;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                 for(j=3; j <=ncovmodel; j++){
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                   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]]]);
   while((c=getc(ficpar))=='#' && c!= EOF){                     ij++;
     ungetc(c,ficpar);                   }
     fgets(line, MAXLINE, ficpar);                   else
     puts(line);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     fputs(line,ficparo);                 }
   }                 fprintf(ficgp,")");
   ungetc(c,ficpar);               }
                 fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
    dateprev1=anprev1+mprev1/12.+jprev1/365.;               i=i+ncovmodel;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;             }
            } /* end k */
   fscanf(ficpar,"pop_based=%d\n",&popbased);         } /* end k2 */
   fprintf(ficparo,"pop_based=%d\n",popbased);         } /* end jk */
   fprintf(ficres,"pop_based=%d\n",popbased);       } /* end ng */
       fclose(ficgp); 
   while((c=getc(ficpar))=='#' && c!= EOF){  }  /* end gnuplot */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /*************** Moving average **************/
     fputs(line,ficparo);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   }  
   ungetc(c,ficpar);    int i, cpt, cptcod;
     int modcovmax =1;
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);    int mobilavrange, mob;
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    double age;
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
 while((c=getc(ficpar))=='#' && c!= EOF){    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     puts(line);      if(mobilav==1) mobilavrange=5; /* default */
     fputs(line,ficparo);      else mobilavrange=mobilav;
   }      for (age=bage; age<=fage; age++)
   ungetc(c,ficpar);        for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      /* We keep the original values on the extreme ages bage, fage and for 
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);         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. 
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
 /*------------ gnuplot -------------*/        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);          for (i=1; i<=nlstate;i++){
              for (cptcod=1;cptcod<=modcovmax;cptcod++){
 /*------------ free_vector  -------------*/              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
  chdir(path);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                    mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
  free_ivector(wav,1,imx);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                }
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
  free_ivector(num,1,n);            }
  free_vector(agedc,1,n);          }
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        }/* end age */
  fclose(ficparo);      }/* end mob */
  fclose(ficres);    }else return -1;
     return 0;
 /*--------- index.htm --------*/  }/* End movingaverage */
   
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
   /************** 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){
   /*--------------- Prevalence limit --------------*/    /* proj1, year, month, day of starting projection 
         agemin, agemax range of age
   strcpy(filerespl,"pl");       dateprev1 dateprev2 range of dates during which prevalence is computed
   strcat(filerespl,fileres);       anproj2 year of en of projection (same day and month as proj1).
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   }    int *popage;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double agec; /* generic age */
   fprintf(ficrespl,"#Prevalence limit\n");    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   fprintf(ficrespl,"#Age ");    double *popeffectif,*popcount;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double ***p3mat;
   fprintf(ficrespl,"\n");    double ***mobaverage;
      char fileresf[FILENAMELENGTH];
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    agelim=AGESUP;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    strcpy(fileresf,"f"); 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    strcat(fileresf,fileres);
   k=0;    if((ficresf=fopen(fileresf,"w"))==NULL) {
   agebase=ageminpar;      printf("Problem with forecast resultfile: %s\n", fileresf);
   agelim=agemaxpar;      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   ftolpl=1.e-10;    }
   i1=cptcoveff;    printf("Computing forecasting: result on file '%s' \n", fileresf);
   if (cptcovn < 1){i1=1;}    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
   for(cptcov=1;cptcov<=i1;cptcov++){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;    if (mobilav!=0) {
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         fprintf(ficrespl,"\n#******");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         for(j=1;j<=cptcoveff;j++)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         fprintf(ficrespl,"******\n");      }
            }
         for (age=agebase; age<=agelim; age++){  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    stepsize=(int) (stepm+YEARM-1)/YEARM;
           fprintf(ficrespl,"%.0f",age );    if (stepm<=12) stepsize=1;
           for(i=1; i<=nlstate;i++)    if(estepm < stepm){
           fprintf(ficrespl," %.5f", prlim[i][i]);      printf ("Problem %d lower than %d\n",estepm, stepm);
           fprintf(ficrespl,"\n");    }
         }    else  hstepm=estepm;   
       }  
     }    hstepm=hstepm/stepm; 
   fclose(ficrespl);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
   /*------------- h Pij x at various ages ------------*/    anprojmean=yp;
      yp2=modf((yp1*12),&yp);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    mprojmean=yp;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    yp1=modf((yp2*30.5),&yp);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    jprojmean=yp;
   }    if(jprojmean==0) jprojmean=1;
   printf("Computing pij: result on file '%s' \n", filerespij);    if(mprojmean==0) jprojmean=1;
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;    i1=cptcoveff;
   /*if (stepm<=24) stepsize=2;*/    if (cptcovn < 1){i1=1;}
     
   agelim=AGESUP;    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   hstepm=stepsize*YEARM; /* Every year of age */    
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    fprintf(ficresf,"#****** Routine prevforecast **\n");
    
   k=0;  /*            if (h==(int)(YEARM*yearp)){ */
   for(cptcov=1;cptcov<=i1;cptcov++){    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       k=k+1;        k=k+1;
         fprintf(ficrespij,"\n#****** ");        fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++)        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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(ficrespij,"******\n");        }
                fprintf(ficresf,"******\n");
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(j=1; j<=nlstate+ndeath;j++){ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          for(i=1; i<=nlstate;i++)              
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            fprintf(ficresf," p%d%d",i,j);
           oldm=oldms;savm=savms;          fprintf(ficresf," p.%d",j);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }
           fprintf(ficrespij,"# Age");        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           for(i=1; i<=nlstate;i++)          fprintf(ficresf,"\n");
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");          for (agec=fage; agec>=(ageminpar-1); agec--){ 
            for (h=0; h<=nhstepm; h++){            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            nhstepm = nhstepm/hstepm; 
             for(i=1; i<=nlstate;i++)            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               for(j=1; j<=nlstate+ndeath;j++)            oldm=oldms;savm=savms;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"\n");          
              }            for (h=0; h<=nhstepm; h++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if (h*hstepm/YEARM*stepm ==yearp) {
           fprintf(ficrespij,"\n");                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);
               } 
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);              for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
   fclose(ficrespij);                for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   /*---------- Forecasting ------------------*/                  else {
   if((stepm == 1) && (strcmp(model,".")==0)){                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);                  }
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);                  if (h*hstepm/YEARM*stepm== yearp) {
   }                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
   else{                  }
     erreur=108;                } /* end i */
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);                if (h*hstepm/YEARM*stepm==yearp) {
   }                  fprintf(ficresf," %.3f", ppij);
                  }
               }/* end j */
   /*---------- Health expectancies and variances ------------*/            } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcpy(filerest,"t");          } /* end agec */
   strcat(filerest,fileres);        } /* end yearp */
   if((ficrest=fopen(filerest,"w"))==NULL) {      } /* end cptcod */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    } /* end  cptcov */
   }         
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   strcpy(filerese,"e");  }
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {  /************** Forecasting *****not tested NB*************/
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  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){
   }    
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
  strcpy(fileresv,"v");    double calagedatem, agelim, kk1, kk2;
   strcat(fileresv,fileres);    double *popeffectif,*popcount;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    double ***p3mat,***tabpop,***tabpopprev;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    double ***mobaverage;
   }    char filerespop[FILENAMELENGTH];
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
   calagedate=-1;    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
   k=0;    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       k=k+1;    
       fprintf(ficrest,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    strcpy(filerespop,"pop"); 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcat(filerespop,fileres);
       fprintf(ficrest,"******\n");    if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficreseij,"\n#****** ");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    printf("Computing forecasting: result on file '%s' \n", filerespop);
       fprintf(ficreseij,"******\n");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
       fprintf(ficresvij,"\n#****** ");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if (mobilav!=0) {
       fprintf(ficresvij,"******\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       oldm=oldms;savm=savms;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       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;    stepsize=(int) (stepm+YEARM-1)/YEARM;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    if (stepm<=12) stepsize=1;
        
     agelim=AGESUP;
      
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    hstepm=1;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    hstepm=hstepm/stepm; 
       fprintf(ficrest,"\n");    
     if (popforecast==1) {
       epj=vector(1,nlstate+1);      if((ficpop=fopen(popfile,"r"))==NULL) {
       for(age=bage; age <=fage ;age++){        printf("Problem with population file : %s\n",popfile);exit(0);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
         if (popbased==1) {      } 
           for(i=1; i<=nlstate;i++)      popage=ivector(0,AGESUP);
             prlim[i][i]=probs[(int)age][i][k];      popeffectif=vector(0,AGESUP);
         }      popcount=vector(0,AGESUP);
              
         fprintf(ficrest," %4.0f",age);      i=1;   
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {     
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      imx=i;
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
           }    }
           epj[nlstate+1] +=epj[j];  
         }    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         for(i=1, vepp=0.;i <=nlstate;i++)        k=k+1;
           for(j=1;j <=nlstate;j++)        fprintf(ficrespop,"\n#******");
             vepp += vareij[i][j][(int)age];        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         for(j=1;j <=nlstate;j++){        }
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));        fprintf(ficrespop,"******\n");
         }        fprintf(ficrespop,"# Age");
         fprintf(ficrest,"\n");        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
       }        if (popforecast==1)  fprintf(ficrespop," [Population]");
     }        
   }        for (cpt=0; cpt<=0;cpt++) { 
 free_matrix(mint,1,maxwav,1,n);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          
     free_vector(weight,1,n);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   fclose(ficreseij);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   fclose(ficresvij);            nhstepm = nhstepm/hstepm; 
   fclose(ficrest);            
   fclose(ficpar);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_vector(epj,1,nlstate+1);            oldm=oldms;savm=savms;
              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   /*------- Variance limit prevalence------*/            
             for (h=0; h<=nhstepm; h++){
   strcpy(fileresvpl,"vpl");              if (h==(int) (calagedatem+YEARM*cpt)) {
   strcat(fileresvpl,fileres);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {              } 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);              for(j=1; j<=nlstate+ndeath;j++) {
     exit(0);                kk1=0.;kk2=0;
   }                for(i=1; i<=nlstate;i++) {              
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                  if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   k=0;                  else {
   for(cptcov=1;cptcov<=i1;cptcov++){                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                  }
       k=k+1;                }
       fprintf(ficresvpl,"\n#****** ");                if (h==(int)(calagedatem+12*cpt)){
       for(j=1;j<=cptcoveff;j++)                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    /*fprintf(ficrespop," %.3f", kk1);
       fprintf(ficresvpl,"******\n");                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                      }
       varpl=matrix(1,nlstate,(int) bage, (int) fage);              }
       oldm=oldms;savm=savms;              for(i=1; i<=nlstate;i++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                kk1=0.;
     }                  for(j=1; j<=nlstate;j++){
  }                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
   fclose(ficresvpl);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                  fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            }
          }
   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);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
            fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   free_matrix(matcov,1,npar,1,npar);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   free_vector(delti,1,npar);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   free_matrix(agev,1,maxwav,1,imx);            nhstepm = nhstepm/hstepm; 
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if(erreur >0)            oldm=oldms;savm=savms;
     printf("End of Imach with error or warning %d\n",erreur);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   else   printf("End of Imach\n");            for (h=0; h<=nhstepm; h++){
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */              if (h==(int) (calagedatem+YEARM*cpt)) {
                  fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   /* 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);*/              for(j=1; j<=nlstate+ndeath;j++) {
   /*------ End -----------*/                kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
  end:                }
 #ifdef windows                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   /* chdir(pathcd);*/              }
 #endif            }
  /*system("wgnuplot graph.plt");*/            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  /*system("../gp37mgw/wgnuplot graph.plt");*/          }
  /*system("cd ../gp37mgw");*/        }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/     } 
  strcpy(plotcmd,GNUPLOTPROGRAM);    }
  strcat(plotcmd," ");   
  strcat(plotcmd,optionfilegnuplot);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  system(plotcmd);  
     if (popforecast==1) {
 #ifdef windows      free_ivector(popage,0,AGESUP);
   while (z[0] != 'q') {      free_vector(popeffectif,0,AGESUP);
     /* chdir(path); */      free_vector(popcount,0,AGESUP);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    }
     scanf("%s",z);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if (z[0] == 'c') system("./imach");    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     else if (z[0] == 'e') system(optionfilehtm);    fclose(ficrespop);
     else if (z[0] == 'g') system(plotcmd);  } /* End of popforecast */
     else if (z[0] == 'q') exit(0);  
   }  int fileappend(FILE *fichier, char *optionfile)
 #endif  {
 }    if((fichier=fopen(optionfile,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfile);
       fprintf(ficlog,"Problem with file: %s\n", optionfile);
       return (1);
     }
   
   }
   /***********************************************/
   /**************** 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;
     int jj;
     int numlinepar=0; /* Current linenumber of parameter file */
     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[132],pathc[132],pathcd[132],pathtot[132],model[132];
     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;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char *strt, *strtend;
     char *stratrunc;
     int lstra;
   
     long total_usecs;
     struct timeval start_time, end_time, curr_time;
     struct timezone tzp;
     extern int gettimeofday();
     struct tm tmg, tm, *gmtime(), *localtime();
     long time_value;
     extern long time();
    
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strt=asctime(&tm);
   
   /*  printf("Localtime (at start)=%s",strt); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strt);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strt=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strt); 
   */
   
     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, 132)!= 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,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%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\n%s",version,fullversion);
     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);
   
     printf("Localtime (at start)=%s",strt);
     fprintf(ficlog,"Localtime (at start)=%s",strt);
     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);
       fflush(ficlog);
       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);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     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);
     numlinepar++;
     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);
     fprintf(ficlog,"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);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     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);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         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");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     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);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     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);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%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]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     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);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     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]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       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");
   
     fflush(ficlog);
   
     /*-------- 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=lvector(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);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.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("%ld %.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 %ld 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 %ld 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 %ld 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 %ld 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: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld 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("%ld %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);*/
       
     /*------------ 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);
     /*--------- 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 <br> %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\
   <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>\n\
    - Date and time at start: %s</ul>\n",\
             version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
             model,fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strt);
     fclose(fichtm);
   
     /* 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);
   
     if(fileappend(fichtm, optionfilehtm)){
       fprintf(fichtm,"<br>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",\
           imx,agemin,agemax,jmin,jmax,jmean);
       fclose(fichtm);
     }
       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) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     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);*/
   
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
   
     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_lvector(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 */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strtend=asctime(&tm);
     printf("Localtime at start %s and at end=%s",strt, strtend); 
     fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend); 
     /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
   
     printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     fprintf(ficlog,"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(fileappend(fichtm,optionfilehtm)){
       fprintf(fichtm,"<br>Localtime at start %s and at end=%s<br>",strt, strtend);
       fclose(fichtm);
     }
     /*------ 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.1.46  
changed lines
  Added in v.1.86


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