Diff for /imach/src/imach.c between versions 1.24 and 1.86

version 1.24, 2002/02/22 18:10:15 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
   probabibility 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 "..\\gp37mgw\\wgnuplot"  
 #define FILENAMELENGTH 80    The advantage of this computer programme, compared to a simple
 /*#define DEBUG*/    multinomial logistic model, is clear when the delay between waves is not
 #define windows    identical for each individual. Also, if a individual missed an
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    intermediate interview, the information is lost, but taken into
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    account using an interpolation or extrapolation.  
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    hPijx is the probability to be observed in state i at age x+h
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
 #define NINTERVMAX 8    states. This elementary transition (by month, quarter,
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    semester or year) is modelled as a multinomial logistic.  The hPx
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    matrix is simply the matrix product of nh*stepm elementary matrices
 #define NCOVMAX 8 /* Maximum number of covariates */    and the contribution of each individual to the likelihood is simply
 #define MAXN 20000    hPijx.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Also this programme outputs the covariance matrix of the parameters but also
 #define AGEBASE 40    of the life expectancies. It also computes the stable prevalence. 
     
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int erreur; /* Error number */             Institut national d'études démographiques, Paris.
 int nvar;    This software have been partly granted by Euro-REVES, a concerted action
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    from the European Union.
 int npar=NPARMAX;    It is copyrighted identically to a GNU software product, ie programme and
 int nlstate=2; /* Number of live states */    software can be distributed freely for non commercial use. Latest version
 int ndeath=1; /* Number of dead states */    can be accessed at http://euroreves.ined.fr/imach .
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     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 */  /*
 int mle, weightopt;    main
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    read parameterfile
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    read datafile
 double jmean; /* Mean space between 2 waves */    concatwav
 double **oldm, **newm, **savm; /* Working pointers to matrices */    freqsummary
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    if (mle >= 1)
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;      mlikeli
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    print results files
 FILE *ficreseij;    if mle==1 
   char filerese[FILENAMELENGTH];       computes hessian
  FILE  *ficresvij;    read end of parameter file: agemin, agemax, bage, fage, estepm
   char fileresv[FILENAMELENGTH];        begin-prev-date,...
  FILE  *ficresvpl;    open gnuplot file
   char fileresvpl[FILENAMELENGTH];    open html file
     stable prevalence
 #define NR_END 1     for age prevalim()
 #define FREE_ARG char*    h Pij x
 #define FTOL 1.0e-10    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 #define NRANSI    health expectancies
 #define ITMAX 200    Variance-covariance of DFLE
     prevalence()
 #define TOL 2.0e-4     movingaverage()
     varevsij() 
 #define CGOLD 0.3819660    if popbased==1 varevsij(,popbased)
 #define ZEPS 1.0e-10    total life expectancies
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Variance of stable prevalence
    end
 #define GOLD 1.618034  */
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  
   
 static double maxarg1,maxarg2;   
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #include <math.h>
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #include <stdio.h>
    #include <stdlib.h>
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #include <unistd.h>
 #define rint(a) floor(a+0.5)  
   #include <sys/time.h>
 static double sqrarg;  #include <time.h>
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #include "timeval.h"
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   #define MAXLINE 256
 int imx;  #define GNUPLOTPROGRAM "gnuplot"
 int stepm;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /* Stepm, step in month: minimum step interpolation*/  #define FILENAMELENGTH 132
   /*#define DEBUG*/
 int m,nb;  /*#define windows*/
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 double *weight;  
 int **s; /* Status */  #define NINTERVMAX 8
 double *agedc, **covar, idx;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define MAXN 20000
 double ftolhess; /* Tolerance for computing hessian */  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 /**************** split *************************/  #define AGEBASE 40
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #ifdef unix
 {  #define DIRSEPARATOR '/'
    char *s;                             /* pointer */  #define ODIRSEPARATOR '\\'
    int  l1, l2;                         /* length counters */  #else
   #define DIRSEPARATOR '\\'
    l1 = strlen( path );                 /* length of path */  #define ODIRSEPARATOR '/'
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #endif
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  /* $Id$ */
 #else  /* $State$ */
    s = strrchr( path, '/' );            /* find last / */  
 #endif  char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
    if ( s == NULL ) {                   /* no directory, so use current */  char fullversion[]="$Revision$ $Date$"; 
 #if     defined(__bsd__)                /* get current working directory */  int erreur; /* Error number */
       extern char       *getwd( );  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
       if ( getwd( dirc ) == NULL ) {  int npar=NPARMAX;
 #else  int nlstate=2; /* Number of live states */
       extern char       *getcwd( );  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int popbased=0;
 #endif  
          return( GLOCK_ERROR_GETCWD );  int *wav; /* Number of waves for this individuual 0 is possible */
       }  int maxwav; /* Maxim number of waves */
       strcpy( name, path );             /* we've got it */  int jmin, jmax; /* min, max spacing between 2 waves */
    } else {                             /* strip direcotry from path */  int mle, weightopt;
       s++;                              /* after this, the filename */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       l2 = strlen( s );                 /* length of filename */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       strcpy( name, s );                /* save file name */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  double jmean; /* Mean space between 2 waves */
       dirc[l1-l2] = 0;                  /* add zero */  double **oldm, **newm, **savm; /* Working pointers to matrices */
    }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    l1 = strlen( dirc );                 /* length of directory */  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #ifdef windows  FILE *ficlog, *ficrespow;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int globpr; /* Global variable for printing or not */
 #else  double fretone; /* Only one call to likelihood */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  long ipmx; /* Number of contributions */
 #endif  double sw; /* Sum of weights */
    s = strrchr( name, '.' );            /* find last / */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
    s++;  FILE *ficresilk;
    strcpy(ext,s);                       /* save extension */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    l1= strlen( name);  FILE *ficresprobmorprev;
    l2= strlen( s)+1;  FILE *fichtm; /* Html File */
    strncpy( finame, name, l1-l2);  FILE *ficreseij;
    finame[l1-l2]= 0;  char filerese[FILENAMELENGTH];
    return( 0 );                         /* we're done */  FILE  *ficresvij;
 }  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 /******************************************/  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 void replace(char *s, char*t)  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 {  
   int i;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   int lg=20;  char filelog[FILENAMELENGTH]; /* Log file */
   i=0;  char filerest[FILENAMELENGTH];
   lg=strlen(t);  char fileregp[FILENAMELENGTH];
   for(i=0; i<= lg; i++) {  char popfile[FILENAMELENGTH];
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   }  
 }  #define NR_END 1
   #define FREE_ARG char*
 int nbocc(char *s, char occ)  #define FTOL 1.0e-10
 {  
   int i,j=0;  #define NRANSI 
   int lg=20;  #define ITMAX 200 
   i=0;  
   lg=strlen(s);  #define TOL 2.0e-4 
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  #define CGOLD 0.3819660 
   }  #define ZEPS 1.0e-10 
   return j;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 void cutv(char *u,char *v, char*t, char occ)  #define GLIMIT 100.0 
 {  #define TINY 1.0e-20 
   int i,lg,j,p=0;  
   i=0;  static double maxarg1,maxarg2;
   for(j=0; j<=strlen(t)-1; j++) {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   }    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   lg=strlen(t);  #define rint(a) floor(a+0.5)
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  static double sqrarg;
   }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
      u[p]='\0';  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
    for(j=0; j<= lg; j++) {  int imx; 
     if (j>=(p+1))(v[j-p-1] = t[j]);  int stepm;
   }  /* Stepm, step in month: minimum step interpolation*/
 }  
   int estepm;
 /********************** nrerror ********************/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 void nrerror(char error_text[])  int m,nb;
 {  long *num;
   fprintf(stderr,"ERREUR ...\n");  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   fprintf(stderr,"%s\n",error_text);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   exit(1);  double **pmmij, ***probs;
 }  double dateintmean=0;
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  double *weight;
 {  int **s; /* Status */
   double *v;  double *agedc, **covar, idx;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 }  double ftolhess; /* Tolerance for computing hessian */
   
 /************************ free vector ******************/  /**************** split *************************/
 void free_vector(double*v, int nl, int nh)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
   free((FREE_ARG)(v+nl-NR_END));    char  *ss;                            /* pointer */
 }    int   l1, l2;                         /* length counters */
   
 /************************ivector *******************************/    l1 = strlen(path );                   /* length of path */
 int *ivector(long nl,long nh)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   int *v;    if ( ss == NULL ) {                   /* no directory, so use current */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   if (!v) nrerror("allocation failure in ivector");        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   return v-nl+NR_END;      /* get current working directory */
 }      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 /******************free ivector **************************/        return( GLOCK_ERROR_GETCWD );
 void free_ivector(int *v, long nl, long nh)      }
 {      strcpy( name, path );               /* we've got it */
   free((FREE_ARG)(v+nl-NR_END));    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 /******************* imatrix *******************************/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 int **imatrix(long nrl, long nrh, long ncl, long nch)      strcpy( name, ss );         /* save file name */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 {      dirc[l1-l2] = 0;                    /* add zero */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    }
   int **m;    l1 = strlen( dirc );                  /* length of directory */
      /*#ifdef windows
   /* allocate pointers to rows */    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #else
   if (!m) nrerror("allocation failure 1 in matrix()");    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   m += NR_END;  #endif
   m -= nrl;    */
      ss = strrchr( name, '.' );            /* find last / */
      ss++;
   /* allocate rows and set pointers to them */    strcpy(ext,ss);                       /* save extension */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    l1= strlen( name);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    l2= strlen(ss)+1;
   m[nrl] += NR_END;    strncpy( finame, name, l1-l2);
   m[nrl] -= ncl;    finame[l1-l2]= 0;
      return( 0 );                          /* we're done */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  }
    
   /* return pointer to array of pointers to rows */  
   return m;  /******************************************/
 }  
   void replace(char *s, char*t)
 /****************** free_imatrix *************************/  {
 void free_imatrix(m,nrl,nrh,ncl,nch)    int i;
       int **m;    int lg=20;
       long nch,ncl,nrh,nrl;    i=0;
      /* free an int matrix allocated by imatrix() */    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   free((FREE_ARG) (m[nrl]+ncl-NR_END));      (s[i] = t[i]);
   free((FREE_ARG) (m+nrl-NR_END));      if (t[i]== '\\') s[i]='/';
 }    }
   }
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  int nbocc(char *s, char occ)
 {  {
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    int i,j=0;
   double **m;    int lg=20;
     i=0;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    lg=strlen(s);
   if (!m) nrerror("allocation failure 1 in matrix()");    for(i=0; i<= lg; i++) {
   m += NR_END;    if  (s[i] == occ ) j++;
   m -= nrl;    }
     return j;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  void cutv(char *u,char *v, char*t, char occ)
   m[nrl] -= ncl;  {
     /* cuts string t into u and v where u is ended by char occ excluding it
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   return m;       gives u="abcedf" and v="ghi2j" */
 }    int i,lg,j,p=0;
     i=0;
 /*************************free matrix ************************/    for(j=0; j<=strlen(t)-1; j++) {
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 {    }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    lg=strlen(t);
 }    for(j=0; j<p; j++) {
       (u[j] = t[j]);
 /******************* ma3x *******************************/    }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)       u[p]='\0';
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;     for(j=0; j<= lg; j++) {
   double ***m;      if (j>=(p+1))(v[j-p-1] = t[j]);
     }
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /********************** nrerror ********************/
   m -= nrl;  
   void nrerror(char error_text[])
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    fprintf(stderr,"ERREUR ...\n");
   m[nrl] += NR_END;    fprintf(stderr,"%s\n",error_text);
   m[nrl] -= ncl;    exit(EXIT_FAILURE);
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /*********************** vector *******************/
   double *vector(int nl, int nh)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  {
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    double *v;
   m[nrl][ncl] += NR_END;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   m[nrl][ncl] -= nll;    if (!v) nrerror("allocation failure in vector");
   for (j=ncl+1; j<=nch; j++)    return v-nl+NR_END;
     m[nrl][j]=m[nrl][j-1]+nlay;  }
    
   for (i=nrl+1; i<=nrh; i++) {  /************************ free vector ******************/
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  void free_vector(double*v, int nl, int nh)
     for (j=ncl+1; j<=nch; j++)  {
       m[i][j]=m[i][j-1]+nlay;    free((FREE_ARG)(v+nl-NR_END));
   }  }
   return m;  
 }  /************************ivector *******************************/
   int *ivector(long nl,long nh)
 /*************************free ma3x ************************/  {
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    int *v;
 {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    if (!v) nrerror("allocation failure in ivector");
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    return v-nl+NR_END;
   free((FREE_ARG)(m+nrl-NR_END));  }
 }  
   /******************free ivector **************************/
 /***************** f1dim *************************/  void free_ivector(int *v, long nl, long nh)
 extern int ncom;  {
 extern double *pcom,*xicom;    free((FREE_ARG)(v+nl-NR_END));
 extern double (*nrfunc)(double []);  }
    
 double f1dim(double x)  /************************lvector *******************************/
 {  long *lvector(long nl,long nh)
   int j;  {
   double f;    long *v;
   double *xt;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
      if (!v) nrerror("allocation failure in ivector");
   xt=vector(1,ncom);    return v-nl+NR_END;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  }
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  /******************free lvector **************************/
   return f;  void free_lvector(long *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /*****************brent *************************/  }
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  /******************* imatrix *******************************/
   int iter;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   double a,b,d,etemp;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   double fu,fv,fw,fx;  { 
   double ftemp;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   double p,q,r,tol1,tol2,u,v,w,x,xm;    int **m; 
   double e=0.0;    
      /* allocate pointers to rows */ 
   a=(ax < cx ? ax : cx);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   b=(ax > cx ? ax : cx);    if (!m) nrerror("allocation failure 1 in matrix()"); 
   x=w=v=bx;    m += NR_END; 
   fw=fv=fx=(*f)(x);    m -= nrl; 
   for (iter=1;iter<=ITMAX;iter++) {    
     xm=0.5*(a+b);    
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    /* allocate rows and set pointers to them */ 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     printf(".");fflush(stdout);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 #ifdef DEBUG    m[nrl] += NR_END; 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    m[nrl] -= ncl; 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    
 #endif    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    
       *xmin=x;    /* return pointer to array of pointers to rows */ 
       return fx;    return m; 
     }  } 
     ftemp=fu;  
     if (fabs(e) > tol1) {  /****************** free_imatrix *************************/
       r=(x-w)*(fx-fv);  void free_imatrix(m,nrl,nrh,ncl,nch)
       q=(x-v)*(fx-fw);        int **m;
       p=(x-v)*q-(x-w)*r;        long nch,ncl,nrh,nrl; 
       q=2.0*(q-r);       /* free an int matrix allocated by imatrix() */ 
       if (q > 0.0) p = -p;  { 
       q=fabs(q);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       etemp=e;    free((FREE_ARG) (m+nrl-NR_END)); 
       e=d;  } 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  /******************* matrix *******************************/
       else {  double **matrix(long nrl, long nrh, long ncl, long nch)
         d=p/q;  {
         u=x+d;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         if (u-a < tol2 || b-u < tol2)    double **m;
           d=SIGN(tol1,xm-x);  
       }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     } else {    if (!m) nrerror("allocation failure 1 in matrix()");
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    m += NR_END;
     }    m -= nrl;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (fu <= fx) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       if (u >= x) a=x; else b=x;    m[nrl] += NR_END;
       SHFT(v,w,x,u)    m[nrl] -= ncl;
         SHFT(fv,fw,fx,fu)  
         } else {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
           if (u < x) a=u; else b=u;    return m;
           if (fu <= fw || w == x) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
             v=w;     */
             w=u;  }
             fv=fw;  
             fw=fu;  /*************************free matrix ************************/
           } else if (fu <= fv || v == x || v == w) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
             v=u;  {
             fv=fu;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
           }    free((FREE_ARG)(m+nrl-NR_END));
         }  }
   }  
   nrerror("Too many iterations in brent");  /******************* ma3x *******************************/
   *xmin=x;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   return fx;  {
 }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
 /****************** mnbrak ***********************/  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    if (!m) nrerror("allocation failure 1 in matrix()");
             double (*func)(double))    m += NR_END;
 {    m -= nrl;
   double ulim,u,r,q, dum;  
   double fu;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   *fa=(*func)(*ax);    m[nrl] += NR_END;
   *fb=(*func)(*bx);    m[nrl] -= ncl;
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       SHFT(dum,*fb,*fa,dum)  
       }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   *cx=(*bx)+GOLD*(*bx-*ax);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   *fc=(*func)(*cx);    m[nrl][ncl] += NR_END;
   while (*fb > *fc) {    m[nrl][ncl] -= nll;
     r=(*bx-*ax)*(*fb-*fc);    for (j=ncl+1; j<=nch; j++) 
     q=(*bx-*cx)*(*fb-*fa);      m[nrl][j]=m[nrl][j-1]+nlay;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    for (i=nrl+1; i<=nrh; i++) {
     ulim=(*bx)+GLIMIT*(*cx-*bx);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     if ((*bx-u)*(u-*cx) > 0.0) {      for (j=ncl+1; j<=nch; j++) 
       fu=(*func)(u);        m[i][j]=m[i][j-1]+nlay;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    }
       fu=(*func)(u);    return m; 
       if (fu < *fc) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
           SHFT(*fb,*fc,fu,(*func)(u))    */
           }  }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  /*************************free ma3x ************************/
       fu=(*func)(u);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       fu=(*func)(u);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     }    free((FREE_ARG)(m+nrl-NR_END));
     SHFT(*ax,*bx,*cx,u)  }
       SHFT(*fa,*fb,*fc,fu)  
       }  /***************** f1dim *************************/
 }  extern int ncom; 
   extern double *pcom,*xicom;
 /*************** linmin ************************/  extern double (*nrfunc)(double []); 
    
 int ncom;  double f1dim(double x) 
 double *pcom,*xicom;  { 
 double (*nrfunc)(double []);    int j; 
      double f;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    double *xt; 
 {   
   double brent(double ax, double bx, double cx,    xt=vector(1,ncom); 
                double (*f)(double), double tol, double *xmin);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double f1dim(double x);    f=(*nrfunc)(xt); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    free_vector(xt,1,ncom); 
               double *fc, double (*func)(double));    return f; 
   int j;  } 
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  /*****************brent *************************/
    double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   ncom=n;  { 
   pcom=vector(1,n);    int iter; 
   xicom=vector(1,n);    double a,b,d,etemp;
   nrfunc=func;    double fu,fv,fw,fx;
   for (j=1;j<=n;j++) {    double ftemp;
     pcom[j]=p[j];    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     xicom[j]=xi[j];    double e=0.0; 
   }   
   ax=0.0;    a=(ax < cx ? ax : cx); 
   xx=1.0;    b=(ax > cx ? ax : cx); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    x=w=v=bx; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    fw=fv=fx=(*f)(x); 
 #ifdef DEBUG    for (iter=1;iter<=ITMAX;iter++) { 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      xm=0.5*(a+b); 
 #endif      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for (j=1;j<=n;j++) {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     xi[j] *= xmin;      printf(".");fflush(stdout);
     p[j] += xi[j];      fprintf(ficlog,".");fflush(ficlog);
   }  #ifdef DEBUG
   free_vector(xicom,1,n);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   free_vector(pcom,1,n);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
 /*************** powell ************************/      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,        *xmin=x; 
             double (*func)(double []))        return fx; 
 {      } 
   void linmin(double p[], double xi[], int n, double *fret,      ftemp=fu;
               double (*func)(double []));      if (fabs(e) > tol1) { 
   int i,ibig,j;        r=(x-w)*(fx-fv); 
   double del,t,*pt,*ptt,*xit;        q=(x-v)*(fx-fw); 
   double fp,fptt;        p=(x-v)*q-(x-w)*r; 
   double *xits;        q=2.0*(q-r); 
   pt=vector(1,n);        if (q > 0.0) p = -p; 
   ptt=vector(1,n);        q=fabs(q); 
   xit=vector(1,n);        etemp=e; 
   xits=vector(1,n);        e=d; 
   *fret=(*func)(p);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   for (j=1;j<=n;j++) pt[j]=p[j];          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (*iter=1;;++(*iter)) {        else { 
     fp=(*fret);          d=p/q; 
     ibig=0;          u=x+d; 
     del=0.0;          if (u-a < tol2 || b-u < tol2) 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);            d=SIGN(tol1,xm-x); 
     for (i=1;i<=n;i++)        } 
       printf(" %d %.12f",i, p[i]);      } else { 
     printf("\n");        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for (i=1;i<=n;i++) {      } 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fptt=(*fret);      fu=(*f)(u); 
 #ifdef DEBUG      if (fu <= fx) { 
       printf("fret=%lf \n",*fret);        if (u >= x) a=x; else b=x; 
 #endif        SHFT(v,w,x,u) 
       printf("%d",i);fflush(stdout);          SHFT(fv,fw,fx,fu) 
       linmin(p,xit,n,fret,func);          } else { 
       if (fabs(fptt-(*fret)) > del) {            if (u < x) a=u; else b=u; 
         del=fabs(fptt-(*fret));            if (fu <= fw || w == x) { 
         ibig=i;              v=w; 
       }              w=u; 
 #ifdef DEBUG              fv=fw; 
       printf("%d %.12e",i,(*fret));              fw=fu; 
       for (j=1;j<=n;j++) {            } else if (fu <= fv || v == x || v == w) { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);              v=u; 
         printf(" x(%d)=%.12e",j,xit[j]);              fv=fu; 
       }            } 
       for(j=1;j<=n;j++)          } 
         printf(" p=%.12e",p[j]);    } 
       printf("\n");    nrerror("Too many iterations in brent"); 
 #endif    *xmin=x; 
     }    return fx; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  } 
 #ifdef DEBUG  
       int k[2],l;  /****************** mnbrak ***********************/
       k[0]=1;  
       k[1]=-1;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       printf("Max: %.12e",(*func)(p));              double (*func)(double)) 
       for (j=1;j<=n;j++)  { 
         printf(" %.12e",p[j]);    double ulim,u,r,q, dum;
       printf("\n");    double fu; 
       for(l=0;l<=1;l++) {   
         for (j=1;j<=n;j++) {    *fa=(*func)(*ax); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    *fb=(*func)(*bx); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    if (*fb > *fa) { 
         }      SHFT(dum,*ax,*bx,dum) 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        SHFT(dum,*fb,*fa,dum) 
       }        } 
 #endif    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
     while (*fb > *fc) { 
       free_vector(xit,1,n);      r=(*bx-*ax)*(*fb-*fc); 
       free_vector(xits,1,n);      q=(*bx-*cx)*(*fb-*fa); 
       free_vector(ptt,1,n);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       free_vector(pt,1,n);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       return;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     }      if ((*bx-u)*(u-*cx) > 0.0) { 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        fu=(*func)(u); 
     for (j=1;j<=n;j++) {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       ptt[j]=2.0*p[j]-pt[j];        fu=(*func)(u); 
       xit[j]=p[j]-pt[j];        if (fu < *fc) { 
       pt[j]=p[j];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     }            SHFT(*fb,*fc,fu,(*func)(u)) 
     fptt=(*func)(ptt);            } 
     if (fptt < fp) {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        u=ulim; 
       if (t < 0.0) {        fu=(*func)(u); 
         linmin(p,xit,n,fret,func);      } else { 
         for (j=1;j<=n;j++) {        u=(*cx)+GOLD*(*cx-*bx); 
           xi[j][ibig]=xi[j][n];        fu=(*func)(u); 
           xi[j][n]=xit[j];      } 
         }      SHFT(*ax,*bx,*cx,u) 
 #ifdef DEBUG        SHFT(*fa,*fb,*fc,fu) 
         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++)  } 
           printf(" %.12e",xit[j]);  
         printf("\n");  /*************** linmin ************************/
 #endif  
       }  int ncom; 
     }  double *pcom,*xicom;
   }  double (*nrfunc)(double []); 
 }   
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 /**** Prevalence limit ****************/  { 
     double brent(double ax, double bx, double cx, 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)                 double (*f)(double), double tol, double *xmin); 
 {    double f1dim(double x); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
      matrix by transitions matrix until convergence is reached */                double *fc, double (*func)(double)); 
     int j; 
   int i, ii,j,k;    double xx,xmin,bx,ax; 
   double min, max, maxmin, maxmax,sumnew=0.;    double fx,fb,fa;
   double **matprod2();   
   double **out, cov[NCOVMAX], **pmij();    ncom=n; 
   double **newm;    pcom=vector(1,n); 
   double agefin, delaymax=50 ; /* Max number of years to converge */    xicom=vector(1,n); 
     nrfunc=func; 
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (j=1;j<=n;j++) { 
     for (j=1;j<=nlstate+ndeath;j++){      pcom[j]=p[j]; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      xicom[j]=xi[j]; 
     }    } 
     ax=0.0; 
    cov[1]=1.;    xx=1.0; 
      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #ifdef DEBUG
     newm=savm;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     /* Covariates have to be included here again */    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
      cov[2]=agefin;  #endif
      for (j=1;j<=n;j++) { 
       for (k=1; k<=cptcovn;k++) {      xi[j] *= xmin; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      p[j] += xi[j]; 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    } 
       }    free_vector(xicom,1,n); 
       for (k=1; k<=cptcovage;k++)    free_vector(pcom,1,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]]];  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, 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]);*/  { 
     void linmin(double p[], double xi[], int n, double *fret, 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);                double (*func)(double [])); 
     int i,ibig,j; 
     savm=oldm;    double del,t,*pt,*ptt,*xit;
     oldm=newm;    double fp,fptt;
     maxmax=0.;    double *xits;
     for(j=1;j<=nlstate;j++){    pt=vector(1,n); 
       min=1.;    ptt=vector(1,n); 
       max=0.;    xit=vector(1,n); 
       for(i=1; i<=nlstate; i++) {    xits=vector(1,n); 
         sumnew=0;    *fret=(*func)(p); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    for (j=1;j<=n;j++) pt[j]=p[j]; 
         prlim[i][j]= newm[i][j]/(1-sumnew);    for (*iter=1;;++(*iter)) { 
         max=FMAX(max,prlim[i][j]);      fp=(*fret); 
         min=FMIN(min,prlim[i][j]);      ibig=0; 
       }      del=0.0; 
       maxmin=max-min;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       maxmax=FMAX(maxmax,maxmin);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     }      fprintf(ficrespow,"%d %.12f",*iter,*fret);
     if(maxmax < ftolpl){      for (i=1;i<=n;i++) {
       return prlim;        printf(" %d %.12f",i, p[i]);
     }        fprintf(ficlog," %d %.12lf",i, p[i]);
   }        fprintf(ficrespow," %.12lf", p[i]);
 }      }
       printf("\n");
 /*************** transition probabilities ***************/      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      for (i=1;i<=n;i++) { 
 {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   double s1, s2;        fptt=(*fret); 
   /*double t34;*/  #ifdef DEBUG
   int i,j,j1, nc, ii, jj;        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
     for(i=1; i<= nlstate; i++){  #endif
     for(j=1; j<i;j++){        printf("%d",i);fflush(stdout);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        fprintf(ficlog,"%d",i);fflush(ficlog);
         /*s2 += param[i][j][nc]*cov[nc];*/        linmin(p,xit,n,fret,func); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        if (fabs(fptt-(*fret)) > del) { 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          del=fabs(fptt-(*fret)); 
       }          ibig=i; 
       ps[i][j]=s2;        } 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  #ifdef DEBUG
     }        printf("%d %.12e",i,(*fret));
     for(j=i+1; j<=nlstate+ndeath;j++){        fprintf(ficlog,"%d %.12e",i,(*fret));
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        for (j=1;j<=n;j++) {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          printf(" x(%d)=%.12e",j,xit[j]);
       }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       ps[i][j]=s2;        }
     }        for(j=1;j<=n;j++) {
   }          printf(" p=%.12e",p[j]);
     /*ps[3][2]=1;*/          fprintf(ficlog," p=%.12e",p[j]);
         }
   for(i=1; i<= nlstate; i++){        printf("\n");
      s1=0;        fprintf(ficlog,"\n");
     for(j=1; j<i; j++)  #endif
       s1+=exp(ps[i][j]);      } 
     for(j=i+1; j<=nlstate+ndeath; j++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       s1+=exp(ps[i][j]);  #ifdef DEBUG
     ps[i][i]=1./(s1+1.);        int k[2],l;
     for(j=1; j<i; j++)        k[0]=1;
       ps[i][j]= exp(ps[i][j])*ps[i][i];        k[1]=-1;
     for(j=i+1; j<=nlstate+ndeath; j++)        printf("Max: %.12e",(*func)(p));
       ps[i][j]= exp(ps[i][j])*ps[i][i];        fprintf(ficlog,"Max: %.12e",(*func)(p));
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        for (j=1;j<=n;j++) {
   } /* end i */          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        }
     for(jj=1; jj<= nlstate+ndeath; jj++){        printf("\n");
       ps[ii][jj]=0;        fprintf(ficlog,"\n");
       ps[ii][ii]=1;        for(l=0;l<=1;l++) {
     }          for (j=1;j<=n;j++) {
   }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){          }
     for(jj=1; jj<= nlstate+ndeath; jj++){          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      printf("%lf ",ps[ii][jj]);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
    }        }
     printf("\n ");  #endif
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*        free_vector(xit,1,n); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        free_vector(xits,1,n); 
   goto end;*/        free_vector(ptt,1,n); 
     return ps;        free_vector(pt,1,n); 
 }        return; 
       } 
 /**************** Product of 2 matrices ******************/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        ptt[j]=2.0*p[j]-pt[j]; 
 {        xit[j]=p[j]-pt[j]; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        pt[j]=p[j]; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      } 
   /* in, b, out are matrice of pointers which should have been initialized      fptt=(*func)(ptt); 
      before: only the contents of out is modified. The function returns      if (fptt < fp) { 
      a pointer to pointers identical to out */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   long i, j, k;        if (t < 0.0) { 
   for(i=nrl; i<= nrh; i++)          linmin(p,xit,n,fret,func); 
     for(k=ncolol; k<=ncoloh; k++)          for (j=1;j<=n;j++) { 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)            xi[j][ibig]=xi[j][n]; 
         out[i][k] +=in[i][j]*b[j][k];            xi[j][n]=xit[j]; 
           }
   return out;  #ifdef DEBUG
 }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
 /************* Higher Matrix Product ***************/            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )          }
 {          printf("\n");
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          fprintf(ficlog,"\n");
      duration (i.e. until  #endif
      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).    } 
      Model is determined by parameters x and covariates have to be  } 
      included manually here.  
   /**** Prevalence limit (stable prevalence)  ****************/
      */  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   int i, j, d, h, k;  {
   double **out, cov[NCOVMAX];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   double **newm;       matrix by transitions matrix until convergence is reached */
   
   /* Hstepm could be zero and should return the unit matrix */    int i, ii,j,k;
   for (i=1;i<=nlstate+ndeath;i++)    double min, max, maxmin, maxmax,sumnew=0.;
     for (j=1;j<=nlstate+ndeath;j++){    double **matprod2();
       oldm[i][j]=(i==j ? 1.0 : 0.0);    double **out, cov[NCOVMAX], **pmij();
       po[i][j][0]=(i==j ? 1.0 : 0.0);    double **newm;
     }    double agefin, delaymax=50 ; /* Max number of years to converge */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){    for (ii=1;ii<=nlstate+ndeath;ii++)
     for(d=1; d <=hstepm; d++){      for (j=1;j<=nlstate+ndeath;j++){
       newm=savm;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       /* Covariates have to be included here again */      }
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;     cov[1]=1.;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];   
       for (k=1; k<=cptcovage;k++)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       for (k=1; k<=cptcovprod;k++)      newm=savm;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      /* Covariates have to be included here again */
        cov[2]=agefin;
     
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        for (k=1; k<=cptcovn;k++) {
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          /*      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]]);*/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        }
       savm=oldm;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       oldm=newm;        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(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         po[i][j][h]=newm[i][j];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
          */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       }  
   } /* end h */      savm=oldm;
   return po;      oldm=newm;
 }      maxmax=0.;
       for(j=1;j<=nlstate;j++){
         min=1.;
 /*************** log-likelihood *************/        max=0.;
 double func( double *x)        for(i=1; i<=nlstate; i++) {
 {          sumnew=0;
   int i, ii, j, k, mi, d, kk;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   double l, ll[NLSTATEMAX], cov[NCOVMAX];          prlim[i][j]= newm[i][j]/(1-sumnew);
   double **out;          max=FMAX(max,prlim[i][j]);
   double sw; /* Sum of weights */          min=FMIN(min,prlim[i][j]);
   double lli; /* Individual log likelihood */        }
   long ipmx;        maxmin=max-min;
   /*extern weight */        maxmax=FMAX(maxmax,maxmin);
   /* We are differentiating ll according to initial status */      }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      if(maxmax < ftolpl){
   /*for(i=1;i<imx;i++)        return prlim;
     printf(" %d\n",s[4][i]);      }
   */    }
   cov[1]=1.;  }
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /*************** transition probabilities ***************/ 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for(mi=1; mi<= wav[i]-1; mi++){  {
       for (ii=1;ii<=nlstate+ndeath;ii++)    double s1, s2;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    /*double t34;*/
       for(d=0; d<dh[mi][i]; d++){    int i,j,j1, nc, ii, jj;
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      for(i=1; i<= nlstate; i++){
         for (kk=1; kk<=cptcovage;kk++) {      for(j=1; j<i;j++){
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         }          /*s2 += param[i][j][nc]*cov[nc];*/
                  s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        }
         savm=oldm;        ps[i][j]=s2;
         oldm=newm;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
              }
              for(j=i+1; j<=nlstate+ndeath;j++){
       } /* end mult */        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];
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        }
       ipmx +=1;        ps[i][j]=s2;
       sw += weight[i];      }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    }
     } /* end of wave */      /*ps[3][2]=1;*/
   } /* end of individual */  
     for(i=1; i<= nlstate; i++){
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];       s1=0;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      for(j=1; j<i; j++)
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        s1+=exp(ps[i][j]);
   return -l;      for(j=i+1; j<=nlstate+ndeath; j++)
 }        s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
       for(j=1; j<i; j++)
 /*********** Maximum Likelihood Estimation ***************/        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        ps[i][j]= exp(ps[i][j])*ps[i][i];
 {      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   int i,j, iter;    } /* end i */
   double **xi,*delti;  
   double fret;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   xi=matrix(1,npar,1,npar);      for(jj=1; jj<= nlstate+ndeath; jj++){
   for (i=1;i<=npar;i++)        ps[ii][jj]=0;
     for (j=1;j<=npar;j++)        ps[ii][ii]=1;
       xi[i][j]=(i==j ? 1.0 : 0.0);      }
   printf("Powell\n");    }
   powell(p,xi,npar,ftol,&iter,&fret,func);  
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
 }     }
       printf("\n ");
 /**** Computes Hessian and covariance matrix ***/      }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      printf("\n ");printf("%lf ",cov[2]);*/
 {  /*
   double  **a,**y,*x,pd;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double **hess;    goto end;*/
   int i, j,jk;      return ps;
   int *indx;  }
   
   double hessii(double p[], double delta, int theta, double delti[]);  /**************** Product of 2 matrices ******************/
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   void ludcmp(double **a, int npar, int *indx, double *d) ;  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   hess=matrix(1,npar,1,npar);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
   printf("\nCalculation of the hessian matrix. Wait...\n");       before: only the contents of out is modified. The function returns
   for (i=1;i<=npar;i++){       a pointer to pointers identical to out */
     printf("%d",i);fflush(stdout);    long i, j, k;
     hess[i][i]=hessii(p,ftolhess,i,delti);    for(i=nrl; i<= nrh; i++)
     /*printf(" %f ",p[i]);*/      for(k=ncolol; k<=ncoloh; k++)
     /*printf(" %lf ",hess[i][i]);*/        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   }          out[i][k] +=in[i][j]*b[j][k];
    
   for (i=1;i<=npar;i++) {    return out;
     for (j=1;j<=npar;j++)  {  }
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);  /************* Higher Matrix Product ***************/
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       }  {
     }    /* Computes the transition matrix starting at age 'age' over 
   }       'nhstepm*hstepm*stepm' months (i.e. until
   printf("\n");       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");       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 
   a=matrix(1,npar,1,npar);       for the memory).
   y=matrix(1,npar,1,npar);       Model is determined by parameters x and covariates have to be 
   x=vector(1,npar);       included manually here. 
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)       */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  
   ludcmp(a,npar,indx,&pd);    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
   for (j=1;j<=npar;j++) {    double **newm;
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;    /* Hstepm could be zero and should return the unit matrix */
     lubksb(a,npar,indx,x);    for (i=1;i<=nlstate+ndeath;i++)
     for (i=1;i<=npar;i++){      for (j=1;j<=nlstate+ndeath;j++){
       matcov[i][j]=x[i];        oldm[i][j]=(i==j ? 1.0 : 0.0);
     }        po[i][j][0]=(i==j ? 1.0 : 0.0);
   }      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   printf("\n#Hessian matrix#\n");    for(h=1; h <=nhstepm; h++){
   for (i=1;i<=npar;i++) {      for(d=1; d <=hstepm; d++){
     for (j=1;j<=npar;j++) {        newm=savm;
       printf("%.3e ",hess[i][j]);        /* Covariates have to be included here again */
     }        cov[1]=1.;
     printf("\n");        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
   /* Recompute Inverse */          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for (i=1;i<=npar;i++)        for (k=1; k<=cptcovprod;k++)
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   ludcmp(a,npar,indx,&pd);  
   
   /*  printf("\n#Hessian matrix recomputed#\n");        /*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 (j=1;j<=npar;j++) {        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     for (i=1;i<=npar;i++) x[i]=0;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     x[j]=1;        savm=oldm;
     lubksb(a,npar,indx,x);        oldm=newm;
     for (i=1;i<=npar;i++){      }
       y[i][j]=x[i];      for(i=1; i<=nlstate+ndeath; i++)
       printf("%.3e ",y[i][j]);        for(j=1;j<=nlstate+ndeath;j++) {
     }          po[i][j][h]=newm[i][j];
     printf("\n");          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   }           */
   */        }
     } /* end h */
   free_matrix(a,1,npar,1,npar);    return po;
   free_matrix(y,1,npar,1,npar);  }
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);  /*************** log-likelihood *************/
   double func( double *x)
   {
 }    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
 /*************** hessian matrix ****************/    double **out;
 double hessii( double x[], double delta, int theta, double delti[])    double sw; /* Sum of weights */
 {    double lli; /* Individual log likelihood */
   int i;    int s1, s2;
   int l=1, lmax=20;    double bbh, survp;
   double k1,k2;    long ipmx;
   double p2[NPARMAX+1];    /*extern weight */
   double res;    /* We are differentiating ll according to initial status */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double fx;    /*for(i=1;i<imx;i++) 
   int k=0,kmax=10;      printf(" %d\n",s[4][i]);
   double l1;    */
     cov[1]=1.;
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];    for(k=1; k<=nlstate; k++) ll[k]=0.;
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);    if(mle==1){
     delts=delt;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(k=1 ; k <kmax; k=k+1){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       delt = delta*(l1*k);        for(mi=1; mi<= wav[i]-1; mi++){
       p2[theta]=x[theta] +delt;          for (ii=1;ii<=nlstate+ndeath;ii++)
       k1=func(p2)-fx;            for (j=1;j<=nlstate+ndeath;j++){
       p2[theta]=x[theta]-delt;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       k2=func(p2)-fx;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*res= (k1-2.0*fx+k2)/delt/delt; */            }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          for(d=0; d<dh[mi][i]; d++){
                  newm=savm;
 #ifdef DEBUG            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);            for (kk=1; kk<=cptcovage;kk++) {
 #endif              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         k=kmax;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            oldm=newm;
         k=kmax; l=lmax*10.;          } /* end mult */
       }        
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         delts=delt;          /* 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 
     }           * (in months) between two waves is not a multiple of stepm, we rounded to 
   }           * the nearest (and in case of equal distance, to the lowest) interval but now
   delti[theta]=delts;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   return res;           * (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
 }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
 double hessij( double x[], double delti[], int thetai,int thetaj)           * 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. 
   int i;           */
   int l=1, l1, lmax=20;          s1=s[mw[mi][i]][i];
   double k1,k2,k3,k4,res,fx;          s2=s[mw[mi+1][i]][i];
   double p2[NPARMAX+1];          bbh=(double)bh[mi][i]/(double)stepm; 
   int k;          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   fx=func(x);           */
   for (k=1; k<=2; 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]));*/
     for (i=1;i<=npar;i++) p2[i]=x[i];          if( s2 > nlstate){ 
     p2[thetai]=x[thetai]+delti[thetai]/k;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;               to the likelihood is the probability to die between last step unit time and current 
     k1=func(p2)-fx;               step unit time, which is also the differences between probability to die before dh 
                 and probability to die before dh-stepm . 
     p2[thetai]=x[thetai]+delti[thetai]/k;               In version up to 0.92 likelihood was computed
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          as if date of death was unknown. Death was treated as any other
     k2=func(p2)-fx;          health state: the date of the interview describes the actual state
            and not the date of a change in health state. The former idea was
     p2[thetai]=x[thetai]-delti[thetai]/k;          to consider that at each interview the state was recorded
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          (healthy, disable or death) and IMaCh was corrected; but when we
     k3=func(p2)-fx;          introduced the exact date of death then we should have modified
            the contribution of an exact death to the likelihood. This new
     p2[thetai]=x[thetai]-delti[thetai]/k;          contribution is smaller and very dependent of the step unit
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          stepm. It is no more the probability to die between last interview
     k4=func(p2)-fx;          and month of death but the probability to survive from last
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          interview up to one month before death multiplied by the
 #ifdef DEBUG          probability to die within a month. Thanks to Chris
     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);          Jackson for correcting this bug.  Former versions increased
 #endif          mortality artificially. The bad side is that we add another loop
   }          which slows down the processing. The difference can be up to 10%
   return res;          lower mortality.
 }            */
             lli=log(out[s1][s2] - savm[s1][s2]);
 /************** Inverse of matrix **************/          }else{
 void ludcmp(double **a, int n, int *indx, double *d)            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 */
   int i,imax,j,k;          } 
   double big,dum,sum,temp;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double *vv;          /*if(lli ==000.0)*/
            /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   vv=vector(1,n);          ipmx +=1;
   *d=1.0;          sw += weight[i];
   for (i=1;i<=n;i++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     big=0.0;        } /* end of wave */
     for (j=1;j<=n;j++)      } /* end of individual */
       if ((temp=fabs(a[i][j])) > big) big=temp;    }  else if(mle==2){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     vv[i]=1.0/big;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   for (j=1;j<=n;j++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (i=1;i<j;i++) {            for (j=1;j<=nlstate+ndeath;j++){
       sum=a[i][j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       a[i][j]=sum;            }
     }          for(d=0; d<=dh[mi][i]; d++){
     big=0.0;            newm=savm;
     for (i=j;i<=n;i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       sum=a[i][j];            for (kk=1; kk<=cptcovage;kk++) {
       for (k=1;k<j;k++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         sum -= a[i][k]*a[k][j];            }
       a[i][j]=sum;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if ( (dum=vv[i]*fabs(sum)) >= big) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         big=dum;            savm=oldm;
         imax=i;            oldm=newm;
       }          } /* end mult */
     }        
     if (j != imax) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       for (k=1;k<=n;k++) {          /* But now since version 0.9 we anticipate for bias and large stepm.
         dum=a[imax][k];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         a[imax][k]=a[j][k];           * (in months) between two waves is not a multiple of stepm, we rounded to 
         a[j][k]=dum;           * 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
       *d = -(*d);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       vv[imax]=vv[j];           * 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
     indx[j]=imax;           * -stepm/2 to stepm/2 .
     if (a[j][j] == 0.0) a[j][j]=TINY;           * For stepm=1 the results are the same as for previous versions of Imach.
     if (j != n) {           * For stepm > 1 the results are less biased than in previous versions. 
       dum=1.0/(a[j][j]);           */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
   free_vector(vv,1,n);  /* Doesn't work */          /* bias is positive if real duration
 ;           * is higher than the multiple of stepm and negative otherwise.
 }           */
           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 */
 void lubksb(double **a, int n, int *indx, double b[])          /* 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 */
   int i,ii=0,ip,j;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double sum;          /*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); */
   for (i=1;i<=n;i++) {          ipmx +=1;
     ip=indx[i];          sw += weight[i];
     sum=b[ip];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     b[ip]=b[i];        } /* end of wave */
     if (ii)      } /* end of individual */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    }  else if(mle==3){  /* exponential inter-extrapolation */
     else if (sum) ii=i;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     b[i]=sum;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   for (i=n;i>=1;i--) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     sum=b[i];            for (j=1;j<=nlstate+ndeath;j++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     b[i]=sum/a[i][i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
 }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 /************ Frequencies ********************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 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)            for (kk=1; kk<=cptcovage;kk++) {
 {  /* Some frequencies */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***freq; /* Frequencies */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double *pp;            savm=oldm;
   double pos, k2, dateintsum=0,k2cpt=0;            oldm=newm;
   FILE *ficresp;          } /* end mult */
   char fileresp[FILENAMELENGTH];        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   pp=vector(1,nlstate);          /* But now since version 0.9 we anticipate for bias and large stepm.
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   strcpy(fileresp,"p");           * (in months) between two waves is not a multiple of stepm, we rounded to 
   strcat(fileresp,fileres);           * the nearest (and in case of equal distance, to the lowest) interval but now
   if((ficresp=fopen(fileresp,"w"))==NULL) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     printf("Problem with prevalence resultfile: %s\n", fileresp);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     exit(0);           * 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
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           * -stepm/2 to stepm/2 .
   j1=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. 
   j=cptcoveff;           */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   for(k1=1; k1<=j;k1++){          bbh=(double)bh[mi][i]/(double)stepm; 
    for(i1=1; i1<=ncodemax[k1];i1++){          /* bias is positive if real duration
        j1++;           * is higher than the multiple of stepm and negative otherwise.
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);           */
          scanf("%d", i);*/          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
         for (i=-1; i<=nlstate+ndeath; i++)            lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
          for (jk=-1; jk<=nlstate+ndeath; jk++)            /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            for(m=agemin; m <= agemax+3; m++)          /*if(lli ==000.0)*/
              freq[i][jk][m]=0;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
         dateintsum=0;          sw += weight[i];
         k2cpt=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        for (i=1; i<=imx; i++) {        } /* end of wave */
          bool=1;      } /* end of individual */
          if  (cptcovn>0) {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
            for (z1=1; z1<=cptcoveff; z1++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                bool=0;        for(mi=1; mi<= wav[i]-1; mi++){
          }          for (ii=1;ii<=nlstate+ndeath;ii++)
          if (bool==1) {            for (j=1;j<=nlstate+ndeath;j++){
            for(m=firstpass; m<=lastpass; m++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              k2=anint[m][i]+(mint[m][i]/12.);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              if ((k2>=dateprev1) && (k2<=dateprev2)) {            }
                if(agev[m][i]==0) agev[m][i]=agemax+1;          for(d=0; d<dh[mi][i]; d++){
                if(agev[m][i]==1) agev[m][i]=agemax+2;            newm=savm;
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            for (kk=1; kk<=cptcovage;kk++) {
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                  dateintsum=dateintsum+k2;            }
                  k2cpt++;          
                }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              }            savm=oldm;
            }            oldm=newm;
          }          } /* end mult */
        }        
         if  (cptcovn>0) {          s1=s[mw[mi][i]][i];
          fprintf(ficresp, "\n#********** Variable ");          s2=s[mw[mi+1][i]][i];
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          if( s2 > nlstate){ 
        fprintf(ficresp, "**********\n#");            lli=log(out[s1][s2] - savm[s1][s2]);
         }          }else{
        for(i=1; i<=nlstate;i++)            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          }
        fprintf(ficresp, "\n");          ipmx +=1;
                  sw += weight[i];
   for(i=(int)agemin; i <= (int)agemax+3; i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     if(i==(int)agemax+3)  /*      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]); */
       printf("Total");        } /* end of wave */
     else      } /* end of individual */
       printf("Age %d", i);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for(jk=1; jk <=nlstate ; jk++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         pp[jk] += freq[jk][m][i];        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(jk=1; jk <=nlstate ; jk++){            for (j=1;j<=nlstate+ndeath;j++){
       for(m=-1, pos=0; m <=0 ; m++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         pos += freq[jk][m][i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(pp[jk]>=1.e-10)            }
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          for(d=0; d<dh[mi][i]; d++){
       else            newm=savm;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            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];
      for(jk=1; jk <=nlstate ; jk++){            }
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          
         pp[jk] += freq[jk][m][i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for(jk=1,pos=0; jk <=nlstate ; jk++)            oldm=newm;
       pos += pp[jk];          } /* end mult */
     for(jk=1; jk <=nlstate ; jk++){        
       if(pos>=1.e-5)          s1=s[mw[mi][i]][i];
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          s2=s[mw[mi+1][i]][i];
       else          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          ipmx +=1;
       if( i <= (int) agemax){          sw += weight[i];
         if(pos>=1.e-5){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          /*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]);*/
           probs[i][jk][j1]= pp[jk]/pos;        } /* end of wave */
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      } /* end of individual */
         }    } /* End of if */
       else    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    /* 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 */
     }    return -l;
     for(jk=-1; jk <=nlstate+ndeath; jk++)  }
       for(m=-1; m <=nlstate+ndeath; m++)  
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  /*************** log-likelihood *************/
     if(i <= (int) agemax)  double funcone( double *x)
       fprintf(ficresp,"\n");  {
     printf("\n");    int i, ii, j, k, mi, d, kk;
     }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     }    double **out;
  }    double lli; /* Individual log likelihood */
   dateintmean=dateintsum/k2cpt;    int s1, s2;
      double bbh, survp;
   fclose(ficresp);    /*extern weight */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /* We are differentiating ll according to initial status */
   free_vector(pp,1,nlstate);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
   /* End of Freq */      printf(" %d\n",s[4][i]);
 }    */
     cov[1]=1.;
 /************ Prevalence ********************/  
 void prevalence(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 calagedate)    for(k=1; k<=nlstate; k++) ll[k]=0.;
 {  /* Some frequencies */  
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double ***freq; /* Frequencies */      for(mi=1; mi<= wav[i]-1; mi++){
   double *pp;        for (ii=1;ii<=nlstate+ndeath;ii++)
   double pos, k2;          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   pp=vector(1,nlstate);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
          for(d=0; d<dh[mi][i]; d++){
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          newm=savm;
   j1=0;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
            for (kk=1; kk<=cptcovage;kk++) {
   j=cptcoveff;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  for(k1=1; k1<=j;k1++){                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i1=1; i1<=ncodemax[k1];i1++){          savm=oldm;
       j1++;          oldm=newm;
          } /* end mult */
       for (i=-1; i<=nlstate+ndeath; i++)          
         for (jk=-1; jk<=nlstate+ndeath; jk++)          s1=s[mw[mi][i]][i];
           for(m=agemin; m <= agemax+3; m++)        s2=s[mw[mi+1][i]][i];
             freq[i][jk][m]=0;        bbh=(double)bh[mi][i]/(double)stepm; 
              /* bias is positive if real duration
       for (i=1; i<=imx; i++) {         * is higher than the multiple of stepm and negative otherwise.
         bool=1;         */
         if  (cptcovn>0) {        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           for (z1=1; z1<=cptcoveff; z1++)          lli=log(out[s1][s2] - savm[s1][s2]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        } else if (mle==1){
               bool=0;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         }        } else if(mle==2){
         if (bool==1) {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           for(m=firstpass; m<=lastpass; m++){        } else if(mle==3){  /* exponential inter-extrapolation */
             k2=anint[m][i]+(mint[m][i]/12.);          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 */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
               if(agev[m][i]==0) agev[m][i]=agemax+1;          lli=log(out[s1][s2]); /* Original formula */
               if(agev[m][i]==1) agev[m][i]=agemax+2;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          lli=log(out[s1][s2]); /* Original formula */
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];          } /* End of if */
             }        ipmx +=1;
           }        sw += weight[i];
         }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
              if(globpr){
         for(i=(int)agemin; i <= (int)agemax+3; i++){          fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
           for(jk=1; jk <=nlstate ; jk++){   %10.6f %10.6f %10.6f ", \
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
               pp[jk] += freq[jk][m][i];                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           }          for(k=1,l=0.; k<=nlstate; k++) 
           for(jk=1; jk <=nlstate ; jk++){            fprintf(ficresilk," %10.6f",ll[k]);
             for(m=-1, pos=0; m <=0 ; m++)          fprintf(ficresilk,"\n");
             pos += freq[jk][m][i];        }
         }      } /* end of wave */
            } /* end of individual */
          for(jk=1; jk <=nlstate ; jk++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
              pp[jk] += freq[jk][m][i];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
          }    return -l;
            }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  
   
          for(jk=1; jk <=nlstate ; jk++){            void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpr, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
            if( i <= (int) agemax){  {
              if(pos>=1.e-5){    /* This routine should help understanding what is done with the selection of individuals/waves and
                probs[i][jk][j1]= pp[jk]/pos;       to check the exact contribution to the likelihood.
              }       Plotting could be done.
            }     */
          }    int k;
              if(globpr !=0){ /* Just counts and sums no printings */
         }      strcpy(fileresilk,"ilk"); 
     }      strcat(fileresilk,fileres);
   }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresilk);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      }
   free_vector(pp,1,nlstate);      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");
        fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight out sav ");
 }  /* End of Freq */      /*  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++) 
 /************* Waves Concatenation ***************/        fprintf(ficresilk," ll[%d]",k);
       fprintf(ficresilk,"\n");
 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.    *fretone=(*funcone)(p);
      Death is a valid wave (if date is known).    if(globpr !=0){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      fclose(ficresilk);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
      and mw[mi+1][i]. dh depends on stepm.        printf("Problem with html file: %s\n", optionfilehtm);
      */        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
         exit(0);
   int i, mi, m;      }
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      else{
      double sum=0., jmean=0.;*/        fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",fileresilk);
         fclose(fichtm);
   int j, k=0,jk, ju, jl;      }
   double sum=0.;    }
   jmin=1e+5;    return;
   jmax=-1;  }
   jmean=0.;  
   for(i=1; i<=imx; i++){  /*********** Maximum Likelihood Estimation ***************/
     mi=0;  
     m=firstpass;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     while(s[m][i] <= nlstate){  {
       if(s[m][i]>=1)    int i,j, iter;
         mw[++mi][i]=m;    double **xi;
       if(m >=lastpass)    double fret;
         break;    double fretone; /* Only one call to likelihood */
       else    char filerespow[FILENAMELENGTH];
         m++;    xi=matrix(1,npar,1,npar);
     }/* end while */    for (i=1;i<=npar;i++)
     if (s[m][i] > nlstate){      for (j=1;j<=npar;j++)
       mi++;     /* Death is another wave */        xi[i][j]=(i==j ? 1.0 : 0.0);
       /* if(mi==0)  never been interviewed correctly before death */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
          /* Only death is a correct wave */    strcpy(filerespow,"pow"); 
       mw[mi][i]=m;    strcat(filerespow,fileres);
     }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
     wav[i]=mi;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     if(mi==0)    }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   }    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
   for(i=1; i<=imx; i++){        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     for(mi=1; mi<wav[i];mi++){    fprintf(ficrespow,"\n");
       if (stepm <=0)  
         dh[mi][i]=1;    powell(p,xi,npar,ftol,&iter,&fret,func);
       else{  
         if (s[mw[mi+1][i]][i] > nlstate) {    fclose(ficrespow);
           if (agedc[i] < 2*AGESUP) {    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           if(j==0) j=1;  /* Survives at least one month after exam */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           k=k+1;  
           if (j >= jmax) jmax=j;  }
           if (j <= jmin) jmin=j;  
           sum=sum+j;  /**** Computes Hessian and covariance matrix ***/
           /* if (j<10) printf("j=%d num=%d ",j,i); */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           }  {
         }    double  **a,**y,*x,pd;
         else{    double **hess;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    int i, j,jk;
           k=k+1;    int *indx;
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;    double hessii(double p[], double delta, int theta, double delti[]);
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    double hessij(double p[], double delti[], int i, int j);
           sum=sum+j;    void lubksb(double **a, int npar, int *indx, double b[]) ;
         }    void ludcmp(double **a, int npar, int *indx, double *d) ;
         jk= j/stepm;  
         jl= j -jk*stepm;    hess=matrix(1,npar,1,npar);
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)    printf("\nCalculation of the hessian matrix. Wait...\n");
           dh[mi][i]=jk;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         else    for (i=1;i<=npar;i++){
           dh[mi][i]=jk+1;      printf("%d",i);fflush(stdout);
         if(dh[mi][i]==0)      fprintf(ficlog,"%d",i);fflush(ficlog);
           dh[mi][i]=1; /* At least one step */      hess[i][i]=hessii(p,ftolhess,i,delti);
       }      /*printf(" %f ",p[i]);*/
     }      /*printf(" %lf ",hess[i][i]);*/
   }    }
   jmean=sum/k;    
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    for (i=1;i<=npar;i++) {
  }      for (j=1;j<=npar;j++)  {
 /*********** Tricode ****************************/        if (j>i) { 
 void tricode(int *Tvar, int **nbcode, int imx)          printf(".%d%d",i,j);fflush(stdout);
 {          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   int Ndum[20],ij=1, k, j, i;          hess[i][j]=hessij(p,delti,i,j);
   int cptcode=0;          hess[j][i]=hess[i][j];    
   cptcoveff=0;          /*printf(" %lf ",hess[i][j]);*/
          }
   for (k=0; k<19; k++) Ndum[k]=0;      }
   for (k=1; k<=7; k++) ncodemax[k]=0;    }
     printf("\n");
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    fprintf(ficlog,"\n");
     for (i=1; i<=imx; i++) {  
       ij=(int)(covar[Tvar[j]][i]);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       Ndum[ij]++;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    
       if (ij > cptcode) cptcode=ij;    a=matrix(1,npar,1,npar);
     }    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
     for (i=0; i<=cptcode; i++) {    indx=ivector(1,npar);
       if(Ndum[i]!=0) ncodemax[j]++;    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ij=1;    ludcmp(a,npar,indx,&pd);
   
     for (j=1;j<=npar;j++) {
     for (i=1; i<=ncodemax[j]; i++) {      for (i=1;i<=npar;i++) x[i]=0;
       for (k=0; k<=19; k++) {      x[j]=1;
         if (Ndum[k] != 0) {      lubksb(a,npar,indx,x);
           nbcode[Tvar[j]][ij]=k;      for (i=1;i<=npar;i++){ 
           ij++;        matcov[i][j]=x[i];
         }      }
         if (ij > ncodemax[j]) break;    }
       }    
     }    printf("\n#Hessian matrix#\n");
   }      fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
  for (k=0; k<19; k++) Ndum[k]=0;      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
  for (i=1; i<=ncovmodel-2; i++) {        fprintf(ficlog,"%.3e ",hess[i][j]);
       ij=Tvar[i];      }
       Ndum[ij]++;      printf("\n");
     }      fprintf(ficlog,"\n");
     }
  ij=1;  
  for (i=1; i<=10; i++) {    /* Recompute Inverse */
    if((Ndum[i]!=0) && (i<=ncov)){    for (i=1;i<=npar;i++)
      Tvaraff[ij]=i;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      ij++;    ludcmp(a,npar,indx,&pd);
    }  
  }    /*  printf("\n#Hessian matrix recomputed#\n");
    
     cptcoveff=ij-1;    for (j=1;j<=npar;j++) {
 }      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
 /*********** Health Expectancies ****************/      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        y[i][j]=x[i];
 {        printf("%.3e ",y[i][j]);
   /* Health expectancies */        fprintf(ficlog,"%.3e ",y[i][j]);
   int i, j, nhstepm, hstepm, h;      }
   double age, agelim,hf;      printf("\n");
   double ***p3mat;      fprintf(ficlog,"\n");
      }
   fprintf(ficreseij,"# Health expectancies\n");    */
   fprintf(ficreseij,"# Age");  
   for(i=1; i<=nlstate;i++)    free_matrix(a,1,npar,1,npar);
     for(j=1; j<=nlstate;j++)    free_matrix(y,1,npar,1,npar);
       fprintf(ficreseij," %1d-%1d",i,j);    free_vector(x,1,npar);
   fprintf(ficreseij,"\n");    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
   hstepm=1*YEARM; /*  Every j years of age (in month) */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   }
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  /*************** hessian matrix ****************/
     /* nhstepm age range expressed in number of stepm */  double hessii( double x[], double delta, int theta, double delti[])
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  {
     /* Typically if 20 years = 20*12/6=40 stepm */    int i;
     if (stepm >= YEARM) hstepm=1;    int l=1, lmax=20;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    double k1,k2;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double p2[NPARMAX+1];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double res;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      double fx;
     int k=0,kmax=10;
     double l1;
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++)    fx=func(x);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    for (i=1;i<=npar;i++) p2[i]=x[i];
           eij[i][j][(int)age] +=p3mat[i][j][h];    for(l=0 ; l <=lmax; l++){
         }      l1=pow(10,l);
          delts=delt;
     hf=1;      for(k=1 ; k <kmax; k=k+1){
     if (stepm >= YEARM) hf=stepm/YEARM;        delt = delta*(l1*k);
     fprintf(ficreseij,"%.0f",age );        p2[theta]=x[theta] +delt;
     for(i=1; i<=nlstate;i++)        k1=func(p2)-fx;
       for(j=1; j<=nlstate;j++){        p2[theta]=x[theta]-delt;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);        k2=func(p2)-fx;
       }        /*res= (k1-2.0*fx+k2)/delt/delt; */
     fprintf(ficreseij,"\n");        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
   }  #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);
         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);
 /************ Variance ******************/  #endif
 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)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   /* Variance of health expectancies */          k=kmax;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        }
   double **newm;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   double **dnewm,**doldm;          k=kmax; l=lmax*10.;
   int i, j, nhstepm, hstepm, h;        }
   int k, cptcode;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   double *xp;          delts=delt;
   double **gp, **gm;        }
   double ***gradg, ***trgradg;      }
   double ***p3mat;    }
   double age,agelim;    delti[theta]=delts;
   int theta;    return res; 
     
    fprintf(ficresvij,"# Covariances of life expectancies\n");  }
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)  double hessij( double x[], double delti[], int thetai,int thetaj)
     for(j=1; j<=nlstate;j++)  {
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    int i;
   fprintf(ficresvij,"\n");    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
   xp=vector(1,npar);    double p2[NPARMAX+1];
   dnewm=matrix(1,nlstate,1,npar);    int k;
   doldm=matrix(1,nlstate,1,nlstate);  
      fx=func(x);
   hstepm=1*YEARM; /* Every year of age */    for (k=1; k<=2; k++) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for (i=1;i<=npar;i++) p2[i]=x[i];
   agelim = AGESUP;      p2[thetai]=x[thetai]+delti[thetai]/k;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      k1=func(p2)-fx;
     if (stepm >= YEARM) hstepm=1;    
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      p2[thetai]=x[thetai]+delti[thetai]/k;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      k2=func(p2)-fx;
     gp=matrix(0,nhstepm,1,nlstate);    
     gm=matrix(0,nhstepm,1,nlstate);      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(theta=1; theta <=npar; theta++){      k3=func(p2)-fx;
       for(i=1; i<=npar; i++){ /* Computes gradient */    
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      p2[thetai]=x[thetai]-delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        k4=func(p2)-fx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
       if (popbased==1) {      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         for(i=1; i<=nlstate;i++)      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);
           prlim[i][i]=probs[(int)age][i][ij];  #endif
       }    }
          return res;
       for(j=1; j<= nlstate; j++){  }
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  /************** Inverse of matrix **************/
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  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++) /* Computes gradient */    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); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    *d=1.0; 
     for (i=1;i<=n;i++) { 
       if (popbased==1) {      big=0.0; 
         for(i=1; i<=nlstate;i++)      for (j=1;j<=n;j++) 
           prlim[i][i]=probs[(int)age][i][ij];        if ((temp=fabs(a[i][j])) > big) big=temp; 
       }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
       for(j=1; j<= nlstate; j++){    } 
         for(h=0; h<=nhstepm; h++){    for (j=1;j<=n;j++) { 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for (i=1;i<j;i++) { 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        sum=a[i][j]; 
         }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       }        a[i][j]=sum; 
       } 
       for(j=1; j<= nlstate; j++)      big=0.0; 
         for(h=0; h<=nhstepm; h++){      for (i=j;i<=n;i++) { 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        sum=a[i][j]; 
         }        for (k=1;k<j;k++) 
     } /* End theta */          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
     for(h=0; h<=nhstepm; h++)          imax=i; 
       for(j=1; j<=nlstate;j++)        } 
         for(theta=1; theta <=npar; theta++)      } 
           trgradg[h][j][theta]=gradg[h][theta][j];      if (j != imax) { 
         for (k=1;k<=n;k++) { 
     for(i=1;i<=nlstate;i++)          dum=a[imax][k]; 
       for(j=1;j<=nlstate;j++)          a[imax][k]=a[j][k]; 
         vareij[i][j][(int)age] =0.;          a[j][k]=dum; 
     for(h=0;h<=nhstepm;h++){        } 
       for(k=0;k<=nhstepm;k++){        *d = -(*d); 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        vv[imax]=vv[j]; 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      } 
         for(i=1;i<=nlstate;i++)      indx[j]=imax; 
           for(j=1;j<=nlstate;j++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
             vareij[i][j][(int)age] += doldm[i][j];      if (j != n) { 
       }        dum=1.0/(a[j][j]); 
     }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     h=1;      } 
     if (stepm >= YEARM) h=stepm/YEARM;    } 
     fprintf(ficresvij,"%.0f ",age );    free_vector(vv,1,n);  /* Doesn't work */
     for(i=1; i<=nlstate;i++)  ;
       for(j=1; j<=nlstate;j++){  } 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  
       }  void lubksb(double **a, int n, int *indx, double b[]) 
     fprintf(ficresvij,"\n");  { 
     free_matrix(gp,0,nhstepm,1,nlstate);    int i,ii=0,ip,j; 
     free_matrix(gm,0,nhstepm,1,nlstate);    double sum; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);   
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    for (i=1;i<=n;i++) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      ip=indx[i]; 
   } /* End age */      sum=b[ip]; 
        b[ip]=b[i]; 
   free_vector(xp,1,npar);      if (ii) 
   free_matrix(doldm,1,nlstate,1,npar);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   free_matrix(dnewm,1,nlstate,1,nlstate);      else if (sum) ii=i; 
       b[i]=sum; 
 }    } 
     for (i=n;i>=1;i--) { 
 /************ Variance of prevlim ******************/      sum=b[i]; 
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 {      b[i]=sum/a[i][i]; 
   /* Variance of prevalence limit */    } 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  } 
   double **newm;  
   double **dnewm,**doldm;  /************ Frequencies ********************/
   int i, j, nhstepm, hstepm;  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)
   int k, cptcode;  {  /* Some frequencies */
   double *xp;    
   double *gp, *gm;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   double **gradg, **trgradg;    int first;
   double age,agelim;    double ***freq; /* Frequencies */
   int theta;    double *pp, **prop;
        double pos,posprop, k2, dateintsum=0,k2cpt=0;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    FILE *ficresp;
   fprintf(ficresvpl,"# Age");    char fileresp[FILENAMELENGTH];
   for(i=1; i<=nlstate;i++)    
       fprintf(ficresvpl," %1d-%1d",i,i);    pp=vector(1,nlstate);
   fprintf(ficresvpl,"\n");    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
   xp=vector(1,npar);    strcat(fileresp,fileres);
   dnewm=matrix(1,nlstate,1,npar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   doldm=matrix(1,nlstate,1,nlstate);      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   hstepm=1*YEARM; /* Every year of age */      exit(0);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    }
   agelim = AGESUP;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    j1=0;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    
     if (stepm >= YEARM) hstepm=1;    j=cptcoveff;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);    first=1;
     gm=vector(1,nlstate);  
     for(k1=1; k1<=j;k1++){
     for(theta=1; theta <=npar; theta++){      for(i1=1; i1<=ncodemax[k1];i1++){
       for(i=1; i<=npar; i++){ /* Computes gradient */        j1++;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       }          scanf("%d", i);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (i=-1; i<=nlstate+ndeath; i++)  
       for(i=1;i<=nlstate;i++)          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         gp[i] = prlim[i][i];            for(m=iagemin; m <= iagemax+3; m++)
                  freq[i][jk][m]=0;
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1; i<=nlstate; i++)  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(m=iagemin; m <= iagemax+3; m++)
       for(i=1;i<=nlstate;i++)          prop[i][m]=0;
         gm[i] = prlim[i][i];        
         dateintsum=0;
       for(i=1;i<=nlstate;i++)        k2cpt=0;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        for (i=1; i<=imx; i++) {
     } /* End theta */          bool=1;
           if  (cptcovn>0) {
     trgradg =matrix(1,nlstate,1,npar);            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for(j=1; j<=nlstate;j++)                bool=0;
       for(theta=1; theta <=npar; theta++)          }
         trgradg[j][theta]=gradg[theta][j];          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
     for(i=1;i<=nlstate;i++)              k2=anint[m][i]+(mint[m][i]/12.);
       varpl[i][(int)age] =0.;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     for(i=1;i<=nlstate;i++)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     fprintf(ficresvpl,"%.0f ",age );                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     for(i=1; i<=nlstate;i++)                }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));                
     fprintf(ficresvpl,"\n");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     free_vector(gp,1,nlstate);                  dateintsum=dateintsum+k2;
     free_vector(gm,1,nlstate);                  k2cpt++;
     free_matrix(gradg,1,npar,1,nlstate);                }
     free_matrix(trgradg,1,nlstate,1,npar);                /*}*/
   } /* End age */            }
           }
   free_vector(xp,1,npar);        }
   free_matrix(doldm,1,nlstate,1,npar);         
   free_matrix(dnewm,1,nlstate,1,nlstate);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
 }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
 /************ Variance of one-step probabilities  ******************/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          fprintf(ficresp, "**********\n#");
 {        }
   int i, j;        for(i=1; i<=nlstate;i++) 
   int k=0, cptcode;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double **dnewm,**doldm;        fprintf(ficresp, "\n");
   double *xp;        
   double *gp, *gm;        for(i=iagemin; i <= iagemax+3; i++){
   double **gradg, **trgradg;          if(i==iagemax+3){
   double age,agelim, cov[NCOVMAX];            fprintf(ficlog,"Total");
   int theta;          }else{
   char fileresprob[FILENAMELENGTH];            if(first==1){
               first=0;
   strcpy(fileresprob,"prob");              printf("See log file for details...\n");
   strcat(fileresprob,fileres);            }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            fprintf(ficlog,"Age %d", i);
     printf("Problem with resultfile: %s\n", fileresprob);          }
   }          for(jk=1; jk <=nlstate ; jk++){
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                pp[jk] += freq[jk][m][i]; 
           }
   xp=vector(1,npar);          for(jk=1; jk <=nlstate ; jk++){
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            for(m=-1, pos=0; m <=0 ; m++)
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));              pos += freq[jk][m][i];
              if(pp[jk]>=1.e-10){
   cov[1]=1;              if(first==1){
   for (age=bage; age<=fage; age ++){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     cov[2]=age;              }
     gradg=matrix(1,npar,1,9);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     trgradg=matrix(1,9,1,npar);            }else{
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              if(first==1)
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                  fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for(theta=1; theta <=npar; theta++){            }
       for(i=1; i<=npar; i++)          }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
                for(jk=1; jk <=nlstate ; jk++){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                  pp[jk] += freq[jk][m][i];
       k=0;          }       
       for(i=1; i<= (nlstate+ndeath); i++){          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         for(j=1; j<=(nlstate+ndeath);j++){            pos += pp[jk];
            k=k+1;            posprop += prop[jk][i];
           gp[k]=pmmij[i][j];          }
         }          for(jk=1; jk <=nlstate ; jk++){
       }            if(pos>=1.e-5){
               if(first==1)
       for(i=1; i<=npar; i++)                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                }else{
               if(first==1)
       pmij(pmmij,cov,ncovmodel,xp,nlstate);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       k=0;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(i=1; i<=(nlstate+ndeath); i++){            }
         for(j=1; j<=(nlstate+ndeath);j++){            if( i <= iagemax){
           k=k+1;              if(pos>=1.e-5){
           gm[k]=pmmij[i][j];                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
         }                /*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]);*/
                    }
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)              else
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     }            }
           }
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          
       for(theta=1; theta <=npar; theta++)          for(jk=-1; jk <=nlstate+ndeath; jk++)
       trgradg[j][theta]=gradg[theta][j];            for(m=-1; m <=nlstate+ndeath; m++)
                if(freq[jk][m][i] !=0 ) {
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);              if(first==1)
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
      pmij(pmmij,cov,ncovmodel,x,nlstate);              }
           if(i <= iagemax)
      k=0;            fprintf(ficresp,"\n");
      for(i=1; i<=(nlstate+ndeath); i++){          if(first==1)
        for(j=1; j<=(nlstate+ndeath);j++){            printf("Others in log...\n");
          k=k+1;          fprintf(ficlog,"\n");
          gm[k]=pmmij[i][j];        }
         }      }
      }    }
          dateintmean=dateintsum/k2cpt; 
      /*printf("\n%d ",(int)age);   
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    fclose(ficresp);
            free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
      }*/    /* End of Freq */
   }
   fprintf(ficresprob,"\n%d ",(int)age);  
   /************ Prevalence ********************/
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  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)
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  {  
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   }       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));   
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double ***freq; /* Frequencies */
 }    double *pp, **prop;
  free_vector(xp,1,npar);    double pos,posprop; 
 fclose(ficresprob);    double  y2; /* in fractional years */
  exit(0);    int iagemin, iagemax;
 }  
     iagemin= (int) agemin;
 /***********************************************/    iagemax= (int) agemax;
 /**************** Main Program *****************/    /*pp=vector(1,nlstate);*/
 /***********************************************/    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 int main(int argc, char *argv[])    j1=0;
 {    
     j=cptcoveff;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   double agedeb, agefin,hf;    
   double agemin=1.e20, agemax=-1.e20;    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   double fret;        j1++;
   double **xi,tmp,delta;        
         for (i=1; i<=nlstate; i++)  
   double dum; /* Dummy variable */          for(m=iagemin; m <= iagemax+3; m++)
   double ***p3mat;            prop[i][m]=0.0;
   int *indx;       
   char line[MAXLINE], linepar[MAXLINE];        for (i=1; i<=imx; i++) { /* Each individual */
   char title[MAXLINE];          bool=1;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];          if  (cptcovn>0) {
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];                bool=0;
           } 
   char filerest[FILENAMELENGTH];          if (bool==1) { 
   char fileregp[FILENAMELENGTH];            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   char popfile[FILENAMELENGTH];              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   int firstobs=1, lastobs=10;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   int sdeb, sfin; /* Status at beginning and end */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   int c,  h , cpt,l;                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); 
   int ju,jl, mi;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                  /*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]]);*/
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   int mobilav=0,popforecast=0;                  prop[s[m][i]][iagemax+3] += weight[i]; 
   int hstepm, nhstepm;                } 
   int *popage;/*boolprev=0 if date and zero if wave*/              }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;            } /* end selection of waves */
           }
   double bage, fage, age, agelim, agebase;        }
   double ftolpl=FTOL;        for(i=iagemin; i <= iagemax+3; i++){  
   double **prlim;          
   double *severity;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   double ***param; /* Matrix of parameters */            posprop += prop[jk][i]; 
   double  *p;          } 
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */          for(jk=1; jk <=nlstate ; jk++){     
   double *delti; /* Scale */            if( i <=  iagemax){ 
   double ***eij, ***vareij;              if(posprop>=1.e-5){ 
   double **varpl; /* Variances of prevalence limits by age */                probs[i][jk][j1]= prop[jk][i]/posprop;
   double *epj, vepp;              } 
   double kk1, kk2;            } 
   double *popeffectif,*popcount;          }/* end jk */ 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;        }/* end i */ 
   double yp,yp1,yp2;      } /* end i1 */
     } /* end k1 */
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";    
   char *alph[]={"a","a","b","c","d","e"}, str[4];    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   char z[1]="c", occ;  }  /* End of prevalence */
 #include <sys/time.h>  
 #include <time.h>  /************* Waves Concatenation ***************/
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
    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)
   /* long total_usecs;  {
   struct timeval start_time, end_time;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         Death is a valid wave (if date is known).
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
   printf("\n%s",version);       */
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");    int i, mi, m;
     scanf("%s",pathtot);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   }       double sum=0., jmean=0.;*/
   else{    int first;
     strcpy(pathtot,argv[1]);    int j, k=0,jk, ju, jl;
   }    double sum=0.;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    first=0;
   /*cygwin_split_path(pathtot,path,optionfile);    jmin=1e+5;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    jmax=-1;
   /* cutv(path,optionfile,pathtot,'\\');*/    jmean=0.;
     for(i=1; i<=imx; i++){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      mi=0;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      m=firstpass;
   chdir(path);      while(s[m][i] <= nlstate){
   replace(pathc,path);        if(s[m][i]>=1)
           mw[++mi][i]=m;
 /*-------- arguments in the command line --------*/        if(m >=lastpass)
           break;
   strcpy(fileres,"r");        else
   strcat(fileres, optionfilefiname);          m++;
   strcat(fileres,".txt");    /* Other files have txt extension */      }/* end while */
       if (s[m][i] > nlstate){
   /*---------arguments file --------*/        mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {           /* Only death is a correct wave */
     printf("Problem with optionfile %s\n",optionfile);        mw[mi][i]=m;
     goto end;      }
   }  
       wav[i]=mi;
   strcpy(filereso,"o");      if(mi==0){
   strcat(filereso,fileres);        if(first==0){
   if((ficparo=fopen(filereso,"w"))==NULL) {          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          first=1;
   }        }
         if(first==1){
   /* Reads comments: lines beginning with '#' */          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);      } /* end mi==0 */
     fgets(line, MAXLINE, ficpar);    } /* End individuals */
     puts(line);  
     fputs(line,ficparo);    for(i=1; i<=imx; i++){
   }      for(mi=1; mi<wav[i];mi++){
   ungetc(c,ficpar);        if (stepm <=0)
           dh[mi][i]=1;
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        else{
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);            if (agedc[i] < 2*AGESUP) {
 while((c=getc(ficpar))=='#' && c!= EOF){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     ungetc(c,ficpar);              if(j==0) j=1;  /* Survives at least one month after exam */
     fgets(line, MAXLINE, ficpar);              else if(j<0){
     puts(line);                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]);
     fputs(line,ficparo);                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);
   ungetc(c,ficpar);                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]);
                  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);
                  }
   covar=matrix(0,NCOVMAX,1,n);              k=k+1;
   cptcovn=0;              if (j >= jmax) jmax=j;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;              if (j <= jmin) jmin=j;
               sum=sum+j;
   ncovmodel=2+cptcovn;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
              }
   /* Read guess parameters */          }
   /* Reads comments: lines beginning with '#' */          else{
   while((c=getc(ficpar))=='#' && c!= EOF){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     ungetc(c,ficpar);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     fgets(line, MAXLINE, ficpar);            k=k+1;
     puts(line);            if (j >= jmax) jmax=j;
     fputs(line,ficparo);            else if (j <= jmin)jmin=j;
   }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   ungetc(c,ficpar);            /*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]);*/
              if(j<0){
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              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]);
     for(i=1; i <=nlstate; 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]);
     for(j=1; j <=nlstate+ndeath-1; j++){            }
       fscanf(ficpar,"%1d%1d",&i1,&j1);            sum=sum+j;
       fprintf(ficparo,"%1d%1d",i1,j1);          }
       printf("%1d%1d",i,j);          jk= j/stepm;
       for(k=1; k<=ncovmodel;k++){          jl= j -jk*stepm;
         fscanf(ficpar," %lf",&param[i][j][k]);          ju= j -(jk+1)*stepm;
         printf(" %lf",param[i][j][k]);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         fprintf(ficparo," %lf",param[i][j][k]);            if(jl==0){
       }              dh[mi][i]=jk;
       fscanf(ficpar,"\n");              bh[mi][i]=0;
       printf("\n");            }else{ /* We want a negative bias in order to only have interpolation ie
       fprintf(ficparo,"\n");                    * at the price of an extra matrix product in likelihood */
     }              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            }
           }else{
   p=param[1][1];            if(jl <= -ju){
                dh[mi][i]=jk;
   /* Reads comments: lines beginning with '#' */              bh[mi][i]=jl;       /* bias is positive if real duration
   while((c=getc(ficpar))=='#' && c!= EOF){                                   * is higher than the multiple of stepm and negative otherwise.
     ungetc(c,ficpar);                                   */
     fgets(line, MAXLINE, ficpar);            }
     puts(line);            else{
     fputs(line,ficparo);              dh[mi][i]=jk+1;
   }              bh[mi][i]=ju;
   ungetc(c,ficpar);            }
             if(dh[mi][i]==0){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              dh[mi][i]=1; /* At least one step */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */              bh[mi][i]=ju; /* At least one step */
   for(i=1; i <=nlstate; i++){              /*  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);*/
     for(j=1; j <=nlstate+ndeath-1; j++){            }
       fscanf(ficpar,"%1d%1d",&i1,&j1);          } /* end if mle */
       printf("%1d%1d",i,j);        }
       fprintf(ficparo,"%1d%1d",i1,j1);      } /* end wave */
       for(k=1; k<=ncovmodel;k++){    }
         fscanf(ficpar,"%le",&delti3[i][j][k]);    jmean=sum/k;
         printf(" %le",delti3[i][j][k]);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         fprintf(ficparo," %le",delti3[i][j][k]);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       }   }
       fscanf(ficpar,"\n");  
       printf("\n");  /*********** Tricode ****************************/
       fprintf(ficparo,"\n");  void tricode(int *Tvar, int **nbcode, int imx)
     }  {
   }    
   delti=delti3[1][1];    int Ndum[20],ij=1, k, j, i, maxncov=19;
      int cptcode=0;
   /* Reads comments: lines beginning with '#' */    cptcoveff=0; 
   while((c=getc(ficpar))=='#' && c!= EOF){   
     ungetc(c,ficpar);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     fgets(line, MAXLINE, ficpar);    for (k=1; k<=7; k++) ncodemax[k]=0;
     puts(line);  
     fputs(line,ficparo);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   ungetc(c,ficpar);                                 modality*/ 
          ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   matcov=matrix(1,npar,1,npar);        Ndum[ij]++; /*store the modality */
   for(i=1; i <=npar; i++){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     fscanf(ficpar,"%s",&str);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     printf("%s",str);                                         Tvar[j]. If V=sex and male is 0 and 
     fprintf(ficparo,"%s",str);                                         female is 1, then  cptcode=1.*/
     for(j=1; j <=i; j++){      }
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);      for (i=0; i<=cptcode; i++) {
       fprintf(ficparo," %.5le",matcov[i][j]);        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 */
     }      }
     fscanf(ficpar,"\n");  
     printf("\n");      ij=1; 
     fprintf(ficparo,"\n");      for (i=1; i<=ncodemax[j]; i++) {
   }        for (k=0; k<= maxncov; k++) {
   for(i=1; i <=npar; i++)          if (Ndum[k] != 0) {
     for(j=i+1;j<=npar;j++)            nbcode[Tvar[j]][ij]=k; 
       matcov[i][j]=matcov[j][i];            /* 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; */
                
   printf("\n");            ij++;
           }
           if (ij > ncodemax[j]) break; 
     /*-------- data file ----------*/        }  
     if((ficres =fopen(fileres,"w"))==NULL) {      } 
       printf("Problem with resultfile: %s\n", fileres);goto end;    }  
     }  
     fprintf(ficres,"#%s\n",version);   for (k=0; k< maxncov; k++) Ndum[k]=0;
      
     if((fic=fopen(datafile,"r"))==NULL)    {   for (i=1; i<=ncovmodel-2; i++) { 
       printf("Problem with datafile: %s\n", datafile);goto end;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     }     ij=Tvar[i];
      Ndum[ij]++;
     n= lastobs;   }
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);   ij=1;
     num=ivector(1,n);   for (i=1; i<= maxncov; i++) {
     moisnais=vector(1,n);     if((Ndum[i]!=0) && (i<=ncovcol)){
     annais=vector(1,n);       Tvaraff[ij]=i; /*For printing */
     moisdc=vector(1,n);       ij++;
     andc=vector(1,n);     }
     agedc=vector(1,n);   }
     cod=ivector(1,n);   
     weight=vector(1,n);   cptcoveff=ij-1; /*Number of simple covariates*/
     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);  /*********** Health Expectancies ****************/
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,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 )
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);  {
     /* Health expectancies */
     i=1;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     while (fgets(line, MAXLINE, fic) != NULL)    {    double age, agelim, hf;
       if ((i >= firstobs) && (i <=lastobs)) {    double ***p3mat,***varhe;
            double **dnewm,**doldm;
         for (j=maxwav;j>=1;j--){    double *xp;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    double **gp, **gm;
           strcpy(line,stra);    double ***gradg, ***trgradg;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    int theta;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
            xp=vector(1,npar);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    dnewm=matrix(1,nlstate*nlstate,1,npar);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficreseij,"# Health expectancies\n");
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      for(j=1; j<=nlstate;j++)
         for (j=ncov;j>=1;j--){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficreseij,"\n");
         }  
         num[i]=atol(stra);    if(estepm < stepm){
              printf ("Problem %d lower than %d\n",estepm, stepm);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    }
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
         i=i+1;     * This is mainly to measure the difference between two models: for example
       }     * if stepm=24 months pijx are given only every 2 years and by summing them
     }     * we are calculating an estimate of the Life Expectancy assuming a linear 
     /* printf("ii=%d", ij);     * progression in between and thus overestimating or underestimating according
        scanf("%d",i);*/     * to the curvature of the survival function. If, for the same date, we 
   imx=i-1; /* Number of individuals */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
   /* for (i=1; i<=imx; i++){     * hypothesis. A more precise result, taking into account a more precise
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;     * curvature will be obtained if estepm is as small as stepm. */
     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 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 
     for (i=1; i<=imx; i++)       nstepm is the number of stepm from age to agelin. 
     if (covar[1][i]==0) 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]));*/       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
   /* Calculation of the number of parameter from char model*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   Tvar=ivector(1,15);       survival function given by stepm (the optimization length). Unfortunately it
   Tprod=ivector(1,15);       means that if the survival funtion is printed only each two years of age and if
   Tvaraff=ivector(1,15);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   Tvard=imatrix(1,15,1,2);       results. So we changed our mind and took the option of the best precision.
   Tage=ivector(1,15);          */
        hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;    agelim=AGESUP;
     j=nbocc(model,'+');    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     j1=nbocc(model,'*');      /* nhstepm age range expressed in number of stepm */
     cptcovn=j+1;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     cptcovprod=j1;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
          /* if (stepm >= YEARM) hstepm=1;*/
          nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     strcpy(modelsav,model);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       printf("Error. Non available option model=%s ",model);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       goto end;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     }  
          /* Computed by stepm unit matrices, product of hstepm matrices, stored
     for(i=(j+1); i>=1;i--){         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       cutv(stra,strb,modelsav,'+');      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);   
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');      /* Computing Variances of health expectancies */
         if (strcmp(strc,"age")==0) {  
           cptcovprod--;       for(theta=1; theta <=npar; theta++){
           cutv(strb,stre,strd,'V');        for(i=1; i<=npar; i++){ 
           Tvar[i]=atoi(stre);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           cptcovage++;        }
             Tage[cptcovage]=i;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             /*printf("stre=%s ", stre);*/    
         }        cptj=0;
         else if (strcmp(strd,"age")==0) {        for(j=1; j<= nlstate; j++){
           cptcovprod--;          for(i=1; i<=nlstate; i++){
           cutv(strb,stre,strc,'V');            cptj=cptj+1;
           Tvar[i]=atoi(stre);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           cptcovage++;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           Tage[cptcovage]=i;            }
         }          }
         else {        }
           cutv(strb,stre,strc,'V');       
           Tvar[i]=ncov+k1;       
           cutv(strb,strc,strd,'V');        for(i=1; i<=npar; i++) 
           Tprod[k1]=i;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           Tvard[k1][1]=atoi(strc);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           Tvard[k1][2]=atoi(stre);        
           Tvar[cptcovn+k2]=Tvard[k1][1];        cptj=0;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        for(j=1; j<= nlstate; j++){
           for (k=1; k<=lastobs;k++)          for(i=1;i<=nlstate;i++){
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            cptj=cptj+1;
           k1++;            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
           k2=k2+2;  
         }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       }            }
       else {          }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        }
        /*  scanf("%d",i);*/        for(j=1; j<= nlstate*nlstate; j++)
       cutv(strd,strc,strb,'V');          for(h=0; h<=nhstepm-1; h++){
       Tvar[i]=atoi(strc);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       }          }
       strcpy(modelsav,stra);         } 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);     
         scanf("%d",i);*/  /* End theta */
     }  
 }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
    
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);       for(h=0; h<=nhstepm-1; h++)
   printf("cptcovprod=%d ", cptcovprod);        for(j=1; j<=nlstate*nlstate;j++)
   scanf("%d ",i);*/          for(theta=1; theta <=npar; theta++)
     fclose(fic);            trgradg[h][j][theta]=gradg[h][theta][j];
        
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/       for(i=1;i<=nlstate*nlstate;i++)
       for(i=1;i<=n;i++) weight[i]=1.0;        for(j=1;j<=nlstate*nlstate;j++)
     }          varhe[i][j][(int)age] =0.;
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
    for (i=1; i<=imx; i++)       for(h=0;h<=nhstepm-1;h++){
      for(m=2; (m<= maxwav); m++)        for(k=0;k<=nhstepm-1;k++){
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
          anint[m][i]=9999;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
          s[m][i]=-1;          for(i=1;i<=nlstate*nlstate;i++)
        }            for(j=1;j<=nlstate*nlstate;j++)
                  varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     for (i=1; i<=imx; i++)  {        }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      }
       for(m=1; (m<= maxwav); m++){      /* Computing expectancies */
         if(s[m][i] >0){      for(i=1; i<=nlstate;i++)
           if (s[m][i] == nlstate+1) {        for(j=1; j<=nlstate;j++)
             if(agedc[i]>0)          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
               if(moisdc[i]!=99 && andc[i]!=9999)            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
               agev[m][i]=agedc[i];            
             else {  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
               if (andc[i]!=9999){  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          }
               agev[m][i]=-1;  
               }      fprintf(ficreseij,"%3.0f",age );
             }      cptj=0;
           }      for(i=1; i<=nlstate;i++)
           else if(s[m][i] !=9){ /* Should no more exist */        for(j=1; j<=nlstate;j++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          cptj++;
             if(mint[m][i]==99 || anint[m][i]==9999)          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
               agev[m][i]=1;        }
             else if(agev[m][i] <agemin){      fprintf(ficreseij,"\n");
               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);*/      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
             }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
             else if(agev[m][i] >agemax){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
               agemax=agev[m][i];      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             }    }
             /*agev[m][i]=anint[m][i]-annais[i];*/    printf("\n");
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(ficlog,"\n");
           }  
           else { /* =9 */    free_vector(xp,1,npar);
             agev[m][i]=1;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
             s[m][i]=-1;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         }  }
         else /*= 0 Unknown */  
           agev[m][i]=1;  /************ Variance ******************/
       }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
      {
     }    /* Variance of health expectancies */
     for (i=1; i<=imx; i++)  {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       for(m=1; (m<= maxwav); m++){    /* double **newm;*/
         if (s[m][i] > (nlstate+ndeath)) {    double **dnewm,**doldm;
           printf("Error: Wrong value in nlstate or ndeath\n");      double **dnewmp,**doldmp;
           goto end;    int i, j, nhstepm, hstepm, h, nstepm ;
         }    int k, cptcode;
       }    double *xp;
     }    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     free_vector(severity,1,maxwav);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     free_imatrix(outcome,1,maxwav+1,1,n);    double ***p3mat;
     free_vector(moisnais,1,n);    double age,agelim, hf;
     free_vector(annais,1,n);    double ***mobaverage;
     /* free_matrix(mint,1,maxwav,1,n);    int theta;
        free_matrix(anint,1,maxwav,1,n);*/    char digit[4];
     free_vector(moisdc,1,n);    char digitp[25];
     free_vector(andc,1,n);  
     char fileresprobmorprev[FILENAMELENGTH];
      
     wav=ivector(1,imx);    if(popbased==1){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      if(mobilav!=0)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        strcpy(digitp,"-populbased-mobilav-");
          else strcpy(digitp,"-populbased-nomobil-");
     /* Concatenates waves */    }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    else 
       strcpy(digitp,"-stablbased-");
   
       Tcode=ivector(1,100);    if (mobilav!=0) {
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       ncodemax[1]=1;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
              printf(" Error in movingaverage mobilav=%d\n",mobilav);
    codtab=imatrix(1,100,1,10);      }
    h=0;    }
    m=pow(2,cptcoveff);  
      strcpy(fileresprobmorprev,"prmorprev"); 
    for(k=1;k<=cptcoveff; k++){    sprintf(digit,"%-d",ij);
      for(i=1; i <=(m/pow(2,k));i++){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
        for(j=1; j <= ncodemax[k]; j++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
            h++;    strcat(fileresprobmorprev,fileres);
            if (h>m) h=1;codtab[h][k]=j;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
          }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }    }
    }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
    /*for(i=1; i <=m ;i++){    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      for(k=1; k <=cptcovn; k++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);      fprintf(ficresprobmorprev," p.%-d SE",j);
      }      for(i=1; i<=nlstate;i++)
      printf("\n");        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
    }    }  
    scanf("%d",i);*/    fprintf(ficresprobmorprev,"\n");
        if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
    /* Calculates basic frequencies. Computes observed prevalence at single age      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
        and prints on file fileres'p'. */      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
        }
        else{
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficgp,"\n# Routine varevsij");
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf("Problem with html file: %s\n", optionfilehtm);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
            exit(0);
     /* 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] */    else{
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      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);
     if(mle==1){    }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     }  
        fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
     /*--------- results files --------------*/    fprintf(ficresvij,"# Age");
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
    jk=1;    fprintf(ficresvij,"\n");
    fprintf(ficres,"# Parameters\n");  
    printf("# Parameters\n");    xp=vector(1,npar);
    for(i=1,jk=1; i <=nlstate; i++){    dnewm=matrix(1,nlstate,1,npar);
      for(k=1; k <=(nlstate+ndeath); k++){    doldm=matrix(1,nlstate,1,nlstate);
        if (k != i)    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
          {    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
            for(j=1; j <=ncovmodel; j++){    gpp=vector(nlstate+1,nlstate+ndeath);
              printf("%f ",p[jk]);    gmp=vector(nlstate+1,nlstate+ndeath);
              fprintf(ficres,"%f ",p[jk]);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
              jk++;    
            }    if(estepm < stepm){
            printf("\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
            fprintf(ficres,"\n");    }
          }    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. 
  if(mle==1){       nhstepm is the number of hstepm from age to agelim 
     /* Computing hessian and covariance matrix */       nstepm is the number of stepm from age to agelin. 
     ftolhess=ftol; /* Usually correct */       Look at hpijx to understand the reason of that which relies in memory size
     hesscov(matcov, p, npar, delti, ftolhess, func);       and note for a fixed period like k years */
  }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     fprintf(ficres,"# Scales\n");       survival function given by stepm (the optimization length). Unfortunately it
     printf("# Scales\n");       means that if the survival funtion is printed every two years of age and if
      for(i=1,jk=1; i <=nlstate; i++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for(j=1; j <=nlstate+ndeath; j++){       results. So we changed our mind and took the option of the best precision.
         if (j!=i) {    */
           fprintf(ficres,"%1d%1d",i,j);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           printf("%1d%1d",i,j);    agelim = AGESUP;
           for(k=1; k<=ncovmodel;k++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             printf(" %.5e",delti[jk]);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             fprintf(ficres," %.5e",delti[jk]);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
             jk++;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           printf("\n");      gp=matrix(0,nhstepm,1,nlstate);
           fprintf(ficres,"\n");      gm=matrix(0,nhstepm,1,nlstate);
         }  
       }  
      }      for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     k=1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     fprintf(ficres,"# Covariance\n");        }
     printf("# Covariance\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for(i=1;i<=npar;i++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;        if (popbased==1) {
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          if(mobilav ==0){
       printf("%s%d%d",alph[k],i1,tab[i]);*/            for(i=1; i<=nlstate;i++)
       fprintf(ficres,"%3d",i);              prlim[i][i]=probs[(int)age][i][ij];
       printf("%3d",i);          }else{ /* mobilav */ 
       for(j=1; j<=i;j++){            for(i=1; i<=nlstate;i++)
         fprintf(ficres," %.5e",matcov[i][j]);              prlim[i][i]=mobaverage[(int)age][i][ij];
         printf(" %.5e",matcov[i][j]);          }
       }        }
       fprintf(ficres,"\n");    
       printf("\n");        for(j=1; j<= nlstate; j++){
       k++;          for(h=0; h<=nhstepm; h++){
     }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                  gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     while((c=getc(ficpar))=='#' && c!= EOF){          }
       ungetc(c,ficpar);        }
       fgets(line, MAXLINE, ficpar);        /* This for computing probability of death (h=1 means
       puts(line);           computed over hstepm matrices product = hstepm*stepm months) 
       fputs(line,ficparo);           as a weighted average of prlim.
     }        */
     ungetc(c,ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gpp[j]=0.; i<= nlstate; i++)
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
            }    
     if (fage <= 2) {        /* end probability of death */
       bage = agemin;  
       fage = agemax;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);   
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        if (popbased==1) {
            if(mobilav ==0){
     while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);              prlim[i][i]=probs[(int)age][i][ij];
     fgets(line, MAXLINE, ficpar);          }else{ /* mobilav */ 
     puts(line);            for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   ungetc(c,ficpar);        }
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);        for(j=1; j<= nlstate; j++){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          for(h=0; h<=nhstepm; h++){
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                    gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        /* This for computing probability of death (h=1 means
     puts(line);           computed over hstepm matrices product = hstepm*stepm months) 
     fputs(line,ficparo);           as a weighted average of prlim.
   }        */
   ungetc(c,ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        }    
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        /* end probability of death */
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);        for(j=1; j<= nlstate; j++) /* vareij */
    fprintf(ficparo,"pop_based=%d\n",popbased);            for(h=0; h<=nhstepm; h++){
    fprintf(ficres,"pop_based=%d\n",popbased);              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     fgets(line, MAXLINE, ficpar);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     puts(line);        }
     fputs(line,ficparo);  
   }      } /* End theta */
   ungetc(c,ficpar);  
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);  
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
      
     /*------------ gnuplot -------------*/      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     /*chdir(pathcd);*/        for(theta=1; theta <=npar; theta++)
     strcpy(optionfilegnuplot,optionfilefiname);          trgradgp[j][theta]=gradgp[theta][j];
     strcat(optionfilegnuplot,".plt");    
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
       printf("Problem with file %s",optionfilegnuplot);goto end;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     }      for(i=1;i<=nlstate;i++)
 #ifdef windows        for(j=1;j<=nlstate;j++)
     fprintf(ficgp,"cd \"%s\" \n",pathc);          vareij[i][j][(int)age] =0.;
 #endif  
 m=pow(2,cptcoveff);      for(h=0;h<=nhstepm;h++){
          for(k=0;k<=nhstepm;k++){
  /* 1eme*/          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   for (cpt=1; cpt<= nlstate ; cpt ++) {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
    for (k1=1; k1<= m ; k1 ++) {          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
 #ifdef windows              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);        }
 #endif      }
 #ifdef unix    
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      /* pptj */
 #endif      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
 for (i=1; i<= nlstate ; i ++) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          varppt[j][i]=doldmp[j][i];
 }      /* end ppptj */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      /*  x centered again */
     for (i=1; i<= nlstate ; i ++) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }      if (popbased==1) {
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        if(mobilav ==0){
      for (i=1; i<= nlstate ; i ++) {          for(i=1; i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            prlim[i][i]=probs[(int)age][i][ij];
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }else{ /* mobilav */ 
 }            for(i=1; i<=nlstate;i++)
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            prlim[i][i]=mobaverage[(int)age][i][ij];
 #ifdef unix        }
 fprintf(ficgp,"\nset ter gif small size 400,300");      }
 #endif               
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      /* This for computing probability of death (h=1 means
    }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   }         as a weighted average of prlim.
   /*2 eme*/      */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
   for (k1=1; k1<= m ; k1 ++) {        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
          }    
     for (i=1; i<= nlstate+1 ; i ++) {      /* end probability of death */
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for (j=1; j<= nlstate+1 ; j ++) {      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=1; i<=nlstate;i++){
 }            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      } 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficresprobmorprev,"\n");
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficresvij,"%.0f ",age );
         else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i=1; i<=nlstate;i++)
 }          for(j=1; j<=nlstate;j++){
       fprintf(ficgp,"\" t\"\" w l 0,");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
      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 ++) {      fprintf(ficresvij,"\n");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      free_matrix(gp,0,nhstepm,1,nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      free_matrix(gm,0,nhstepm,1,nlstate);
 }        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       else fprintf(ficgp,"\" t\"\" w l 0,");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    } /* End age */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    free_vector(gpp,nlstate+1,nlstate+ndeath);
   }    free_vector(gmp,nlstate+1,nlstate+ndeath);
      free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   /*3eme*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   for (k1=1; k1<= m ; k1 ++) {    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     for (cpt=1; cpt<= nlstate ; cpt ++) {    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       k=2+nlstate*(cpt-1);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       for (i=1; i< nlstate ; i ++) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    fprintf(ficgp,"\n 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);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
     }    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
      /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   /* CV preval stat */  */
   for (k1=1; k1<= m ; k1 ++) {    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;    free_vector(xp,1,npar);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    free_matrix(doldm,1,nlstate,1,nlstate);
       for (i=1; i< nlstate ; i ++)    free_matrix(dnewm,1,nlstate,1,npar);
         fprintf(ficgp,"+$%d",k+i+1);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
          free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       l=3+(nlstate+ndeath)*cpt;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    fclose(ficresprobmorprev);
       for (i=1; i< nlstate ; i ++) {    fclose(ficgp);
         l=3+(nlstate+ndeath)*cpt;    fclose(fichtm);
         fprintf(ficgp,"+$%d",l+i+1);  }  /* end varevsij */
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    /************ Variance of prevlim ******************/
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  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 */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   /* proba elementaires */    double **newm;
    for(i=1,jk=1; i <=nlstate; i++){    double **dnewm,**doldm;
     for(k=1; k <=(nlstate+ndeath); k++){    int i, j, nhstepm, hstepm;
       if (k != i) {    int k, cptcode;
         for(j=1; j <=ncovmodel; j++){    double *xp;
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    double *gp, *gm;
           /*fprintf(ficgp,"%s",alph[1]);*/    double **gradg, **trgradg;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    double age,agelim;
           jk++;    int theta;
           fprintf(ficgp,"\n");     
         }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
       }    fprintf(ficresvpl,"# Age");
     }    for(i=1; i<=nlstate;i++)
     }        fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   for(jk=1; jk <=m; jk++) {  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    xp=vector(1,npar);
    i=1;    dnewm=matrix(1,nlstate,1,npar);
    for(k2=1; k2<=nlstate; k2++) {    doldm=matrix(1,nlstate,1,nlstate);
      k3=i;    
      for(k=1; k<=(nlstate+ndeath); k++) {    hstepm=1*YEARM; /* Every year of age */
        if (k != k2){    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    agelim = AGESUP;
 ij=1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         for(j=3; j <=ncovmodel; j++) {      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      if (stepm >= YEARM) hstepm=1;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
             ij++;      gradg=matrix(1,npar,1,nlstate);
           }      gp=vector(1,nlstate);
           else      gm=vector(1,nlstate);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
         }      for(theta=1; theta <=npar; theta++){
           fprintf(ficgp,")/(1");        for(i=1; i<=npar; i++){ /* Computes gradient */
                  xp[i] = x[i] + (i==theta ?delti[theta]:0);
         for(k1=1; k1 <=nlstate; k1++){          }
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 ij=1;        for(i=1;i<=nlstate;i++)
           for(j=3; j <=ncovmodel; j++){          gp[i] = prlim[i][i];
           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]]]);        for(i=1; i<=npar; i++) /* Computes gradient */
             ij++;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           else        for(i=1;i<=nlstate;i++)
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          gm[i] = prlim[i][i];
           }  
           fprintf(ficgp,")");        for(i=1;i<=nlstate;i++)
         }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      } /* End theta */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
         i=i+ncovmodel;      trgradg =matrix(1,nlstate,1,npar);
        }  
      }      for(j=1; j<=nlstate;j++)
    }        for(theta=1; theta <=npar; theta++)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          trgradg[j][theta]=gradg[theta][j];
   }  
          for(i=1;i<=nlstate;i++)
   fclose(ficgp);        varpl[i][(int)age] =0.;
   /* end gnuplot */      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 chdir(path);      for(i=1;i<=nlstate;i++)
            varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     free_ivector(wav,1,imx);  
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      fprintf(ficresvpl,"%.0f ",age );
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        for(i=1; i<=nlstate;i++)
     free_ivector(num,1,n);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     free_vector(agedc,1,n);      fprintf(ficresvpl,"\n");
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      free_vector(gp,1,nlstate);
     fclose(ficparo);      free_vector(gm,1,nlstate);
     fclose(ficres);      free_matrix(gradg,1,npar,1,nlstate);
     /*  }*/      free_matrix(trgradg,1,nlstate,1,npar);
        } /* End age */
    /*________fin mle=1_________*/  
        free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
      free_matrix(dnewm,1,nlstate,1,nlstate);
     /* No more information from the sample is required now */  
   /* Reads comments: lines beginning with '#' */  }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /************ Variance of one-step probabilities  ******************/
     fgets(line, MAXLINE, ficpar);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
     puts(line);  {
     fputs(line,ficparo);    int i, j=0,  i1, k1, l1, t, tj;
   }    int k2, l2, j1,  z1;
   ungetc(c,ficpar);    int k=0,l, cptcode;
      int first=1, first1;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    double **dnewm,**doldm;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    double *xp;
 /*--------- index.htm --------*/    double *gp, *gm;
     double **gradg, **trgradg;
   strcpy(optionfilehtm,optionfile);    double **mu;
   strcat(optionfilehtm,".htm");    double age,agelim, cov[NCOVMAX];
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     printf("Problem with %s \n",optionfilehtm);goto end;    int theta;
   }    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    char fileresprobcor[FILENAMELENGTH];
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  
 Total number of observations=%d <br>    double ***varpij;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  
 <hr  size=\"2\" color=\"#EC5E5E\">    strcpy(fileresprob,"prob"); 
 <li>Outputs files<br><br>\n    strcat(fileresprob,fileres);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>      printf("Problem with resultfile: %s\n", fileresprob);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    }
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    strcpy(fileresprobcov,"probcov"); 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    strcat(fileresprobcov,fileres);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      printf("Problem with resultfile: %s\n", fileresprobcov);
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    }
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
  fprintf(fichtm," <li>Graphs</li><p>");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
  m=cptcoveff;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
  j1=0;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
  for(k1=1; k1<=m;k1++){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
        j1++;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
        if (cptcovn > 0) {    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    
          for (cpt=1; cpt<=cptcoveff;cpt++)    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    fprintf(ficresprob,"# Age");
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
        }    fprintf(ficresprobcov,"# Age");
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        fprintf(ficresprobcov,"# Age");
        for(cpt=1; cpt<nlstate;cpt++){  
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    for(i=1; i<=nlstate;i++)
        }      for(j=1; j<=(nlstate+ndeath);j++){
     for(cpt=1; cpt<=nlstate;cpt++) {        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        fprintf(ficresprobcov," p%1d-%1d ",i,j);
 interval) in state (%d): v%s%d%d.gif <br>        fprintf(ficresprobcor," p%1d-%1d ",i,j);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        }  
      }   /* fprintf(ficresprob,"\n");
      for(cpt=1; cpt<=nlstate;cpt++) {    fprintf(ficresprobcov,"\n");
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    fprintf(ficresprobcor,"\n");
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);   */
      }   xp=vector(1,npar);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 health expectancies in states (1) and (2): e%s%d.gif<br>    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
 fprintf(fichtm,"\n</body>");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
    }    first=1;
  }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 fclose(fichtm);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   /*--------------- Prevalence limit --------------*/      exit(0);
      }
   strcpy(filerespl,"pl");    else{
   strcat(filerespl,fileres);      fprintf(ficgp,"\n# Routine varprob");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   }      printf("Problem with html file: %s\n", optionfilehtm);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   fprintf(ficrespl,"#Prevalence limit\n");      exit(0);
   fprintf(ficrespl,"#Age ");    }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    else{
   fprintf(ficrespl,"\n");      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
        fprintf(fichtm,"\n");
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      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");
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      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");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    }
   k=0;  
   agebase=agemin;    cov[1]=1;
   agelim=agemax;    tj=cptcoveff;
   ftolpl=1.e-10;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   i1=cptcoveff;    j1=0;
   if (cptcovn < 1){i1=1;}    for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
   for(cptcov=1;cptcov<=i1;cptcov++){        j1++;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        if  (cptcovn>0) {
         k=k+1;          fprintf(ficresprob, "\n#********** Variable "); 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficrespl,"\n#******");          fprintf(ficresprob, "**********\n#\n");
         for(j=1;j<=cptcoveff;j++)          fprintf(ficresprobcov, "\n#********** Variable "); 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficrespl,"******\n");          fprintf(ficresprobcov, "**********\n#\n");
                  
         for (age=agebase; age<=agelim; age++){          fprintf(ficgp, "\n#********** Variable "); 
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficrespl,"%.0f",age );          fprintf(ficgp, "**********\n#\n");
           for(i=1; i<=nlstate;i++)          
           fprintf(ficrespl," %.5f", prlim[i][i]);          
           fprintf(ficrespl,"\n");          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     }          
   fclose(ficrespl);          fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /*------------- h Pij x at various ages ------------*/          fprintf(ficresprobcor, "**********\n#");    
          }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        for (age=bage; age<=fage; age ++){ 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          cov[2]=age;
   }          for (k=1; k<=cptcovn;k++) {
   printf("Computing pij: result on file '%s' \n", filerespij);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
            }
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /*if (stepm<=24) stepsize=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]]];
   agelim=AGESUP;          
   hstepm=stepsize*YEARM; /* Every year of age */          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
            gp=vector(1,(nlstate)*(nlstate+ndeath));
   k=0;          gm=vector(1,(nlstate)*(nlstate+ndeath));
   for(cptcov=1;cptcov<=i1;cptcov++){      
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for(theta=1; theta <=npar; theta++){
       k=k+1;            for(i=1; i<=npar; i++)
         fprintf(ficrespij,"\n#****** ");              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
         for(j=1;j<=cptcoveff;j++)            
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         fprintf(ficrespij,"******\n");            
                    k=0;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            for(i=1; i<= (nlstate); i++){
           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 */                k=k+1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                gp[k]=pmmij[i][j];
           oldm=oldms;savm=savms;              }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              }
           fprintf(ficrespij,"# Age");            
           for(i=1; i<=nlstate;i++)            for(i=1; i<=npar; i++)
             for(j=1; j<=nlstate+ndeath;j++)              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
               fprintf(ficrespij," %1d-%1d",i,j);      
           fprintf(ficrespij,"\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           for (h=0; h<=nhstepm; h++){            k=0;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            for(i=1; i<=(nlstate); i++){
             for(i=1; i<=nlstate;i++)              for(j=1; j<=(nlstate+ndeath);j++){
               for(j=1; j<=nlstate+ndeath;j++)                k=k+1;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                gm[k]=pmmij[i][j];
             fprintf(ficrespij,"\n");              }
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       
           fprintf(ficrespij,"\n");            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     }          }
   }  
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/            for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
   fclose(ficrespij);          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   if(stepm == 1) {          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   /*---------- Forecasting ------------------*/          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   /*printf("calage= %f", calagedate);*/          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
   strcpy(fileresf,"f");          for(i=1; i<=(nlstate); i++){
   strcat(fileresf,fileres);            for(j=1; j<=(nlstate+ndeath);j++){
   if((ficresf=fopen(fileresf,"w"))==NULL) {              k=k+1;
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;              mu[k][(int) age]=pmmij[i][j];
   }            }
   printf("Computing forecasting: result on file '%s' \n", fileresf);          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   free_matrix(mint,1,maxwav,1,n);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   free_matrix(anint,1,maxwav,1,n);              varpij[i][j][(int)age] = doldm[i][j];
   free_matrix(agev,1,maxwav,1,imx);  
   /* Mobile average */          /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   if (mobilav==1) {            }*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)          fprintf(ficresprob,"\n%d ",(int)age);
       for (i=1; i<=nlstate;i++)          fprintf(ficresprobcov,"\n%d ",(int)age);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          fprintf(ficresprobcor,"\n%d ",(int)age);
           mobaverage[(int)agedeb][i][cptcod]=0.;  
              for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     for (agedeb=bage+4; agedeb<=fage; agedeb++){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       for (i=1; i<=nlstate;i++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
           for (cpt=0;cpt<=4;cpt++){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          }
           }          i=0;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          for (k=1; k<=(nlstate);k++){
         }            for (l=1; l<=(nlstate+ndeath);l++){ 
       }              i=i++;
     }                fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   if (stepm<=12) stepsize=1;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
   agelim=AGESUP;            }
   /*hstepm=stepsize*YEARM; *//* Every year of age */          }/* end of loop for state */
   hstepm=1;        } /* end of loop for age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */  
   yp1=modf(dateintmean,&yp);        /* Confidence intervalle of pij  */
   anprojmean=yp;        /*
   yp2=modf((yp1*12),&yp);          fprintf(ficgp,"\nset noparametric;unset label");
   mprojmean=yp;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   yp1=modf((yp2*30.5),&yp);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   jprojmean=yp;          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(jprojmean==0) jprojmean=1;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   if(mprojmean==0) jprojmean=1;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        */
   
   if (popforecast==1) {        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     if((ficpop=fopen(popfile,"r"))==NULL)    {        first1=1;
       printf("Problem with population file : %s\n",popfile);goto end;        for (k2=1; k2<=(nlstate);k2++){
     }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     popage=ivector(0,AGESUP);            if(l2==k2) continue;
     popeffectif=vector(0,AGESUP);            j=(k2-1)*(nlstate+ndeath)+l2;
     popcount=vector(0,AGESUP);            for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     i=1;                  if(l1==k1) continue;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)                i=(k1-1)*(nlstate+ndeath)+l1;
       {                if(i<=j) continue;
         i=i+1;                for (age=bage; age<=fage; age ++){ 
       }                  if ((int)age %5==0){
     imx=i;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                        v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
   for(cptcov=1;cptcov<=i1;cptcov++){                    c12=cv12/sqrt(v1*v2);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                    /* Computing eigen value of matrix of covariance */
       k=k+1;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       fprintf(ficresf,"\n#******");                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       for(j=1;j<=cptcoveff;j++) {                    /* Eigen vectors */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       }                    /*v21=sqrt(1.-v11*v11); *//* error */
       fprintf(ficresf,"******\n");                    v21=(lc1-v1)/cv12*v11;
       fprintf(ficresf,"# StartingAge FinalAge");                    v12=-v21;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                    v22=v11;
       if (popforecast==1)  fprintf(ficresf," [Population]");                    tnalp=v21/v11;
                        if(first1==1){
       for (cpt=0; cpt<4;cpt++) {                      first1=0;
         fprintf(ficresf,"\n");                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                      }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */                    /*printf(fignu*/
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         nhstepm = nhstepm/hstepm;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/                    if(first==1){
                       first=0;
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      fprintf(ficgp,"\nset parametric;unset label");
         oldm=oldms;savm=savms;                      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);
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                        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);
         for (h=0; h<=nhstepm; h++){                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
           if (h==(int) (calagedate+YEARM*cpt)) {                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
           }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           for(j=1; j<=nlstate+ndeath;j++) {                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
             kk1=0.;kk2=0;                      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",\
             for(i=1; i<=nlstate;i++) {                                      mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
               if (mobilav==1)                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                    }else{
               else {                      first=0;
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
               }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
             }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                              }/* if first */
             if (h==(int)(calagedate+12*cpt)){                  } /* age mod 5 */
               fprintf(ficresf," %.3f", kk1);                } /* end loop age */
                              fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);                first=1;
             }              } /*l12 */
           }            } /* k12 */
         }          } /*l1 */
         /*      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);*/        }/* k1 */
       }      } /* loop covariates */
       }    }
     }    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   /*  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_vector(xp,1,npar);
   if (popforecast==1) {    fclose(ficresprob);
     free_ivector(popage,0,AGESUP);    fclose(ficresprobcov);
     free_vector(popeffectif,0,AGESUP);    fclose(ficresprobcor);
     free_vector(popcount,0,AGESUP);    fclose(ficgp);
   }    fclose(fichtm);
   free_imatrix(s,1,maxwav+1,1,n);  }
   free_vector(weight,1,n);*/  
   fclose(ficresf);  
   }/* End forecasting */  /******************* Printing html file ***********/
   else{  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     erreur=108;                    int lastpass, int stepm, int weightopt, char model[],\
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   }                    int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
   /*---------- Health expectancies and variances ------------*/                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   strcpy(filerest,"t");    /*char optionfilehtm[FILENAMELENGTH];*/
   strcat(filerest,fileres);    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   if((ficrest=fopen(filerest,"w"))==NULL) {      printf("Problem with %s \n",optionfilehtm), exit(0);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   }    }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n \
   strcpy(filerese,"e");   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
   strcat(filerese,fileres);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
   if((ficreseij=fopen(filerese,"w"))==NULL) {   - Life expectancies by age and initial health status (estepm=%2d months): \
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   }    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
  strcpy(fileresv,"v");  
   strcat(fileresv,fileres);   m=cptcoveff;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }   jj1=0;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   k=0;       jj1++;
   for(cptcov=1;cptcov<=i1;cptcov++){       if (cptcovn > 0) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       k=k+1;         for (cpt=1; cpt<=cptcoveff;cpt++) 
       fprintf(ficrest,"\n#****** ");           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       for(j=1;j<=cptcoveff;j++)         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       }
       fprintf(ficrest,"******\n");       /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br> \
       fprintf(ficreseij,"\n#****** ");  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
       for(j=1;j<=cptcoveff;j++)       /* Quasi-incidences */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
       fprintf(ficreseij,"******\n");   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); 
       fprintf(ficresvij,"\n#****** ");         /* Stable prevalence in each health state */
       for(j=1;j<=cptcoveff;j++)         for(cpt=1; cpt<nlstate;cpt++){
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
       fprintf(ficresvij,"******\n");  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       for(cpt=1; cpt<=nlstate;cpt++) {
       oldm=oldms;savm=savms;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       }
       oldm=oldms;savm=savms;       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  health expectancies in states (1) and (2): e%s%d.png<br>\
        <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");     } /* end i1 */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   }/* End k1 */
       fprintf(ficrest,"\n");   fprintf(fichtm,"</ul>");
          
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
       epj=vector(1,nlstate+1);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
       for(age=bage; age <=fage ;age++){   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
         if (popbased==1) {   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
           for(i=1; i<=nlstate;i++)   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
             prlim[i][i]=probs[(int)age][i][k];   - 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);
          
         fprintf(ficrest," %.0f",age);  /*  if(popforecast==1) fprintf(fichtm,"\n */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  /*      <br>",fileres,fileres,fileres,fileres); */
           }  /*  else  */
           epj[nlstate+1] +=epj[j];  /*    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>");
         for(i=1, vepp=0.;i <=nlstate;i++)  
           for(j=1;j <=nlstate;j++)   m=cptcoveff;
             vepp += vareij[i][j][(int)age];   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  
         for(j=1;j <=nlstate;j++){   jj1=0;
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));   for(k1=1; k1<=m;k1++){
         }     for(i1=1; i1<=ncodemax[k1];i1++){
         fprintf(ficrest,"\n");       jj1++;
       }       if (cptcovn > 0) {
     }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   }         for (cpt=1; cpt<=cptcoveff;cpt++) 
                   fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                 fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
  fclose(ficreseij);         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
  fclose(ficresvij);  interval) in state (%d): v%s%d%d.png <br>\
   fclose(ficrest);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
   fclose(ficpar);       }
   free_vector(epj,1,nlstate+1);     } /* end i1 */
   /*  scanf("%d ",i); */   }/* End k1 */
    fprintf(fichtm,"</ul>");
   /*------- Variance limit prevalence------*/    fclose(fichtm);
   }
 strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);  /******************* Gnuplot file **************/
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   }    int ng;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
  k=0;      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
  for(cptcov=1;cptcov<=i1;cptcov++){    }
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
      k=k+1;    /*#ifdef windows */
      fprintf(ficresvpl,"\n#****** ");      fprintf(ficgp,"cd \"%s\" \n",pathc);
      for(j=1;j<=cptcoveff;j++)      /*#endif */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  m=pow(2,cptcoveff);
      fprintf(ficresvpl,"******\n");    
         /* 1eme*/
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    for (cpt=1; cpt<= nlstate ; cpt ++) {
      oldm=oldms;savm=savms;     for (k1=1; k1<= m ; k1 ++) {
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
    }       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
  }  
        for (i=1; i<= nlstate ; i ++) {
   fclose(ficresvpl);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   /*---------- End : free ----------------*/       }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
         for (i=1; i<= nlstate ; i ++) {
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         } 
         fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);       for (i=1; i<= nlstate ; i ++) {
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       }  
         fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
   free_matrix(matcov,1,npar,1,npar);     }
   free_vector(delti,1,npar);    }
      /*2 eme*/
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    
     for (k1=1; k1<= m ; k1 ++) { 
   if(erreur >0)      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
     printf("End of Imach with error %d\n",erreur);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   else   printf("End of Imach\n");      
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      for (i=1; i<= nlstate+1 ; i ++) {
          k=2*i;
   /* 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(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
   /*printf("Total time was %d uSec.\n", total_usecs);*/        for (j=1; j<= nlstate+1 ; j ++) {
   /*------ End -----------*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
  end:        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
 #ifdef windows        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   /* chdir(pathcd);*/        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
 #endif        for (j=1; j<= nlstate+1 ; j ++) {
  /*system("wgnuplot graph.plt");*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  /*system("../gp37mgw/wgnuplot graph.plt");*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
  /*system("cd ../gp37mgw");*/        }   
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        fprintf(ficgp,"\" t\"\" w l 0,");
  strcpy(plotcmd,GNUPLOTPROGRAM);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
  strcat(plotcmd," ");        for (j=1; j<= nlstate+1 ; j ++) {
  strcat(plotcmd,optionfilegnuplot);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  system(plotcmd);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
 #ifdef windows        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   while (z[0] != 'q') {        else fprintf(ficgp,"\" t\"\" w l 0,");
     chdir(path);      }
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    }
     scanf("%s",z);    
     if (z[0] == 'c') system("./imach");    /*3eme*/
     else if (z[0] == 'e') {    
       chdir(path);    for (k1=1; k1<= m ; k1 ++) { 
       system(optionfilehtm);      for (cpt=1; cpt<= nlstate ; cpt ++) {
     }        k=2+nlstate*(2*cpt-2);
     else if (z[0] == 'q') exit(0);        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   }        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
 #endif        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fclose(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfile)
   {
     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.1.24  
changed lines
  Added in v.1.86


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