Diff for /imach/src/imach.c between versions 1.50 and 1.84

version 1.50, 2002/06/26 23:25:02 version 1.84, 2003/06/13 21:44:43
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.84  2003/06/13 21:44:43  brouard
      * imach.c (Repository): Replace "freqsummary" at a correct
   This program computes Healthy Life Expectancies from    place. It differs from routine "prevalence" which may be called
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    many times. Probs is memory consuming and must be used with
   first survey ("cross") where individuals from different ages are    parcimony.
   interviewed on their health status or degree of disability (in the    Version 0.95a2 (should output exactly the same maximization than 0.8a2)
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.83  2003/06/10 13:39:11  lievre
   (if any) in individual health status.  Health expectancies are    *** empty log message ***
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.82  2003/06/05 15:57:20  brouard
   Maximum Likelihood of the parameters involved in the model.  The    Add log in  imach.c and  fullversion number is now printed.
   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  /*
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where     Interpolated Markov Chain
   '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    Short summary of the programme:
   where the markup *Covariates have to be included here again* invites    
   you to do it.  More covariates you add, slower the    This program computes Healthy Life Expectancies from
   convergence.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
   The advantage of this computer programme, compared to a simple    interviewed on their health status or degree of disability (in the
   multinomial logistic model, is clear when the delay between waves is not    case of a health survey which is our main interest) -2- at least a
   identical for each individual. Also, if a individual missed an    second wave of interviews ("longitudinal") which measure each change
   intermediate interview, the information is lost, but taken into    (if any) in individual health status.  Health expectancies are
   account using an interpolation or extrapolation.      computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
   hPijx is the probability to be observed in state i at age x+h    Maximum Likelihood of the parameters involved in the model.  The
   conditional to the observed state i at age x. The delay 'h' can be    simplest model is the multinomial logistic model where pij is the
   split into an exact number (nh*stepm) of unobserved intermediate    probability to be observed in state j at the second wave
   states. This elementary transition (by month or quarter trimester,    conditional to be observed in state i at the first wave. Therefore
   semester or year) is model as a multinomial logistic.  The hPx    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   matrix is simply the matrix product of nh*stepm elementary matrices    'age' is age and 'sex' is a covariate. If you want to have a more
   and the contribution of each individual to the likelihood is simply    complex model than "constant and age", you should modify the program
   hPijx.    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
   Also this programme outputs the covariance matrix of the parameters but also    convergence.
   of the life expectancies. It also computes the prevalence limits.  
      The advantage of this computer programme, compared to a simple
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    multinomial logistic model, is clear when the delay between waves is not
            Institut national d'études démographiques, Paris.    identical for each individual. Also, if a individual missed an
   This software have been partly granted by Euro-REVES, a concerted action    intermediate interview, the information is lost, but taken into
   from the European Union.    account using an interpolation or extrapolation.  
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    hPijx is the probability to be observed in state i at age x+h
   can be accessed at http://euroreves.ined.fr/imach .    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, quarter,
 #include <math.h>    semester or year) is modelled as a multinomial logistic.  The hPx
 #include <stdio.h>    matrix is simply the matrix product of nh*stepm elementary matrices
 #include <stdlib.h>    and the contribution of each individual to the likelihood is simply
 #include <unistd.h>    hPijx.
   
 #define MAXLINE 256    Also this programme outputs the covariance matrix of the parameters but also
 #define GNUPLOTPROGRAM "gnuplot"    of the life expectancies. It also computes the stable prevalence. 
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    
 #define FILENAMELENGTH 80    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 /*#define DEBUG*/             Institut national d'études démographiques, Paris.
 #define windows    This software have been partly granted by Euro-REVES, a concerted action
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    from the European Union.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    can be accessed at http://euroreves.ined.fr/imach .
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define NINTERVMAX 8    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    **********************************************************************/
 #define NCOVMAX 8 /* Maximum number of covariates */  /*
 #define MAXN 20000    main
 #define YEARM 12. /* Number of months per year */    read parameterfile
 #define AGESUP 130    read datafile
 #define AGEBASE 40    concatwav
 #ifdef windows    freqsummary
 #define DIRSEPARATOR '\\'    if (mle >= 1)
 #define ODIRSEPARATOR '/'      mlikeli
 #else    print results files
 #define DIRSEPARATOR '/'    if mle==1 
 #define ODIRSEPARATOR '\\'       computes hessian
 #endif    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    open gnuplot file
 int erreur; /* Error number */    open html file
 int nvar;    stable prevalence
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;     for age prevalim()
 int npar=NPARMAX;    h Pij x
 int nlstate=2; /* Number of live states */    variance of p varprob
 int ndeath=1; /* Number of dead states */    forecasting if prevfcast==1 prevforecast call prevalence()
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    health expectancies
 int popbased=0;    Variance-covariance of DFLE
     prevalence()
 int *wav; /* Number of waves for this individuual 0 is possible */     movingaverage()
 int maxwav; /* Maxim number of waves */    varevsij() 
 int jmin, jmax; /* min, max spacing between 2 waves */    if popbased==1 varevsij(,popbased)
 int mle, weightopt;    total life expectancies
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Variance of stable prevalence
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */   end
 double jmean; /* Mean space between 2 waves */  */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficlog;   
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  #include <math.h>
 FILE *ficresprobmorprev;  #include <stdio.h>
 FILE *fichtm; /* Html File */  #include <stdlib.h>
 FILE *ficreseij;  #include <unistd.h>
 char filerese[FILENAMELENGTH];  
 FILE  *ficresvij;  #define MAXLINE 256
 char fileresv[FILENAMELENGTH];  #define GNUPLOTPROGRAM "gnuplot"
 FILE  *ficresvpl;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 char fileresvpl[FILENAMELENGTH];  #define FILENAMELENGTH 80
 char title[MAXLINE];  /*#define DEBUG*/
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  #define windows
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
 char filelog[FILENAMELENGTH]; /* Log file */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 char filerest[FILENAMELENGTH];  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 char fileregp[FILENAMELENGTH];  
 char popfile[FILENAMELENGTH];  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 #define NR_END 1  #define MAXN 20000
 #define FREE_ARG char*  #define YEARM 12. /* Number of months per year */
 #define FTOL 1.0e-10  #define AGESUP 130
   #define AGEBASE 40
 #define NRANSI  #ifdef windows
 #define ITMAX 200  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 #define TOL 2.0e-4  #else
   #define DIRSEPARATOR '/'
 #define CGOLD 0.3819660  #define ODIRSEPARATOR '\\'
 #define ZEPS 1.0e-10  #endif
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
   /* $Id$ */
 #define GOLD 1.618034  /* $State$ */
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
 static double maxarg1,maxarg2;  int erreur; /* Error number */
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  int nvar;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    int npar=NPARMAX;
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int nlstate=2; /* Number of live states */
 #define rint(a) floor(a+0.5)  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 static double sqrarg;  int popbased=0;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 int imx;  int jmin, jmax; /* min, max spacing between 2 waves */
 int stepm;  int mle, weightopt;
 /* Stepm, step in month: minimum step interpolation*/  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 int estepm;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 int m,nb;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 double **pmmij, ***probs, ***mobaverage;  FILE *ficlog, *ficrespow;
 double dateintmean=0;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 double *weight;  FILE *fichtm; /* Html File */
 int **s; /* Status */  FILE *ficreseij;
 double *agedc, **covar, idx;  char filerese[FILENAMELENGTH];
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  FILE  *ficresvpl;
 double ftolhess; /* Tolerance for computing hessian */  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 /**************** split *************************/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 {  
    char *s;                             /* pointer */  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    int  l1, l2;                         /* length counters */  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
    l1 = strlen( path );                 /* length of path */  char fileregp[FILENAMELENGTH];
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  char popfile[FILENAMELENGTH];
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  #define NR_END 1
 #if     defined(__bsd__)                /* get current working directory */  #define FREE_ARG char*
       extern char       *getwd( );  #define FTOL 1.0e-10
   
       if ( getwd( dirc ) == NULL ) {  #define NRANSI 
 #else  #define ITMAX 200 
       extern char       *getcwd( );  
   #define TOL 2.0e-4 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  #define CGOLD 0.3819660 
          return( GLOCK_ERROR_GETCWD );  #define ZEPS 1.0e-10 
       }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  #define GOLD 1.618034 
       s++;                              /* after this, the filename */  #define GLIMIT 100.0 
       l2 = strlen( s );                 /* length of filename */  #define TINY 1.0e-20 
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */  static double maxarg1,maxarg2;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       dirc[l1-l2] = 0;                  /* add zero */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    }    
    l1 = strlen( dirc );                 /* length of directory */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #ifdef windows  #define rint(a) floor(a+0.5)
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  static double sqrarg;
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #endif  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    s = strrchr( name, '.' );            /* find last / */  
    s++;  int imx; 
    strcpy(ext,s);                       /* save extension */  int stepm;
    l1= strlen( name);  /* Stepm, step in month: minimum step interpolation*/
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);  int estepm;
    finame[l1-l2]= 0;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    return( 0 );                         /* we're done */  
 }  int m,nb;
   int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 /******************************************/  double **pmmij, ***probs;
   double dateintmean=0;
 void replace(char *s, char*t)  
 {  double *weight;
   int i;  int **s; /* Status */
   int lg=20;  double *agedc, **covar, idx;
   i=0;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     (s[i] = t[i]);  double ftolhess; /* Tolerance for computing hessian */
     if (t[i]== '\\') s[i]='/';  
   }  /**************** split *************************/
 }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 int nbocc(char *s, char occ)    char  *ss;                            /* pointer */
 {    int   l1, l2;                         /* length counters */
   int i,j=0;  
   int lg=20;    l1 = strlen(path );                   /* length of path */
   i=0;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   lg=strlen(s);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   for(i=0; i<= lg; i++) {    if ( ss == NULL ) {                   /* no directory, so use current */
   if  (s[i] == occ ) j++;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   return j;      /* get current working directory */
 }      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 void cutv(char *u,char *v, char*t, char occ)        return( GLOCK_ERROR_GETCWD );
 {      }
   /* cuts string t into u and v where u is ended by char occ excluding it      strcpy( name, path );               /* we've got it */
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    } else {                              /* strip direcotry from path */
      gives u="abcedf" and v="ghi2j" */      ss++;                               /* after this, the filename */
   int i,lg,j,p=0;      l2 = strlen( ss );                  /* length of filename */
   i=0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(j=0; j<=strlen(t)-1; j++) {      strcpy( name, ss );         /* save file name */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   }      dirc[l1-l2] = 0;                    /* add zero */
     }
   lg=strlen(t);    l1 = strlen( dirc );                  /* length of directory */
   for(j=0; j<p; j++) {  #ifdef windows
     (u[j] = t[j]);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   }  #else
      u[p]='\0';    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
    for(j=0; j<= lg; j++) {    ss = strrchr( name, '.' );            /* find last / */
     if (j>=(p+1))(v[j-p-1] = t[j]);    ss++;
   }    strcpy(ext,ss);                       /* save extension */
 }    l1= strlen( name);
     l2= strlen(ss)+1;
 /********************** nrerror ********************/    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 void nrerror(char error_text[])    return( 0 );                          /* we're done */
 {  }
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  /******************************************/
 }  
 /*********************** vector *******************/  void replace(char *s, char*t)
 double *vector(int nl, int nh)  {
 {    int i;
   double *v;    int lg=20;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    i=0;
   if (!v) nrerror("allocation failure in vector");    lg=strlen(t);
   return v-nl+NR_END;    for(i=0; i<= lg; i++) {
 }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /************************ free vector ******************/    }
 void free_vector(double*v, int nl, int nh)  }
 {  
   free((FREE_ARG)(v+nl-NR_END));  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /************************ivector *******************************/    int lg=20;
 int *ivector(long nl,long nh)    i=0;
 {    lg=strlen(s);
   int *v;    for(i=0; i<= lg; i++) {
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    if  (s[i] == occ ) j++;
   if (!v) nrerror("allocation failure in ivector");    }
   return v-nl+NR_END;    return j;
 }  }
   
 /******************free ivector **************************/  void cutv(char *u,char *v, char*t, char occ)
 void free_ivector(int *v, long nl, long nh)  {
 {    /* cuts string t into u and v where u is ended by char occ excluding it
   free((FREE_ARG)(v+nl-NR_END));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 }       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
 /******************* imatrix *******************************/    i=0;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    for(j=0; j<=strlen(t)-1; j++) {
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 {    }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    lg=strlen(t);
      for(j=0; j<p; j++) {
   /* allocate pointers to rows */      (u[j] = t[j]);
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");       u[p]='\0';
   m += NR_END;  
   m -= nrl;     for(j=0; j<= lg; j++) {
        if (j>=(p+1))(v[j-p-1] = t[j]);
      }
   /* allocate rows and set pointers to them */  }
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /********************** nrerror ********************/
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  void nrerror(char error_text[])
    {
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
   /* return pointer to array of pointers to rows */    exit(EXIT_FAILURE);
   return m;  }
 }  /*********************** vector *******************/
   double *vector(int nl, int nh)
 /****************** free_imatrix *************************/  {
 void free_imatrix(m,nrl,nrh,ncl,nch)    double *v;
       int **m;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       long nch,ncl,nrh,nrl;    if (!v) nrerror("allocation failure in vector");
      /* free an int matrix allocated by imatrix() */    return v-nl+NR_END;
 {  }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /******************* matrix *******************************/    free((FREE_ARG)(v+nl-NR_END));
 double **matrix(long nrl, long nrh, long ncl, long nch)  }
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  /************************ivector *******************************/
   double **m;  char *cvector(long nl,long nh)
   {
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    char *v;
   if (!m) nrerror("allocation failure 1 in matrix()");    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   m += NR_END;    if (!v) nrerror("allocation failure in cvector");
   m -= nrl;    return v-nl+NR_END;
   }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /******************free ivector **************************/
   m[nrl] += NR_END;  void free_cvector(char *v, long nl, long nh)
   m[nrl] -= ncl;  {
     free((FREE_ARG)(v+nl-NR_END));
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  
 }  /************************ivector *******************************/
   int *ivector(long nl,long nh)
 /*************************free matrix ************************/  {
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    int *v;
 {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!v) nrerror("allocation failure in ivector");
   free((FREE_ARG)(m+nrl-NR_END));    return v-nl+NR_END;
 }  }
   
 /******************* ma3x *******************************/  /******************free ivector **************************/
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  void free_ivector(int *v, long nl, long nh)
 {  {
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    free((FREE_ARG)(v+nl-NR_END));
   double ***m;  }
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /******************* imatrix *******************************/
   if (!m) nrerror("allocation failure 1 in matrix()");  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   m += NR_END;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   m -= nrl;  { 
     long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    int **m; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    /* allocate pointers to rows */ 
   m[nrl] -= ncl;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    m += NR_END; 
     m -= nrl; 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    
   m[nrl][ncl] += NR_END;    /* allocate rows and set pointers to them */ 
   m[nrl][ncl] -= nll;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   for (j=ncl+1; j<=nch; j++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl][j]=m[nrl][j-1]+nlay;    m[nrl] += NR_END; 
      m[nrl] -= ncl; 
   for (i=nrl+1; i<=nrh; i++) {    
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     for (j=ncl+1; j<=nch; j++)    
       m[i][j]=m[i][j-1]+nlay;    /* return pointer to array of pointers to rows */ 
   }    return m; 
   return m;  } 
 }  
   /****************** free_imatrix *************************/
 /*************************free ma3x ************************/  void free_imatrix(m,nrl,nrh,ncl,nch)
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)        int **m;
 {        long nch,ncl,nrh,nrl; 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));       /* free an int matrix allocated by imatrix() */ 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  { 
   free((FREE_ARG)(m+nrl-NR_END));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 }    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 /***************** f1dim *************************/  
 extern int ncom;  /******************* matrix *******************************/
 extern double *pcom,*xicom;  double **matrix(long nrl, long nrh, long ncl, long nch)
 extern double (*nrfunc)(double []);  {
      long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 double f1dim(double x)    double **m;
 {  
   int j;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double f;    if (!m) nrerror("allocation failure 1 in matrix()");
   double *xt;    m += NR_END;
      m -= nrl;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   f=(*nrfunc)(xt);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free_vector(xt,1,ncom);    m[nrl] += NR_END;
   return f;    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /*****************brent *************************/    return m;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
 {     */
   int iter;  }
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  /*************************free matrix ************************/
   double ftemp;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double p,q,r,tol1,tol2,u,v,w,x,xm;  {
   double e=0.0;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
   a=(ax < cx ? ax : cx);  }
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  /******************* ma3x *******************************/
   fw=fv=fx=(*f)(x);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (iter=1;iter<=ITMAX;iter++) {  {
     xm=0.5*(a+b);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    double ***m;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     fprintf(ficlog,".");fflush(ficlog);    if (!m) nrerror("allocation failure 1 in matrix()");
 #ifdef DEBUG    m += 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;
     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)))) { */    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 #endif    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    m[nrl] += NR_END;
       *xmin=x;    m[nrl] -= ncl;
       return fx;  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     ftemp=fu;  
     if (fabs(e) > tol1) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       r=(x-w)*(fx-fv);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       q=(x-v)*(fx-fw);    m[nrl][ncl] += NR_END;
       p=(x-v)*q-(x-w)*r;    m[nrl][ncl] -= nll;
       q=2.0*(q-r);    for (j=ncl+1; j<=nch; j++) 
       if (q > 0.0) p = -p;      m[nrl][j]=m[nrl][j-1]+nlay;
       q=fabs(q);    
       etemp=e;    for (i=nrl+1; i<=nrh; i++) {
       e=d;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      for (j=ncl+1; j<=nch; j++) 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));        m[i][j]=m[i][j-1]+nlay;
       else {    }
         d=p/q;    return m; 
         u=x+d;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         if (u-a < tol2 || b-u < tol2)             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
           d=SIGN(tol1,xm-x);    */
       }  }
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  {
     fu=(*f)(u);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     if (fu <= fx) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       if (u >= x) a=x; else b=x;    free((FREE_ARG)(m+nrl-NR_END));
       SHFT(v,w,x,u)  }
         SHFT(fv,fw,fx,fu)  
         } else {  /***************** f1dim *************************/
           if (u < x) a=u; else b=u;  extern int ncom; 
           if (fu <= fw || w == x) {  extern double *pcom,*xicom;
             v=w;  extern double (*nrfunc)(double []); 
             w=u;   
             fv=fw;  double f1dim(double x) 
             fw=fu;  { 
           } else if (fu <= fv || v == x || v == w) {    int j; 
             v=u;    double f;
             fv=fu;    double *xt; 
           }   
         }    xt=vector(1,ncom); 
   }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   nrerror("Too many iterations in brent");    f=(*nrfunc)(xt); 
   *xmin=x;    free_vector(xt,1,ncom); 
   return fx;    return f; 
 }  } 
   
 /****************** mnbrak ***********************/  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  { 
             double (*func)(double))    int iter; 
 {    double a,b,d,etemp;
   double ulim,u,r,q, dum;    double fu,fv,fw,fx;
   double fu;    double ftemp;
      double p,q,r,tol1,tol2,u,v,w,x,xm; 
   *fa=(*func)(*ax);    double e=0.0; 
   *fb=(*func)(*bx);   
   if (*fb > *fa) {    a=(ax < cx ? ax : cx); 
     SHFT(dum,*ax,*bx,dum)    b=(ax > cx ? ax : cx); 
       SHFT(dum,*fb,*fa,dum)    x=w=v=bx; 
       }    fw=fv=fx=(*f)(x); 
   *cx=(*bx)+GOLD*(*bx-*ax);    for (iter=1;iter<=ITMAX;iter++) { 
   *fc=(*func)(*cx);      xm=0.5*(a+b); 
   while (*fb > *fc) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     r=(*bx-*ax)*(*fb-*fc);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     q=(*bx-*cx)*(*fb-*fa);      printf(".");fflush(stdout);
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      fprintf(ficlog,".");fflush(ficlog);
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #ifdef DEBUG
     ulim=(*bx)+GLIMIT*(*cx-*bx);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     if ((*bx-u)*(u-*cx) > 0.0) {      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);
       fu=(*func)(u);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #endif
       fu=(*func)(u);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       if (fu < *fc) {        *xmin=x; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        return fx; 
           SHFT(*fb,*fc,fu,(*func)(u))      } 
           }      ftemp=fu;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      if (fabs(e) > tol1) { 
       u=ulim;        r=(x-w)*(fx-fv); 
       fu=(*func)(u);        q=(x-v)*(fx-fw); 
     } else {        p=(x-v)*q-(x-w)*r; 
       u=(*cx)+GOLD*(*cx-*bx);        q=2.0*(q-r); 
       fu=(*func)(u);        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
     SHFT(*ax,*bx,*cx,u)        etemp=e; 
       SHFT(*fa,*fb,*fc,fu)        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)); 
         else { 
 /*************** linmin ************************/          d=p/q; 
           u=x+d; 
 int ncom;          if (u-a < tol2 || b-u < tol2) 
 double *pcom,*xicom;            d=SIGN(tol1,xm-x); 
 double (*nrfunc)(double []);        } 
        } else { 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 {      } 
   double brent(double ax, double bx, double cx,      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
                double (*f)(double), double tol, double *xmin);      fu=(*f)(u); 
   double f1dim(double x);      if (fu <= fx) { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        if (u >= x) a=x; else b=x; 
               double *fc, double (*func)(double));        SHFT(v,w,x,u) 
   int j;          SHFT(fv,fw,fx,fu) 
   double xx,xmin,bx,ax;          } else { 
   double fx,fb,fa;            if (u < x) a=u; else b=u; 
              if (fu <= fw || w == x) { 
   ncom=n;              v=w; 
   pcom=vector(1,n);              w=u; 
   xicom=vector(1,n);              fv=fw; 
   nrfunc=func;              fw=fu; 
   for (j=1;j<=n;j++) {            } else if (fu <= fv || v == x || v == w) { 
     pcom[j]=p[j];              v=u; 
     xicom[j]=xi[j];              fv=fu; 
   }            } 
   ax=0.0;          } 
   xx=1.0;    } 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    nrerror("Too many iterations in brent"); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    *xmin=x; 
 #ifdef DEBUG    return fx; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  } 
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  /****************** mnbrak ***********************/
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     p[j] += xi[j];              double (*func)(double)) 
   }  { 
   free_vector(xicom,1,n);    double ulim,u,r,q, dum;
   free_vector(pcom,1,n);    double fu; 
 }   
     *fa=(*func)(*ax); 
 /*************** powell ************************/    *fb=(*func)(*bx); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    if (*fb > *fa) { 
             double (*func)(double []))      SHFT(dum,*ax,*bx,dum) 
 {        SHFT(dum,*fb,*fa,dum) 
   void linmin(double p[], double xi[], int n, double *fret,        } 
               double (*func)(double []));    *cx=(*bx)+GOLD*(*bx-*ax); 
   int i,ibig,j;    *fc=(*func)(*cx); 
   double del,t,*pt,*ptt,*xit;    while (*fb > *fc) { 
   double fp,fptt;      r=(*bx-*ax)*(*fb-*fc); 
   double *xits;      q=(*bx-*cx)*(*fb-*fa); 
   pt=vector(1,n);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   ptt=vector(1,n);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   xit=vector(1,n);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   xits=vector(1,n);      if ((*bx-u)*(u-*cx) > 0.0) { 
   *fret=(*func)(p);        fu=(*func)(u); 
   for (j=1;j<=n;j++) pt[j]=p[j];      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   for (*iter=1;;++(*iter)) {        fu=(*func)(u); 
     fp=(*fret);        if (fu < *fc) { 
     ibig=0;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     del=0.0;            SHFT(*fb,*fc,fu,(*func)(u)) 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);            } 
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     for (i=1;i<=n;i++)        u=ulim; 
       printf(" %d %.12f",i, p[i]);        fu=(*func)(u); 
     fprintf(ficlog," %d %.12f",i, p[i]);      } else { 
     printf("\n");        u=(*cx)+GOLD*(*cx-*bx); 
     fprintf(ficlog,"\n");        fu=(*func)(u); 
     for (i=1;i<=n;i++) {      } 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      SHFT(*ax,*bx,*cx,u) 
       fptt=(*fret);        SHFT(*fa,*fb,*fc,fu) 
 #ifdef DEBUG        } 
       printf("fret=%lf \n",*fret);  } 
       fprintf(ficlog,"fret=%lf \n",*fret);  
 #endif  /*************** linmin ************************/
       printf("%d",i);fflush(stdout);  
       fprintf(ficlog,"%d",i);fflush(ficlog);  int ncom; 
       linmin(p,xit,n,fret,func);  double *pcom,*xicom;
       if (fabs(fptt-(*fret)) > del) {  double (*nrfunc)(double []); 
         del=fabs(fptt-(*fret));   
         ibig=i;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       }  { 
 #ifdef DEBUG    double brent(double ax, double bx, double cx, 
       printf("%d %.12e",i,(*fret));                 double (*f)(double), double tol, double *xmin); 
       fprintf(ficlog,"%d %.12e",i,(*fret));    double f1dim(double x); 
       for (j=1;j<=n;j++) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);                double *fc, double (*func)(double)); 
         printf(" x(%d)=%.12e",j,xit[j]);    int j; 
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);    double xx,xmin,bx,ax; 
       }    double fx,fb,fa;
       for(j=1;j<=n;j++) {   
         printf(" p=%.12e",p[j]);    ncom=n; 
         fprintf(ficlog," p=%.12e",p[j]);    pcom=vector(1,n); 
       }    xicom=vector(1,n); 
       printf("\n");    nrfunc=func; 
       fprintf(ficlog,"\n");    for (j=1;j<=n;j++) { 
 #endif      pcom[j]=p[j]; 
     }      xicom[j]=xi[j]; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    } 
 #ifdef DEBUG    ax=0.0; 
       int k[2],l;    xx=1.0; 
       k[0]=1;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       k[1]=-1;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       printf("Max: %.12e",(*func)(p));  #ifdef DEBUG
       fprintf(ficlog,"Max: %.12e",(*func)(p));    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (j=1;j<=n;j++) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         printf(" %.12e",p[j]);  #endif
         fprintf(ficlog," %.12e",p[j]);    for (j=1;j<=n;j++) { 
       }      xi[j] *= xmin; 
       printf("\n");      p[j] += xi[j]; 
       fprintf(ficlog,"\n");    } 
       for(l=0;l<=1;l++) {    free_vector(xicom,1,n); 
         for (j=1;j<=n;j++) {    free_vector(pcom,1,n); 
           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]);  /*************** powell ************************/
         }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));              double (*func)(double [])) 
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  { 
       }    void linmin(double p[], double xi[], int n, double *fret, 
 #endif                double (*func)(double [])); 
     int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
       free_vector(xit,1,n);    double fp,fptt;
       free_vector(xits,1,n);    double *xits;
       free_vector(ptt,1,n);    pt=vector(1,n); 
       free_vector(pt,1,n);    ptt=vector(1,n); 
       return;    xit=vector(1,n); 
     }    xits=vector(1,n); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    *fret=(*func)(p); 
     for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
       ptt[j]=2.0*p[j]-pt[j];    for (*iter=1;;++(*iter)) { 
       xit[j]=p[j]-pt[j];      fp=(*fret); 
       pt[j]=p[j];      ibig=0; 
     }      del=0.0; 
     fptt=(*func)(ptt);      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     if (fptt < fp) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       if (t < 0.0) {      for (i=1;i<=n;i++) {
         linmin(p,xit,n,fret,func);        printf(" %d %.12f",i, p[i]);
         for (j=1;j<=n;j++) {        fprintf(ficlog," %d %.12lf",i, p[i]);
           xi[j][ibig]=xi[j][n];        fprintf(ficrespow," %.12lf", p[i]);
           xi[j][n]=xit[j];      }
         }      printf("\n");
 #ifdef DEBUG      fprintf(ficlog,"\n");
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      fprintf(ficrespow,"\n");
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      for (i=1;i<=n;i++) { 
         for(j=1;j<=n;j++){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
           printf(" %.12e",xit[j]);        fptt=(*fret); 
           fprintf(ficlog," %.12e",xit[j]);  #ifdef DEBUG
         }        printf("fret=%lf \n",*fret);
         printf("\n");        fprintf(ficlog,"fret=%lf \n",*fret);
         fprintf(ficlog,"\n");  #endif
 #endif        printf("%d",i);fflush(stdout);
       }        fprintf(ficlog,"%d",i);fflush(ficlog);
     }        linmin(p,xit,n,fret,func); 
   }        if (fabs(fptt-(*fret)) > del) { 
 }          del=fabs(fptt-(*fret)); 
           ibig=i; 
 /**** Prevalence limit ****************/        } 
   #ifdef DEBUG
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        printf("%d %.12e",i,(*fret));
 {        fprintf(ficlog,"%d %.12e",i,(*fret));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        for (j=1;j<=n;j++) {
      matrix by transitions matrix until convergence is reached */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
   int i, ii,j,k;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double min, max, maxmin, maxmax,sumnew=0.;        }
   double **matprod2();        for(j=1;j<=n;j++) {
   double **out, cov[NCOVMAX], **pmij();          printf(" p=%.12e",p[j]);
   double **newm;          fprintf(ficlog," p=%.12e",p[j]);
   double agefin, delaymax=50 ; /* Max number of years to converge */        }
         printf("\n");
   for (ii=1;ii<=nlstate+ndeath;ii++)        fprintf(ficlog,"\n");
     for (j=1;j<=nlstate+ndeath;j++){  #endif
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      } 
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
    cov[1]=1.;        int k[2],l;
          k[0]=1;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        k[1]=-1;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        printf("Max: %.12e",(*func)(p));
     newm=savm;        fprintf(ficlog,"Max: %.12e",(*func)(p));
     /* Covariates have to be included here again */        for (j=1;j<=n;j++) {
      cov[2]=agefin;          printf(" %.12e",p[j]);
            fprintf(ficlog," %.12e",p[j]);
       for (k=1; k<=cptcovn;k++) {        }
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        printf("\n");
         /*      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]]);*/        fprintf(ficlog,"\n");
       }        for(l=0;l<=1;l++) {
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          for (j=1;j<=n;j++) {
       for (k=1; k<=cptcovprod;k++)            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          }
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        }
   #endif
     savm=oldm;  
     oldm=newm;  
     maxmax=0.;        free_vector(xit,1,n); 
     for(j=1;j<=nlstate;j++){        free_vector(xits,1,n); 
       min=1.;        free_vector(ptt,1,n); 
       max=0.;        free_vector(pt,1,n); 
       for(i=1; i<=nlstate; i++) {        return; 
         sumnew=0;      } 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         prlim[i][j]= newm[i][j]/(1-sumnew);      for (j=1;j<=n;j++) { 
         max=FMAX(max,prlim[i][j]);        ptt[j]=2.0*p[j]-pt[j]; 
         min=FMIN(min,prlim[i][j]);        xit[j]=p[j]-pt[j]; 
       }        pt[j]=p[j]; 
       maxmin=max-min;      } 
       maxmax=FMAX(maxmax,maxmin);      fptt=(*func)(ptt); 
     }      if (fptt < fp) { 
     if(maxmax < ftolpl){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       return prlim;        if (t < 0.0) { 
     }          linmin(p,xit,n,fret,func); 
   }          for (j=1;j<=n;j++) { 
 }            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
 /*************** transition probabilities ***************/          }
   #ifdef DEBUG
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          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);
   double s1, s2;          for(j=1;j<=n;j++){
   /*double t34;*/            printf(" %.12e",xit[j]);
   int i,j,j1, nc, ii, jj;            fprintf(ficlog," %.12e",xit[j]);
           }
     for(i=1; i<= nlstate; i++){          printf("\n");
     for(j=1; j<i;j++){          fprintf(ficlog,"\n");
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #endif
         /*s2 += param[i][j][nc]*cov[nc];*/        }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      } 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    } 
       }  } 
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /**** Prevalence limit (stable prevalence)  ****************/
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       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];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/       matrix by transitions matrix until convergence is reached */
       }  
       ps[i][j]=s2;    int i, ii,j,k;
     }    double min, max, maxmin, maxmax,sumnew=0.;
   }    double **matprod2();
     /*ps[3][2]=1;*/    double **out, cov[NCOVMAX], **pmij();
     double **newm;
   for(i=1; i<= nlstate; i++){    double agefin, delaymax=50 ; /* Max number of years to converge */
      s1=0;  
     for(j=1; j<i; j++)    for (ii=1;ii<=nlstate+ndeath;ii++)
       s1+=exp(ps[i][j]);      for (j=1;j<=nlstate+ndeath;j++){
     for(j=i+1; j<=nlstate+ndeath; j++)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       s1+=exp(ps[i][j]);      }
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)     cov[1]=1.;
       ps[i][j]= exp(ps[i][j])*ps[i][i];   
     for(j=i+1; j<=nlstate+ndeath; j++)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       ps[i][j]= exp(ps[i][j])*ps[i][i];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      newm=savm;
   } /* end i */      /* Covariates have to be included here again */
        cov[2]=agefin;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    
     for(jj=1; jj<= nlstate+ndeath; jj++){        for (k=1; k<=cptcovn;k++) {
       ps[ii][jj]=0;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       ps[ii][ii]=1;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     }        }
   }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      printf("%lf ",ps[ii][jj]);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
    }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     printf("\n ");      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     }  
     printf("\n ");printf("%lf ",cov[2]);*/      savm=oldm;
 /*      oldm=newm;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      maxmax=0.;
   goto end;*/      for(j=1;j<=nlstate;j++){
     return ps;        min=1.;
 }        max=0.;
         for(i=1; i<=nlstate; i++) {
 /**************** Product of 2 matrices ******************/          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)          prlim[i][j]= newm[i][j]/(1-sumnew);
 {          max=FMAX(max,prlim[i][j]);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          min=FMIN(min,prlim[i][j]);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        }
   /* in, b, out are matrice of pointers which should have been initialized        maxmin=max-min;
      before: only the contents of out is modified. The function returns        maxmax=FMAX(maxmax,maxmin);
      a pointer to pointers identical to out */      }
   long i, j, k;      if(maxmax < ftolpl){
   for(i=nrl; i<= nrh; i++)        return prlim;
     for(k=ncolol; k<=ncoloh; k++)      }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    }
         out[i][k] +=in[i][j]*b[j][k];  }
   
   return out;  /*************** transition probabilities ***************/ 
 }  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
 /************* Higher Matrix Product ***************/    double s1, s2;
     /*double t34;*/
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    int i,j,j1, nc, ii, jj;
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      for(i=1; i<= nlstate; i++){
      duration (i.e. until      for(j=1; j<i;j++){
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          /*s2 += param[i][j][nc]*cov[nc];*/
      (typically every 2 years instead of every month which is too big).          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      Model is determined by parameters x and covariates have to be          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
      included manually here.        }
         ps[i][j]=s2;
      */        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
   int i, j, d, h, k;      for(j=i+1; j<=nlstate+ndeath;j++){
   double **out, cov[NCOVMAX];        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double **newm;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   /* Hstepm could be zero and should return the unit matrix */        }
   for (i=1;i<=nlstate+ndeath;i++)        ps[i][j]=s2;
     for (j=1;j<=nlstate+ndeath;j++){      }
       oldm[i][j]=(i==j ? 1.0 : 0.0);    }
       po[i][j][0]=(i==j ? 1.0 : 0.0);      /*ps[3][2]=1;*/
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for(i=1; i<= nlstate; i++){
   for(h=1; h <=nhstepm; h++){       s1=0;
     for(d=1; d <=hstepm; d++){      for(j=1; j<i; j++)
       newm=savm;        s1+=exp(ps[i][j]);
       /* Covariates have to be included here again */      for(j=i+1; j<=nlstate+ndeath; j++)
       cov[1]=1.;        s1+=exp(ps[i][j]);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      ps[i][i]=1./(s1+1.);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      for(j=1; j<i; j++)
       for (k=1; k<=cptcovage;k++)        ps[i][j]= exp(ps[i][j])*ps[i][i];
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      for(j=i+1; j<=nlstate+ndeath; j++)
       for (k=1; k<=cptcovprod;k++)        ps[i][j]= exp(ps[i][j])*ps[i][i];
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     } /* end i */
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      for(jj=1; jj<= nlstate+ndeath; jj++){
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        ps[ii][jj]=0;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        ps[ii][ii]=1;
       savm=oldm;      }
       oldm=newm;    }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
         po[i][j][h]=newm[i][j];      for(jj=1; jj<= nlstate+ndeath; jj++){
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);       printf("%lf ",ps[ii][jj]);
          */     }
       }      printf("\n ");
   } /* end h */      }
   return po;      printf("\n ");printf("%lf ",cov[2]);*/
 }  /*
     for(i=1; i<= npar; i++) printf("%f ",x[i]);
     goto end;*/
 /*************** log-likelihood *************/      return ps;
 double func( double *x)  }
 {  
   int i, ii, j, k, mi, d, kk;  /**************** Product of 2 matrices ******************/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   double sw; /* Sum of weights */  {
   double lli; /* Individual log likelihood */    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   long ipmx;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   /*extern weight */    /* in, b, out are matrice of pointers which should have been initialized 
   /* We are differentiating ll according to initial status */       before: only the contents of out is modified. The function returns
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/       a pointer to pointers identical to out */
   /*for(i=1;i<imx;i++)    long i, j, k;
     printf(" %d\n",s[4][i]);    for(i=nrl; i<= nrh; i++)
   */      for(k=ncolol; k<=ncoloh; k++)
   cov[1]=1.;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    return out;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  }
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /************* Higher Matrix Product ***************/
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  {
         for (kk=1; kk<=cptcovage;kk++) {    /* Computes the transition matrix starting at age 'age' over 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];       'nhstepm*hstepm*stepm' months (i.e. until
         }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
               nhstepm*hstepm matrices. 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       (typically every 2 years instead of every month which is too big 
         savm=oldm;       for the memory).
         oldm=newm;       Model is determined by parameters x and covariates have to be 
               included manually here. 
          
       } /* end mult */       */
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    int i, j, d, h, k;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double **out, cov[NCOVMAX];
       ipmx +=1;    double **newm;
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    /* Hstepm could be zero and should return the unit matrix */
     } /* end of wave */    for (i=1;i<=nlstate+ndeath;i++)
   } /* end of individual */      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        po[i][j][0]=(i==j ? 1.0 : 0.0);
   /* 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 */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   return -l;    for(h=1; h <=nhstepm; h++){
 }      for(d=1; d <=hstepm; d++){
         newm=savm;
         /* Covariates have to be included here again */
 /*********** Maximum Likelihood Estimation ***************/        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 {        for (k=1; k<=cptcovage;k++)
   int i,j, iter;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double **xi,*delti;        for (k=1; k<=cptcovprod;k++)
   double fret;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   xi=matrix(1,npar,1,npar);  
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       xi[i][j]=(i==j ? 1.0 : 0.0);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   printf("Powell\n");  fprintf(ficlog,"Powell\n");        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   powell(p,xi,npar,ftol,&iter,&fret,func);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        oldm=newm;
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
 }          po[i][j][h]=newm[i][j];
           /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
 /**** Computes Hessian and covariance matrix ***/           */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        }
 {    } /* end h */
   double  **a,**y,*x,pd;    return po;
   double **hess;  }
   int i, j,jk;  
   int *indx;  
   /*************** log-likelihood *************/
   double hessii(double p[], double delta, int theta, double delti[]);  double func( double *x)
   double hessij(double p[], double delti[], int i, int j);  {
   void lubksb(double **a, int npar, int *indx, double b[]) ;    int i, ii, j, k, mi, d, kk;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
   hess=matrix(1,npar,1,npar);    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
   printf("\nCalculation of the hessian matrix. Wait...\n");    int s1, s2;
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    double bbh, survp;
   for (i=1;i<=npar;i++){    long ipmx;
     printf("%d",i);fflush(stdout);    /*extern weight */
     fprintf(ficlog,"%d",i);fflush(ficlog);    /* We are differentiating ll according to initial status */
     hess[i][i]=hessii(p,ftolhess,i,delti);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*printf(" %f ",p[i]);*/    /*for(i=1;i<imx;i++) 
     /*printf(" %lf ",hess[i][i]);*/      printf(" %d\n",s[4][i]);
   }    */
      cov[1]=1.;
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {    for(k=1; k<=nlstate; k++) ll[k]=0.;
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);    if(mle==1){
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         hess[i][j]=hessij(p,delti,i,j);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         hess[j][i]=hess[i][j];            for(mi=1; mi<= wav[i]-1; mi++){
         /*printf(" %lf ",hess[i][j]);*/          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("\n");            }
   fprintf(ficlog,"\n");          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   a=matrix(1,npar,1,npar);            }
   y=matrix(1,npar,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   x=vector(1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   indx=ivector(1,npar);            savm=oldm;
   for (i=1;i<=npar;i++)            oldm=newm;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          } /* end mult */
   ludcmp(a,npar,indx,&pd);        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   for (j=1;j<=npar;j++) {          /* But now since version 0.9 we anticipate for bias and large stepm.
     for (i=1;i<=npar;i++) x[i]=0;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     x[j]=1;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     lubksb(a,npar,indx,x);           * the nearest (and in case of equal distance, to the lowest) interval but now
     for (i=1;i<=npar;i++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       matcov[i][j]=x[i];           * (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 .
   printf("\n#Hessian matrix#\n");           * For stepm=1 the results are the same as for previous versions of Imach.
   fprintf(ficlog,"\n#Hessian matrix#\n");           * For stepm > 1 the results are less biased than in previous versions. 
   for (i=1;i<=npar;i++) {           */
     for (j=1;j<=npar;j++) {          s1=s[mw[mi][i]][i];
       printf("%.3e ",hess[i][j]);          s2=s[mw[mi+1][i]][i];
       fprintf(ficlog,"%.3e ",hess[i][j]);          bbh=(double)bh[mi][i]/(double)stepm; 
     }          /* bias is positive if real duration
     printf("\n");           * is higher than the multiple of stepm and negative otherwise.
     fprintf(ficlog,"\n");           */
   }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
   /* Recompute Inverse */            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   for (i=1;i<=npar;i++)               to the likelihood is the probability to die between last step unit time and current 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];               step unit time, which is also the differences between probability to die before dh 
   ludcmp(a,npar,indx,&pd);               and probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
   /*  printf("\n#Hessian matrix recomputed#\n");          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
   for (j=1;j<=npar;j++) {          and not the date of a change in health state. The former idea was
     for (i=1;i<=npar;i++) x[i]=0;          to consider that at each interview the state was recorded
     x[j]=1;          (healthy, disable or death) and IMaCh was corrected; but when we
     lubksb(a,npar,indx,x);          introduced the exact date of death then we should have modified
     for (i=1;i<=npar;i++){          the contribution of an exact death to the likelihood. This new
       y[i][j]=x[i];          contribution is smaller and very dependent of the step unit
       printf("%.3e ",y[i][j]);          stepm. It is no more the probability to die between last interview
       fprintf(ficlog,"%.3e ",y[i][j]);          and month of death but the probability to survive from last
     }          interview up to one month before death multiplied by the
     printf("\n");          probability to die within a month. Thanks to Chris
     fprintf(ficlog,"\n");          Jackson for correcting this bug.  Former versions increased
   }          mortality artificially. The bad side is that we add another loop
   */          which slows down the processing. The difference can be up to 10%
           lower mortality.
   free_matrix(a,1,npar,1,npar);            */
   free_matrix(y,1,npar,1,npar);            lli=log(out[s1][s2] - savm[s1][s2]);
   free_vector(x,1,npar);          }else{
   free_ivector(indx,1,npar);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   free_matrix(hess,1,npar,1,npar);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 }          /*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); */
 /*************** hessian matrix ****************/          ipmx +=1;
 double hessii( double x[], double delta, int theta, double delti[])          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i;        } /* end of wave */
   int l=1, lmax=20;      } /* end of individual */
   double k1,k2;    }  else if(mle==2){
   double p2[NPARMAX+1];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double res;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        for(mi=1; mi<= wav[i]-1; mi++){
   double fx;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int k=0,kmax=10;            for (j=1;j<=nlstate+ndeath;j++){
   double l1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fx=func(x);            }
   for (i=1;i<=npar;i++) p2[i]=x[i];          for(d=0; d<=dh[mi][i]; d++){
   for(l=0 ; l <=lmax; l++){            newm=savm;
     l1=pow(10,l);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     delts=delt;            for (kk=1; kk<=cptcovage;kk++) {
     for(k=1 ; k <kmax; k=k+1){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       delt = delta*(l1*k);            }
       p2[theta]=x[theta] +delt;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       k1=func(p2)-fx;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       p2[theta]=x[theta]-delt;            savm=oldm;
       k2=func(p2)-fx;            oldm=newm;
       /*res= (k1-2.0*fx+k2)/delt/delt; */          } /* end mult */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        
                /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 #ifdef DEBUG          /* But now since version 0.9 we anticipate for bias and large stepm.
       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);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       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);           * (in months) between two waves is not a multiple of stepm, we rounded to 
 #endif           * the nearest (and in case of equal distance, to the lowest) interval but now
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         k=kmax;           * 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
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */           * -stepm/2 to stepm/2 .
         k=kmax; l=lmax*10.;           * 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. 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){           */
         delts=delt;          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
     }          bbh=(double)bh[mi][i]/(double)stepm; 
   }          /* bias is positive if real duration
   delti[theta]=delts;           * is higher than the multiple of stepm and negative otherwise.
   return res;           */
            lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
 double hessij( double x[], double delti[], int thetai,int thetaj)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 {          /*if(lli ==000.0)*/
   int i;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   int l=1, l1, lmax=20;          ipmx +=1;
   double k1,k2,k3,k4,res,fx;          sw += weight[i];
   double p2[NPARMAX+1];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int k;        } /* end of wave */
       } /* end of individual */
   fx=func(x);    }  else if(mle==3){  /* exponential inter-extrapolation */
   for (k=1; k<=2; k++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (i=1;i<=npar;i++) p2[i]=x[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
     k1=func(p2)-fx;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]+delti[thetai]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            }
     k2=func(p2)-fx;          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
     p2[thetai]=x[thetai]-delti[thetai]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            for (kk=1; kk<=cptcovage;kk++) {
     k3=func(p2)-fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
     p2[thetai]=x[thetai]-delti[thetai]/k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     k4=func(p2)-fx;            savm=oldm;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            oldm=newm;
 #ifdef DEBUG          } /* end mult */
     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);        
     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);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 #endif          /* 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 
   return res;           * (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
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
 /************** Inverse of matrix **************/           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 void ludcmp(double **a, int n, int *indx, double *d)           * 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
   int i,imax,j,k;           * -stepm/2 to stepm/2 .
   double big,dum,sum,temp;           * For stepm=1 the results are the same as for previous versions of Imach.
   double *vv;           * For stepm > 1 the results are less biased than in previous versions. 
             */
   vv=vector(1,n);          s1=s[mw[mi][i]][i];
   *d=1.0;          s2=s[mw[mi+1][i]][i];
   for (i=1;i<=n;i++) {          bbh=(double)bh[mi][i]/(double)stepm; 
     big=0.0;          /* bias is positive if real duration
     for (j=1;j<=n;j++)           * is higher than the multiple of stepm and negative otherwise.
       if ((temp=fabs(a[i][j])) > big) big=temp;           */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          /* 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 */
     vv[i]=1.0/big;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for (j=1;j<=n;j++) {          /*if(lli ==000.0)*/
     for (i=1;i<j;i++) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       sum=a[i][j];          ipmx +=1;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          sw += weight[i];
       a[i][j]=sum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     big=0.0;      } /* end of individual */
     for (i=j;i<=n;i++) {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       sum=a[i][j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1;k<j;k++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         sum -= a[i][k]*a[k][j];        for(mi=1; mi<= wav[i]-1; mi++){
       a[i][j]=sum;          for (ii=1;ii<=nlstate+ndeath;ii++)
       if ( (dum=vv[i]*fabs(sum)) >= big) {            for (j=1;j<=nlstate+ndeath;j++){
         big=dum;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         imax=i;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
     }          for(d=0; d<dh[mi][i]; d++){
     if (j != imax) {            newm=savm;
       for (k=1;k<=n;k++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         dum=a[imax][k];            for (kk=1; kk<=cptcovage;kk++) {
         a[imax][k]=a[j][k];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         a[j][k]=dum;            }
       }          
       *d = -(*d);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       vv[imax]=vv[j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     indx[j]=imax;            oldm=newm;
     if (a[j][j] == 0.0) a[j][j]=TINY;          } /* end mult */
     if (j != n) {        
       dum=1.0/(a[j][j]);          s1=s[mw[mi][i]][i];
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          s2=s[mw[mi+1][i]][i];
     }          if( s2 > nlstate){ 
   }            lli=log(out[s1][s2] - savm[s1][s2]);
   free_vector(vv,1,n);  /* Doesn't work */          }else{
 ;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 }          }
           ipmx +=1;
 void lubksb(double **a, int n, int *indx, double b[])          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i,ii=0,ip,j;          /*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]);*/
   double sum;        } /* end of wave */
        } /* end of individual */
   for (i=1;i<=n;i++) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     ip=indx[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     sum=b[ip];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     b[ip]=b[i];        for(mi=1; mi<= wav[i]-1; mi++){
     if (ii)          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            for (j=1;j<=nlstate+ndeath;j++){
     else if (sum) ii=i;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     b[i]=sum;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   for (i=n;i>=1;i--) {          for(d=0; d<dh[mi][i]; d++){
     sum=b[i];            newm=savm;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     b[i]=sum/a[i][i];            for (kk=1; kk<=cptcovage;kk++) {
   }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 }            }
           
 /************ Frequencies ********************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {  /* Some frequencies */            savm=oldm;
              oldm=newm;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          } /* end mult */
   int first;        
   double ***freq; /* Frequencies */          s1=s[mw[mi][i]][i];
   double *pp;          s2=s[mw[mi+1][i]][i];
   double pos, k2, dateintsum=0,k2cpt=0;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   FILE *ficresp;          ipmx +=1;
   char fileresp[FILENAMELENGTH];          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   pp=vector(1,nlstate);          /*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= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        } /* end of wave */
   strcpy(fileresp,"p");      } /* end of individual */
   strcat(fileresp,fileres);    } /* End of if */
   if((ficresp=fopen(fileresp,"w"))==NULL) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     printf("Problem with prevalence resultfile: %s\n", fileresp);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     exit(0);    /*exit(0); */
   }    return -l;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  }
   j1=0;  
    
   j=cptcoveff;  /*********** Maximum Likelihood Estimation ***************/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   first=1;  {
     int i,j, iter;
   for(k1=1; k1<=j;k1++){    double **xi;
     for(i1=1; i1<=ncodemax[k1];i1++){    double fret;
       j1++;    char filerespow[FILENAMELENGTH];
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    xi=matrix(1,npar,1,npar);
         scanf("%d", i);*/    for (i=1;i<=npar;i++)
       for (i=-1; i<=nlstate+ndeath; i++)        for (j=1;j<=npar;j++)
         for (jk=-1; jk<=nlstate+ndeath; jk++)          xi[i][j]=(i==j ? 1.0 : 0.0);
           for(m=agemin; m <= agemax+3; m++)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
             freq[i][jk][m]=0;    strcpy(filerespow,"pow"); 
          strcat(filerespow,fileres);
       dateintsum=0;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       k2cpt=0;      printf("Problem with resultfile: %s\n", filerespow);
       for (i=1; i<=imx; i++) {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         bool=1;    }
         if  (cptcovn>0) {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
           for (z1=1; z1<=cptcoveff; z1++)    for (i=1;i<=nlstate;i++)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for(j=1;j<=nlstate+ndeath;j++)
               bool=0;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         }    fprintf(ficrespow,"\n");
         if (bool==1) {    powell(p,xi,npar,ftol,&iter,&fret,func);
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);    fclose(ficrespow);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
               if(agev[m][i]==0) agev[m][i]=agemax+1;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
               if(agev[m][i]==1) agev[m][i]=agemax+2;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  }
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  
               }  /**** Computes Hessian and covariance matrix ***/
                void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  {
                 dateintsum=dateintsum+k2;    double  **a,**y,*x,pd;
                 k2cpt++;    double **hess;
               }    int i, j,jk;
             }    int *indx;
           }  
         }    double hessii(double p[], double delta, int theta, double delti[]);
       }    double hessij(double p[], double delti[], int i, int j);
            void lubksb(double **a, int npar, int *indx, double b[]) ;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   
       if  (cptcovn>0) {    hess=matrix(1,npar,1,npar);
         fprintf(ficresp, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    printf("\nCalculation of the hessian matrix. Wait...\n");
         fprintf(ficresp, "**********\n#");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       }    for (i=1;i<=npar;i++){
       for(i=1; i<=nlstate;i++)      printf("%d",i);fflush(stdout);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      fprintf(ficlog,"%d",i);fflush(ficlog);
       fprintf(ficresp, "\n");      hess[i][i]=hessii(p,ftolhess,i,delti);
            /*printf(" %f ",p[i]);*/
       for(i=(int)agemin; i <= (int)agemax+3; i++){      /*printf(" %lf ",hess[i][i]);*/
         if(i==(int)agemax+3){    }
           fprintf(ficlog,"Total");    
         }else{    for (i=1;i<=npar;i++) {
           if(first==1){      for (j=1;j<=npar;j++)  {
             first=0;        if (j>i) { 
             printf("See log file for details...\n");          printf(".%d%d",i,j);fflush(stdout);
           }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           fprintf(ficlog,"Age %d", i);          hess[i][j]=hessij(p,delti,i,j);
         }          hess[j][i]=hess[i][j];    
         for(jk=1; jk <=nlstate ; jk++){          /*printf(" %lf ",hess[i][j]);*/
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        }
             pp[jk] += freq[jk][m][i];      }
         }    }
         for(jk=1; jk <=nlstate ; jk++){    printf("\n");
           for(m=-1, pos=0; m <=0 ; m++)    fprintf(ficlog,"\n");
             pos += freq[jk][m][i];  
           if(pp[jk]>=1.e-10){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
             if(first==1){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    
             }    a=matrix(1,npar,1,npar);
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    y=matrix(1,npar,1,npar);
           }else{    x=vector(1,npar);
             if(first==1)    indx=ivector(1,npar);
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    for (i=1;i<=npar;i++)
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           }    ludcmp(a,npar,indx,&pd);
         }  
     for (j=1;j<=npar;j++) {
         for(jk=1; jk <=nlstate ; jk++){      for (i=1;i<=npar;i++) x[i]=0;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      x[j]=1;
             pp[jk] += freq[jk][m][i];      lubksb(a,npar,indx,x);
         }      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
         for(jk=1,pos=0; jk <=nlstate ; jk++)      }
           pos += pp[jk];    }
         for(jk=1; jk <=nlstate ; jk++){  
           if(pos>=1.e-5){    printf("\n#Hessian matrix#\n");
             if(first==1)    fprintf(ficlog,"\n#Hessian matrix#\n");
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    for (i=1;i<=npar;i++) { 
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      for (j=1;j<=npar;j++) { 
           }else{        printf("%.3e ",hess[i][j]);
             if(first==1)        fprintf(ficlog,"%.3e ",hess[i][j]);
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      }
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      printf("\n");
           }      fprintf(ficlog,"\n");
           if( i <= (int) agemax){    }
             if(pos>=1.e-5){  
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    /* Recompute Inverse */
               probs[i][jk][j1]= pp[jk]/pos;    for (i=1;i<=npar;i++)
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
             }    ludcmp(a,npar,indx,&pd);
             else  
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    /*  printf("\n#Hessian matrix recomputed#\n");
           }  
         }    for (j=1;j<=npar;j++) {
              for (i=1;i<=npar;i++) x[i]=0;
         for(jk=-1; jk <=nlstate+ndeath; jk++)      x[j]=1;
           for(m=-1; m <=nlstate+ndeath; m++)      lubksb(a,npar,indx,x);
             if(freq[jk][m][i] !=0 ) {      for (i=1;i<=npar;i++){ 
             if(first==1)        y[i][j]=x[i];
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        printf("%.3e ",y[i][j]);
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);        fprintf(ficlog,"%.3e ",y[i][j]);
             }      }
         if(i <= (int) agemax)      printf("\n");
           fprintf(ficresp,"\n");      fprintf(ficlog,"\n");
         if(first==1)    }
           printf("Others in log...\n");    */
         fprintf(ficlog,"\n");  
       }    free_matrix(a,1,npar,1,npar);
     }    free_matrix(y,1,npar,1,npar);
   }    free_vector(x,1,npar);
   dateintmean=dateintsum/k2cpt;    free_ivector(indx,1,npar);
      free_matrix(hess,1,npar,1,npar);
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  }
    
   /* End of Freq */  /*************** hessian matrix ****************/
 }  double hessii( double x[], double delta, int theta, double delti[])
   {
 /************ Prevalence ********************/    int i;
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    int l=1, lmax=20;
 {  /* Some frequencies */    double k1,k2;
      double p2[NPARMAX+1];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    double res;
   double ***freq; /* Frequencies */    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double *pp;    double fx;
   double pos, k2;    int k=0,kmax=10;
     double l1;
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    fx=func(x);
      for (i=1;i<=npar;i++) p2[i]=x[i];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    for(l=0 ; l <=lmax; l++){
   j1=0;      l1=pow(10,l);
        delts=delt;
   j=cptcoveff;      for(k=1 ; k <kmax; k=k+1){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        delt = delta*(l1*k);
          p2[theta]=x[theta] +delt;
   for(k1=1; k1<=j;k1++){        k1=func(p2)-fx;
     for(i1=1; i1<=ncodemax[k1];i1++){        p2[theta]=x[theta]-delt;
       j1++;        k2=func(p2)-fx;
              /*res= (k1-2.0*fx+k2)/delt/delt; */
       for (i=-1; i<=nlstate+ndeath; i++)          res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         for (jk=-1; jk<=nlstate+ndeath; jk++)          
           for(m=agemin; m <= agemax+3; m++)  #ifdef DEBUG
             freq[i][jk][m]=0;        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);
       for (i=1; i<=imx; i++) {  #endif
         bool=1;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if  (cptcovn>0) {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           for (z1=1; z1<=cptcoveff; z1++)          k=kmax;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        }
               bool=0;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         }          k=kmax; l=lmax*10.;
         if (bool==1) {        }
           for(m=firstpass; m<=lastpass; m++){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
             k2=anint[m][i]+(mint[m][i]/12.);          delts=delt;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        }
               if(agev[m][i]==0) agev[m][i]=agemax+1;      }
               if(agev[m][i]==1) agev[m][i]=agemax+2;    }
               if (m<lastpass) {    delti[theta]=delts;
                 if (calagedate>0)    return res; 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    
                 else  }
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  double hessij( double x[], double delti[], int thetai,int thetaj)
               }  {
             }    int i;
           }    int l=1, l1, lmax=20;
         }    double k1,k2,k3,k4,res,fx;
       }    double p2[NPARMAX+1];
       for(i=(int)agemin; i <= (int)agemax+3; i++){    int k;
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    fx=func(x);
             pp[jk] += freq[jk][m][i];    for (k=1; k<=2; k++) {
         }      for (i=1;i<=npar;i++) p2[i]=x[i];
         for(jk=1; jk <=nlstate ; jk++){      p2[thetai]=x[thetai]+delti[thetai]/k;
           for(m=-1, pos=0; m <=0 ; m++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
             pos += freq[jk][m][i];      k1=func(p2)-fx;
         }    
              p2[thetai]=x[thetai]+delti[thetai]/k;
         for(jk=1; jk <=nlstate ; jk++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      k2=func(p2)-fx;
             pp[jk] += freq[jk][m][i];    
         }      p2[thetai]=x[thetai]-delti[thetai]/k;
              p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      k3=func(p2)-fx;
            
         for(jk=1; jk <=nlstate ; jk++){          p2[thetai]=x[thetai]-delti[thetai]/k;
           if( i <= (int) agemax){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             if(pos>=1.e-5){      k4=func(p2)-fx;
               probs[i][jk][j1]= pp[jk]/pos;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
             }  #ifdef DEBUG
           }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         }/* end jk */      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);
       }/* end i */  #endif
     } /* end i1 */    }
   } /* end k1 */    return res;
   }
    
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /************** Inverse of matrix **************/
   free_vector(pp,1,nlstate);  void ludcmp(double **a, int n, int *indx, double *d) 
    { 
 }  /* End of Freq */    int i,imax,j,k; 
     double big,dum,sum,temp; 
 /************* Waves Concatenation ***************/    double *vv; 
    
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    vv=vector(1,n); 
 {    *d=1.0; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    for (i=1;i<=n;i++) { 
      Death is a valid wave (if date is known).      big=0.0; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      for (j=1;j<=n;j++) 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        if ((temp=fabs(a[i][j])) > big) big=temp; 
      and mw[mi+1][i]. dh depends on stepm.      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
      */      vv[i]=1.0/big; 
     } 
   int i, mi, m;    for (j=1;j<=n;j++) { 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      for (i=1;i<j;i++) { 
      double sum=0., jmean=0.;*/        sum=a[i][j]; 
   int first;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   int j, k=0,jk, ju, jl;        a[i][j]=sum; 
   double sum=0.;      } 
   first=0;      big=0.0; 
   jmin=1e+5;      for (i=j;i<=n;i++) { 
   jmax=-1;        sum=a[i][j]; 
   jmean=0.;        for (k=1;k<j;k++) 
   for(i=1; i<=imx; i++){          sum -= a[i][k]*a[k][j]; 
     mi=0;        a[i][j]=sum; 
     m=firstpass;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     while(s[m][i] <= nlstate){          big=dum; 
       if(s[m][i]>=1)          imax=i; 
         mw[++mi][i]=m;        } 
       if(m >=lastpass)      } 
         break;      if (j != imax) { 
       else        for (k=1;k<=n;k++) { 
         m++;          dum=a[imax][k]; 
     }/* end while */          a[imax][k]=a[j][k]; 
     if (s[m][i] > nlstate){          a[j][k]=dum; 
       mi++;     /* Death is another wave */        } 
       /* if(mi==0)  never been interviewed correctly before death */        *d = -(*d); 
          /* Only death is a correct wave */        vv[imax]=vv[j]; 
       mw[mi][i]=m;      } 
     }      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
     wav[i]=mi;      if (j != n) { 
     if(mi==0){        dum=1.0/(a[j][j]); 
       if(first==0){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);      } 
         first=1;    } 
       }    free_vector(vv,1,n);  /* Doesn't work */
       if(first==1){  ;
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);  } 
       }  
     } /* end mi==0 */  void lubksb(double **a, int n, int *indx, double b[]) 
   }  { 
     int i,ii=0,ip,j; 
   for(i=1; i<=imx; i++){    double sum; 
     for(mi=1; mi<wav[i];mi++){   
       if (stepm <=0)    for (i=1;i<=n;i++) { 
         dh[mi][i]=1;      ip=indx[i]; 
       else{      sum=b[ip]; 
         if (s[mw[mi+1][i]][i] > nlstate) {      b[ip]=b[i]; 
           if (agedc[i] < 2*AGESUP) {      if (ii) 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           if(j==0) j=1;  /* Survives at least one month after exam */      else if (sum) ii=i; 
           k=k+1;      b[i]=sum; 
           if (j >= jmax) jmax=j;    } 
           if (j <= jmin) jmin=j;    for (i=n;i>=1;i--) { 
           sum=sum+j;      sum=b[i]; 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           }      b[i]=sum/a[i][i]; 
         }    } 
         else{  } 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;  /************ Frequencies ********************/
           if (j >= jmax) jmax=j;  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)
           else if (j <= jmin)jmin=j;  {  /* Some frequencies */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    
           sum=sum+j;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         }    int first;
         jk= j/stepm;    double ***freq; /* Frequencies */
         jl= j -jk*stepm;    double *pp, **prop;
         ju= j -(jk+1)*stepm;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         if(jl <= -ju)    FILE *ficresp;
           dh[mi][i]=jk;    char fileresp[FILENAMELENGTH];
         else    
           dh[mi][i]=jk+1;    pp=vector(1,nlstate);
         if(dh[mi][i]==0)    prop=matrix(1,nlstate,iagemin,iagemax+3);
           dh[mi][i]=1; /* At least one step */    strcpy(fileresp,"p");
       }    strcat(fileresp,fileres);
     }    if((ficresp=fopen(fileresp,"w"))==NULL) {
   }      printf("Problem with prevalence resultfile: %s\n", fileresp);
   jmean=sum/k;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      exit(0);
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    }
  }    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
 /*********** Tricode ****************************/    
 void tricode(int *Tvar, int **nbcode, int imx)    j=cptcoveff;
 {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;    first=1;
   cptcoveff=0;  
      for(k1=1; k1<=j;k1++){
   for (k=0; k<19; k++) Ndum[k]=0;      for(i1=1; i1<=ncodemax[k1];i1++){
   for (k=1; k<=7; k++) ncodemax[k]=0;        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          scanf("%d", i);*/
     for (i=1; i<=imx; i++) {        for (i=-1; i<=nlstate+ndeath; i++)  
       ij=(int)(covar[Tvar[j]][i]);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       Ndum[ij]++;            for(m=iagemin; m <= iagemax+3; m++)
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              freq[i][jk][m]=0;
       if (ij > cptcode) cptcode=ij;  
     }      for (i=1; i<=nlstate; i++)  
         for(m=iagemin; m <= iagemax+3; m++)
     for (i=0; i<=cptcode; i++) {          prop[i][m]=0;
       if(Ndum[i]!=0) ncodemax[j]++;        
     }        dateintsum=0;
     ij=1;        k2cpt=0;
         for (i=1; i<=imx; i++) {
           bool=1;
     for (i=1; i<=ncodemax[j]; i++) {          if  (cptcovn>0) {
       for (k=0; k<=19; k++) {            for (z1=1; z1<=cptcoveff; z1++) 
         if (Ndum[k] != 0) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           nbcode[Tvar[j]][ij]=k;                bool=0;
                    }
           ij++;          if (bool==1){
         }            for(m=firstpass; m<=lastpass; m++){
         if (ij > ncodemax[j]) break;              k2=anint[m][i]+(mint[m][i]/12.);
       }                /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   }                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
  for (k=0; k<19; k++) Ndum[k]=0;                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
  for (i=1; i<=ncovmodel-2; i++) {                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    ij=Tvar[i];                }
    Ndum[ij]++;                
  }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
  ij=1;                  k2cpt++;
  for (i=1; i<=10; i++) {                }
    if((Ndum[i]!=0) && (i<=ncovcol)){                /*}*/
      Tvaraff[ij]=i;            }
      ij++;          }
    }        }
  }         
          /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
  cptcoveff=ij-1;  
 }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
 /*********** Health Expectancies ****************/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\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 )        }
         for(i=1; i<=nlstate;i++) 
 {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   /* Health expectancies */        fprintf(ficresp, "\n");
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        
   double age, agelim, hf;        for(i=iagemin; i <= iagemax+3; i++){
   double ***p3mat,***varhe;          if(i==iagemax+3){
   double **dnewm,**doldm;            fprintf(ficlog,"Total");
   double *xp;          }else{
   double **gp, **gm;            if(first==1){
   double ***gradg, ***trgradg;              first=0;
   int theta;              printf("See log file for details...\n");
             }
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            fprintf(ficlog,"Age %d", i);
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate*2,1,npar);          for(jk=1; jk <=nlstate ; jk++){
   doldm=matrix(1,nlstate*2,1,nlstate*2);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                pp[jk] += freq[jk][m][i]; 
   fprintf(ficreseij,"# Health expectancies\n");          }
   fprintf(ficreseij,"# Age");          for(jk=1; jk <=nlstate ; jk++){
   for(i=1; i<=nlstate;i++)            for(m=-1, pos=0; m <=0 ; m++)
     for(j=1; j<=nlstate;j++)              pos += freq[jk][m][i];
       fprintf(ficreseij," %1d-%1d (SE)",i,j);            if(pp[jk]>=1.e-10){
   fprintf(ficreseij,"\n");              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   if(estepm < stepm){              }
     printf ("Problem %d lower than %d\n",estepm, stepm);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }            }else{
   else  hstepm=estepm;                if(first==1)
   /* We compute the life expectancy from trapezoids spaced every estepm months                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    * This is mainly to measure the difference between two models: for example              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    * if stepm=24 months pijx are given only every 2 years and by summing them            }
    * we are calculating an estimate of the Life Expectancy assuming a linear          }
    * progression inbetween and thus overestimating or underestimating according  
    * to the curvature of the survival function. If, for the same date, we          for(jk=1; jk <=nlstate ; jk++){
    * estimate the model with stepm=1 month, we can keep estepm to 24 months            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
    * to compare the new estimate of Life expectancy with the same linear              pp[jk] += freq[jk][m][i];
    * hypothesis. A more precise result, taking into account a more precise          }       
    * curvature will be obtained if estepm is as small as stepm. */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
   /* For example we decided to compute the life expectancy with the smallest unit */            posprop += prop[jk][i];
   /* 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(jk=1; jk <=nlstate ; jk++){
      nstepm is the number of stepm from age to agelin.            if(pos>=1.e-5){
      Look at hpijx to understand the reason of that which relies in memory size              if(first==1)
      and note for a fixed period like estepm months */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      survival function given by stepm (the optimization length). Unfortunately it            }else{
      means that if the survival funtion is printed only each two years of age and if              if(first==1)
      you sum them up and add 1 year (area under the trapezoids) you won't get the same                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      results. So we changed our mind and took the option of the best precision.              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            if( i <= iagemax){
               if(pos>=1.e-5){
   agelim=AGESUP;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                /*probs[i][jk][j1]= pp[jk]/pos;*/
     /* nhstepm age range expressed in number of stepm */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     nstepm=(int) rint((agelim-age)*YEARM/stepm);              }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */              else
     /* if (stepm >= YEARM) hstepm=1;*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          
     gp=matrix(0,nhstepm,1,nlstate*2);          for(jk=-1; jk <=nlstate+ndeath; jk++)
     gm=matrix(0,nhstepm,1,nlstate*2);            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              if(first==1)
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                }
           if(i <= iagemax)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            fprintf(ficresp,"\n");
           if(first==1)
     /* Computing Variances of health expectancies */            printf("Others in log...\n");
           fprintf(ficlog,"\n");
      for(theta=1; theta <=npar; theta++){        }
       for(i=1; i<=npar; i++){      }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }    dateintmean=dateintsum/k2cpt; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     
      fclose(ficresp);
       cptj=0;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
       for(j=1; j<= nlstate; j++){    free_vector(pp,1,nlstate);
         for(i=1; i<=nlstate; i++){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
           cptj=cptj+1;    /* End of Freq */
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){  }
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  /************ Prevalence ********************/
         }  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       }  {  
          /* 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).
       for(i=1; i<=npar; i++)       We still use firstpass and lastpass as another selection.
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     
          int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       cptj=0;    double ***freq; /* Frequencies */
       for(j=1; j<= nlstate; j++){    double *pp, **prop;
         for(i=1;i<=nlstate;i++){    double pos,posprop; 
           cptj=cptj+1;    double  y2; /* in fractional years */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    int iagemin, iagemax;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }    iagemin= (int) agemin;
         }    iagemax= (int) agemax;
       }    /*pp=vector(1,nlstate);*/
       for(j=1; j<= nlstate*2; j++)    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         for(h=0; h<=nhstepm-1; h++){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    j1=0;
         }    
      }    j=cptcoveff;
        if (cptcovn<1) {j=1;ncodemax[1]=1;}
 /* End theta */    
     for(k1=1; k1<=j;k1++){
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
      for(h=0; h<=nhstepm-1; h++)        
       for(j=1; j<=nlstate*2;j++)        for (i=1; i<=nlstate; i++)  
         for(theta=1; theta <=npar; theta++)          for(m=iagemin; m <= iagemax+3; m++)
           trgradg[h][j][theta]=gradg[h][theta][j];            prop[i][m]=0.0;
             
         for (i=1; i<=imx; i++) { /* Each individual */
      for(i=1;i<=nlstate*2;i++)          bool=1;
       for(j=1;j<=nlstate*2;j++)          if  (cptcovn>0) {
         varhe[i][j][(int)age] =0.;            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      printf("%d|",(int)age);fflush(stdout);                bool=0;
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);          } 
      for(h=0;h<=nhstepm-1;h++){          if (bool==1) { 
       for(k=0;k<=nhstepm-1;k++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         for(i=1;i<=nlstate*2;i++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           for(j=1;j<=nlstate*2;j++)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     /* Computing expectancies */                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     for(i=1; i<=nlstate;i++)                  prop[s[m][i]][iagemax+3] += weight[i]; 
       for(j=1; j<=nlstate;j++)                } 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){              }
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            } /* end selection of waves */
                    }
 /* 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]);*/        }
         for(i=iagemin; i <= iagemax+3; i++){  
         }          
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     fprintf(ficreseij,"%3.0f",age );            posprop += prop[jk][i]; 
     cptj=0;          } 
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){          for(jk=1; jk <=nlstate ; jk++){     
         cptj++;            if( i <=  iagemax){ 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );              if(posprop>=1.e-5){ 
       }                probs[i][jk][j1]= prop[jk][i]/posprop;
     fprintf(ficreseij,"\n");              } 
                } 
     free_matrix(gm,0,nhstepm,1,nlstate*2);          }/* end jk */ 
     free_matrix(gp,0,nhstepm,1,nlstate*2);        }/* end i */ 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      } /* end i1 */
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    } /* end k1 */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
   }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   printf("\n");    /*free_vector(pp,1,nlstate);*/
   fprintf(ficlog,"\n");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   free_vector(xp,1,npar);  
   free_matrix(dnewm,1,nlstate*2,1,npar);  /************* Waves Concatenation ***************/
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  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)
 }  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 /************ Variance ******************/       Death is a valid wave (if date is known).
 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)       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]
   /* Variance of health expectancies */       and mw[mi+1][i]. dh depends on stepm.
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       */
   /* double **newm;*/  
   double **dnewm,**doldm;    int i, mi, m;
   double **dnewmp,**doldmp;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   int i, j, nhstepm, hstepm, h, nstepm ;       double sum=0., jmean=0.;*/
   int k, cptcode;    int first;
   double *xp;    int j, k=0,jk, ju, jl;
   double **gp, **gm;  /* for var eij */    double sum=0.;
   double ***gradg, ***trgradg; /*for var eij */    first=0;
   double **gradgp, **trgradgp; /* for var p point j */    jmin=1e+5;
   double *gpp, *gmp; /* for var p point j */    jmax=-1;
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */    jmean=0.;
   double ***p3mat;    for(i=1; i<=imx; i++){
   double age,agelim, hf;      mi=0;
   int theta;      m=firstpass;
   char digit[4];      while(s[m][i] <= nlstate){
   char digitp[16];        if(s[m][i]>=1)
           mw[++mi][i]=m;
   char fileresprobmorprev[FILENAMELENGTH];        if(m >=lastpass)
           break;
   if(popbased==1)        else
     strcpy(digitp,"-populbased-");          m++;
   else      }/* end while */
     strcpy(digitp,"-stablbased-");      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
   strcpy(fileresprobmorprev,"prmorprev");        /* if(mi==0)  never been interviewed correctly before death */
   sprintf(digit,"%-d",ij);           /* Only death is a correct wave */
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/        mw[mi][i]=m;
   strcat(fileresprobmorprev,digit); /* Tvar to be done */      }
   strcat(fileresprobmorprev,digitp); /* Popbased or not */  
   strcat(fileresprobmorprev,fileres);      wav[i]=mi;
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {      if(mi==0){
     printf("Problem with resultfile: %s\n", fileresprobmorprev);        if(first==0){
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
   }          first=1;
   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);        if(first==1){
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);        }
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){      } /* end mi==0 */
     fprintf(ficresprobmorprev," p.%-d SE",j);    } /* End individuals */
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);    for(i=1; i<=imx; i++){
   }        for(mi=1; mi<wav[i];mi++){
   fprintf(ficresprobmorprev,"\n");        if (stepm <=0)
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          dh[mi][i]=1;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);        else{
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     exit(0);            if (agedc[i] < 2*AGESUP) {
   }            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   else{            if(j==0) j=1;  /* Survives at least one month after exam */
     fprintf(ficgp,"\n# Routine varevsij");            k=k+1;
   }            if (j >= jmax) jmax=j;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {            if (j <= jmin) jmin=j;
     printf("Problem with html file: %s\n", optionfilehtm);            sum=sum+j;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     exit(0);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   }            if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   else{            }
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");          }
   }          else{
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   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");            k=k+1;
   fprintf(ficresvij,"# Age");            if (j >= jmax) jmax=j;
   for(i=1; i<=nlstate;i++)            else if (j <= jmin)jmin=j;
     for(j=1; j<=nlstate;j++)            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            /*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]);*/
   fprintf(ficresvij,"\n");            if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             sum=sum+j;
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate,1,npar);          jk= j/stepm;
   doldm=matrix(1,nlstate,1,nlstate);          jl= j -jk*stepm;
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);          ju= j -(jk+1)*stepm;
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          if(mle <=1){ 
             if(jl==0){
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);              dh[mi][i]=jk;
   gpp=vector(nlstate+1,nlstate+ndeath);              bh[mi][i]=0;
   gmp=vector(nlstate+1,nlstate+ndeath);            }else{ /* We want a negative bias in order to only have interpolation ie
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/                    * at the price of an extra matrix product in likelihood */
                dh[mi][i]=jk+1;
   if(estepm < stepm){              bh[mi][i]=ju;
     printf ("Problem %d lower than %d\n",estepm, stepm);            }
   }          }else{
   else  hstepm=estepm;              if(jl <= -ju){
   /* For example we decided to compute the life expectancy with the smallest unit */              dh[mi][i]=jk;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              bh[mi][i]=jl;       /* bias is positive if real duration
      nhstepm is the number of hstepm from age to agelim                                   * is higher than the multiple of stepm and negative otherwise.
      nstepm is the number of stepm from age to agelin.                                   */
      Look at hpijx to understand the reason of that which relies in memory size            }
      and note for a fixed period like k years */            else{
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              dh[mi][i]=jk+1;
      survival function given by stepm (the optimization length). Unfortunately it              bh[mi][i]=ju;
      means that if the survival funtion is printed only each two years of age and if            }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            if(dh[mi][i]==0){
      results. So we changed our mind and took the option of the best precision.              dh[mi][i]=1; /* At least one step */
   */              bh[mi][i]=ju; /* At least one step */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */              /*  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);*/
   agelim = AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        } /* end if mle */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      } /* end wave */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    jmean=sum/k;
     gp=matrix(0,nhstepm,1,nlstate);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     gm=matrix(0,nhstepm,1,nlstate);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    }
   
     for(theta=1; theta <=npar; theta++){  /*********** Tricode ****************************/
       for(i=1; i<=npar; i++){ /* Computes gradient */  void tricode(int *Tvar, int **nbcode, int imx)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int Ndum[20],ij=1, k, j, i, maxncov=19;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int cptcode=0;
     cptcoveff=0; 
       if (popbased==1) {   
         for(i=1; i<=nlstate;i++)    for (k=0; k<maxncov; k++) Ndum[k]=0;
           prlim[i][i]=probs[(int)age][i][ij];    for (k=1; k<=7; k++) ncodemax[k]=0;
       }  
      for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for(j=1; j<= nlstate; j++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         for(h=0; h<=nhstepm; h++){                                 modality*/ 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        Ndum[ij]++; /*store the modality */
         }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       /* This for computing forces of mortality (h=1)as a weighted average */                                         Tvar[j]. If V=sex and male is 0 and 
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){                                         female is 1, then  cptcode=1.*/
         for(i=1; i<= nlstate; i++)      }
           gpp[j] += prlim[i][i]*p3mat[i][j][1];  
       }          for (i=0; i<=cptcode; i++) {
       /* end force of mortality */        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 */
       }
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      ij=1; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (i=1; i<=ncodemax[j]; i++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (k=0; k<= maxncov; k++) {
            if (Ndum[k] != 0) {
       if (popbased==1) {            nbcode[Tvar[j]][ij]=k; 
         for(i=1; i<=nlstate;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; */
           prlim[i][i]=probs[(int)age][i][ij];            
       }            ij++;
           }
       for(j=1; j<= nlstate; j++){          if (ij > ncodemax[j]) break; 
         for(h=0; h<=nhstepm; h++){        }  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      } 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    }  
         }  
       }   for (k=0; k< maxncov; k++) Ndum[k]=0;
       /* This for computing force of mortality (h=1)as a weighted average */  
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){   for (i=1; i<=ncovmodel-2; i++) { 
         for(i=1; i<= nlstate; i++)     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           gmp[j] += prlim[i][i]*p3mat[i][j][1];     ij=Tvar[i];
       }         Ndum[ij]++;
       /* end force of mortality */   }
   
       for(j=1; j<= nlstate; j++) /* vareij */   ij=1;
         for(h=0; h<=nhstepm; h++){   for (i=1; i<= maxncov; i++) {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];     if((Ndum[i]!=0) && (i<=ncovcol)){
         }       Tvaraff[ij]=i; /*For printing */
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */       ij++;
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];     }
       }   }
    
     } /* End theta */   cptcoveff=ij-1; /*Number of simple covariates*/
   }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */  
   /*********** Health Expectancies ****************/
     for(h=0; h<=nhstepm; h++) /* veij */  
       for(j=1; j<=nlstate;j++)  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 )
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];  {
     /* Health expectancies */
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       for(theta=1; theta <=npar; theta++)    double age, agelim, hf;
         trgradgp[j][theta]=gradgp[theta][j];    double ***p3mat,***varhe;
     double **dnewm,**doldm;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    double *xp;
     for(i=1;i<=nlstate;i++)    double **gp, **gm;
       for(j=1;j<=nlstate;j++)    double ***gradg, ***trgradg;
         vareij[i][j][(int)age] =0.;    int theta;
   
     for(h=0;h<=nhstepm;h++){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       for(k=0;k<=nhstepm;k++){    xp=vector(1,npar);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    dnewm=matrix(1,nlstate*nlstate,1,npar);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         for(i=1;i<=nlstate;i++)    
           for(j=1;j<=nlstate;j++)    fprintf(ficreseij,"# Health expectancies\n");
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    fprintf(ficreseij,"# Age");
       }    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
     /* pptj */    fprintf(ficreseij,"\n");
     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);    if(estepm < stepm){
     for(j=nlstate+1;j<=nlstate+ndeath;j++)      printf ("Problem %d lower than %d\n",estepm, stepm);
       for(i=nlstate+1;i<=nlstate+ndeath;i++)    }
         varppt[j][i]=doldmp[j][i];    else  hstepm=estepm;   
     /* end ppptj */    /* We compute the life expectancy from trapezoids spaced every estepm months
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);       * This is mainly to measure the difference between two models: for example
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);     * 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 
     if (popbased==1) {     * progression in between and thus overestimating or underestimating according
       for(i=1; i<=nlstate;i++)     * to the curvature of the survival function. If, for the same date, we 
         prlim[i][i]=probs[(int)age][i][ij];     * 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 
         * hypothesis. A more precise result, taking into account a more precise
     /* This for computing force of mortality (h=1)as a weighted average */     * curvature will be obtained if estepm is as small as stepm. */
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){  
       for(i=1; i<= nlstate; i++)    /* For example we decided to compute the life expectancy with the smallest unit */
         gmp[j] += prlim[i][i]*p3mat[i][j][1];    /* 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 
     /* end force of mortality */       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);       and note for a fixed period like estepm months */
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));       survival function given by stepm (the optimization length). Unfortunately it
       for(i=1; i<=nlstate;i++){       means that if the survival funtion is printed only each two years of age and if
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       }       results. So we changed our mind and took the option of the best precision.
     }    */
     fprintf(ficresprobmorprev,"\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     fprintf(ficresvij,"%.0f ",age );    agelim=AGESUP;
     for(i=1; i<=nlstate;i++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       for(j=1; j<=nlstate;j++){      /* nhstepm age range expressed in number of stepm */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fprintf(ficresvij,"\n");      /* if (stepm >= YEARM) hstepm=1;*/
     free_matrix(gp,0,nhstepm,1,nlstate);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     free_matrix(gm,0,nhstepm,1,nlstate);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   } /* End age */  
   free_vector(gpp,nlstate+1,nlstate+ndeath);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   free_vector(gmp,nlstate+1,nlstate+ndeath);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   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(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");  
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);      /* Computing Variances of health expectancies */
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);  
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);       for(theta=1; theta <=npar; theta++){
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);        for(i=1; i<=npar; i++){ 
   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);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   free_vector(xp,1,npar);    
   free_matrix(doldm,1,nlstate,1,nlstate);        cptj=0;
   free_matrix(dnewm,1,nlstate,1,npar);        for(j=1; j<= nlstate; j++){
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          for(i=1; i<=nlstate; i++){
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);            cptj=cptj+1;
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   fclose(ficresprobmorprev);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   fclose(ficgp);            }
   fclose(fichtm);          }
         }
 }       
        
 /************ Variance of prevlim ******************/        for(i=1; i<=npar; 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)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /* Variance of prevalence limit */        
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        cptj=0;
   double **newm;        for(j=1; j<= nlstate; j++){
   double **dnewm,**doldm;          for(i=1;i<=nlstate;i++){
   int i, j, nhstepm, hstepm;            cptj=cptj+1;
   int k, cptcode;            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   double *xp;  
   double *gp, *gm;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   double **gradg, **trgradg;            }
   double age,agelim;          }
   int theta;        }
            for(j=1; j<= nlstate*nlstate; j++)
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");          for(h=0; h<=nhstepm-1; h++){
   fprintf(ficresvpl,"# Age");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   for(i=1; i<=nlstate;i++)          }
       fprintf(ficresvpl," %1d-%1d",i,i);       } 
   fprintf(ficresvpl,"\n");     
   /* End theta */
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);  
         for(h=0; h<=nhstepm-1; h++)
   hstepm=1*YEARM; /* Every year of age */        for(j=1; j<=nlstate*nlstate;j++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          for(theta=1; theta <=npar; theta++)
   agelim = AGESUP;            trgradg[h][j][theta]=gradg[h][theta][j];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;       for(i=1;i<=nlstate*nlstate;i++)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for(j=1;j<=nlstate*nlstate;j++)
     gradg=matrix(1,npar,1,nlstate);          varhe[i][j][(int)age] =0.;
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     for(theta=1; theta <=npar; theta++){       for(h=0;h<=nhstepm-1;h++){
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(k=0;k<=nhstepm-1;k++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(i=1;i<=nlstate*nlstate;i++)
       for(i=1;i<=nlstate;i++)            for(j=1;j<=nlstate*nlstate;j++)
         gp[i] = prlim[i][i];              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
            }
       for(i=1; i<=npar; i++) /* Computes gradient */      }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      /* Computing expectancies */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for(i=1; i<=nlstate;i++)
       for(i=1;i<=nlstate;i++)        for(j=1; j<=nlstate;j++)
         gm[i] = prlim[i][i];          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       for(i=1;i<=nlstate;i++)            
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  /* 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]);*/
     } /* End theta */  
           }
     trgradg =matrix(1,nlstate,1,npar);  
       fprintf(ficreseij,"%3.0f",age );
     for(j=1; j<=nlstate;j++)      cptj=0;
       for(theta=1; theta <=npar; theta++)      for(i=1; i<=nlstate;i++)
         trgradg[j][theta]=gradg[theta][j];        for(j=1; j<=nlstate;j++){
           cptj++;
     for(i=1;i<=nlstate;i++)          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       varpl[i][(int)age] =0.;        }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      fprintf(ficreseij,"\n");
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);     
     for(i=1;i<=nlstate;i++)      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     fprintf(ficresvpl,"%.0f ",age );      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     for(i=1; i<=nlstate;i++)      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    }
     fprintf(ficresvpl,"\n");    printf("\n");
     free_vector(gp,1,nlstate);    fprintf(ficlog,"\n");
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);    free_vector(xp,1,npar);
     free_matrix(trgradg,1,nlstate,1,npar);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   } /* End age */    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   free_vector(xp,1,npar);  }
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
 }  {
     /* Variance of health expectancies */
 /************ Variance of one-step probabilities  ******************/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    /* double **newm;*/
 {    double **dnewm,**doldm;
   int i, j=0,  i1, k1, l1, t, tj;    double **dnewmp,**doldmp;
   int k2, l2, j1,  z1;    int i, j, nhstepm, hstepm, h, nstepm ;
   int k=0,l, cptcode;    int k, cptcode;
   int first=1, first1;    double *xp;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;    double **gp, **gm;  /* for var eij */
   double **dnewm,**doldm;    double ***gradg, ***trgradg; /*for var eij */
   double *xp;    double **gradgp, **trgradgp; /* for var p point j */
   double *gp, *gm;    double *gpp, *gmp; /* for var p point j */
   double **gradg, **trgradg;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   double **mu;    double ***p3mat;
   double age,agelim, cov[NCOVMAX];    double age,agelim, hf;
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    double ***mobaverage;
   int theta;    int theta;
   char fileresprob[FILENAMELENGTH];    char digit[4];
   char fileresprobcov[FILENAMELENGTH];    char digitp[25];
   char fileresprobcor[FILENAMELENGTH];  
     char fileresprobmorprev[FILENAMELENGTH];
   double ***varpij;  
     if(popbased==1){
   strcpy(fileresprob,"prob");      if(mobilav!=0)
   strcat(fileresprob,fileres);        strcpy(digitp,"-populbased-mobilav-");
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      else strcpy(digitp,"-populbased-nomobil-");
     printf("Problem with resultfile: %s\n", fileresprob);    }
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);    else 
   }      strcpy(digitp,"-stablbased-");
   strcpy(fileresprobcov,"probcov");  
   strcat(fileresprobcov,fileres);    if (mobilav!=0) {
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("Problem with resultfile: %s\n", fileresprobcov);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   strcpy(fileresprobcor,"probcor");      }
   strcat(fileresprobcor,fileres);    }
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcor);    strcpy(fileresprobmorprev,"prmorprev"); 
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);    sprintf(digit,"%-d",ij);
   }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    strcat(fileresprobmorprev,fileres);
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fprintf(ficresprob,"# Age");    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   fprintf(ficresprobcov,"# Age");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   fprintf(ficresprobcov,"# Age");      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   for(i=1; i<=nlstate;i++)    }  
     for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficresprobmorprev,"\n");
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       fprintf(ficresprobcov," p%1d-%1d ",i,j);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficresprobcor," p%1d-%1d ",i,j);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     }        exit(0);
   fprintf(ficresprob,"\n");    }
   fprintf(ficresprobcov,"\n");    else{
   fprintf(ficresprobcor,"\n");      fprintf(ficgp,"\n# Routine varevsij");
   xp=vector(1,npar);    }
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));      printf("Problem with html file: %s\n", optionfilehtm);
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);      exit(0);
   first=1;    }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    else{
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);      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(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     exit(0);    }
   }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   else{  
     fprintf(ficgp,"\n# Routine varprob");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   }    fprintf(ficresvij,"# Age");
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    for(i=1; i<=nlstate;i++)
     printf("Problem with html file: %s\n", optionfilehtm);      for(j=1; j<=nlstate;j++)
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     exit(0);    fprintf(ficresvij,"\n");
   }  
   else{    xp=vector(1,npar);
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    dnewm=matrix(1,nlstate,1,npar);
     fprintf(fichtm,"\n");    doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");  
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
   }    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      
   cov[1]=1;    if(estepm < stepm){
   tj=cptcoveff;      printf ("Problem %d lower than %d\n",estepm, stepm);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    }
   j1=0;    else  hstepm=estepm;   
   for(t=1; t<=tj;t++){    /* For example we decided to compute the life expectancy with the smallest unit */
     for(i1=1; i1<=ncodemax[t];i1++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       j1++;       nhstepm is the number of hstepm from age to agelim 
             nstepm is the number of stepm from age to agelin. 
       if  (cptcovn>0) {       Look at hpijx to understand the reason of that which relies in memory size
         fprintf(ficresprob, "\n#********** Variable ");       and note for a fixed period like k years */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fprintf(ficresprob, "**********\n#");       survival function given by stepm (the optimization length). Unfortunately it
         fprintf(ficresprobcov, "\n#********** Variable ");       means that if the survival funtion is printed every two years of age and if
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficresprobcov, "**********\n#");       results. So we changed our mind and took the option of the best precision.
            */
         fprintf(ficgp, "\n#********** Variable ");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    agelim = AGESUP;
         fprintf(ficgp, "**********\n#");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
              nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
              nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");      gp=matrix(0,nhstepm,1,nlstate);
              gm=matrix(0,nhstepm,1,nlstate);
         fprintf(ficresprobcor, "\n#********** Variable ");      
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficgp, "**********\n#");          for(theta=1; theta <=npar; theta++){
       }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for (age=bage; age<=fage; age ++){        }
         cov[2]=age;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         for (k=1; k<=cptcovn;k++) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  
         }        if (popbased==1) {
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          if(mobilav ==0){
         for (k=1; k<=cptcovprod;k++)            for(i=1; i<=nlstate;i++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              prlim[i][i]=probs[(int)age][i][ij];
                  }else{ /* mobilav */ 
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));            for(i=1; i<=nlstate;i++)
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);              prlim[i][i]=mobaverage[(int)age][i][ij];
         gp=vector(1,(nlstate)*(nlstate+ndeath));          }
         gm=vector(1,(nlstate)*(nlstate+ndeath));        }
        
         for(theta=1; theta <=npar; theta++){        for(j=1; j<= nlstate; j++){
           for(i=1; i<=npar; i++)          for(h=0; h<=nhstepm; h++){
             xp[i] = x[i] + (i==theta ?delti[theta]:0);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                        gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          }
                  }
           k=0;        /* This for computing probability of death (h=1 means
           for(i=1; i<= (nlstate); i++){           computed over hstepm matrices product = hstepm*stepm months) 
             for(j=1; j<=(nlstate+ndeath);j++){           as a weighted average of prlim.
               k=k+1;        */
               gp[k]=pmmij[i][j];        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
           }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
                  }    
           for(i=1; i<=npar; i++)        /* end probability of death */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);  
            for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           k=0;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           for(i=1; i<=(nlstate); i++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             for(j=1; j<=(nlstate+ndeath);j++){   
               k=k+1;        if (popbased==1) {
               gm[k]=pmmij[i][j];          if(mobilav ==0){
             }            for(i=1; i<=nlstate;i++)
           }              prlim[i][i]=probs[(int)age][i][ij];
                }else{ /* mobilav */ 
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)            for(i=1; i<=nlstate;i++)
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                prlim[i][i]=mobaverage[(int)age][i][ij];
         }          }
         }
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)  
           for(theta=1; theta <=npar; theta++)        for(j=1; j<= nlstate; j++){
             trgradg[j][theta]=gradg[theta][j];          for(h=0; h<=nhstepm; h++){
                    for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);          }
                }
         pmij(pmmij,cov,ncovmodel,x,nlstate);        /* This for computing probability of death (h=1 means
                   computed over hstepm matrices product = hstepm*stepm months) 
         k=0;           as a weighted average of prlim.
         for(i=1; i<=(nlstate); i++){        */
           for(j=1; j<=(nlstate+ndeath);j++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             k=k+1;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
             mu[k][(int) age]=pmmij[i][j];           gmp[j] += prlim[i][i]*p3mat[i][j][1];
           }        }    
         }        /* end probability of death */
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)  
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)        for(j=1; j<= nlstate; j++) /* vareij */
             varpij[i][j][(int)age] = doldm[i][j];          for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         /*printf("\n%d ",(int)age);          }
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
      }*/        }
   
         fprintf(ficresprob,"\n%d ",(int)age);      } /* End theta */
         fprintf(ficresprobcov,"\n%d ",(int)age);  
         fprintf(ficresprobcor,"\n%d ",(int)age);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)      for(h=0; h<=nhstepm; h++) /* veij */
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));        for(j=1; j<=nlstate;j++)
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          for(theta=1; theta <=npar; theta++)
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);            trgradg[h][j][theta]=gradg[h][theta][j];
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);  
         }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         i=0;        for(theta=1; theta <=npar; theta++)
         for (k=1; k<=(nlstate);k++){          trgradgp[j][theta]=gradgp[theta][j];
           for (l=1; l<=(nlstate+ndeath);l++){    
             i=i++;  
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);      for(i=1;i<=nlstate;i++)
             for (j=1; j<=i;j++){        for(j=1;j<=nlstate;j++)
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);          vareij[i][j][(int)age] =0.;
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));  
             }      for(h=0;h<=nhstepm;h++){
           }        for(k=0;k<=nhstepm;k++){
         }/* end of loop for state */          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       } /* end of loop for age */          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
       /* Confidence intervalle of pij  */            for(j=1;j<=nlstate;j++)
       /*              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficgp,"\nset noparametric;unset label");        }
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");      }
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);      /* pptj */
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       */        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/      /* end ppptj */
       first1=1;      /*  x centered again */
       for (k1=1; k1<=(nlstate);k1++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         for (l1=1; l1<=(nlstate+ndeath);l1++){      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           if(l1==k1) continue;   
           i=(k1-1)*(nlstate+ndeath)+l1;      if (popbased==1) {
           for (k2=1; k2<=(nlstate);k2++){        if(mobilav ==0){
             for (l2=1; l2<=(nlstate+ndeath);l2++){          for(i=1; i<=nlstate;i++)
               if(l2==k2) continue;            prlim[i][i]=probs[(int)age][i][ij];
               j=(k2-1)*(nlstate+ndeath)+l2;        }else{ /* mobilav */ 
               if(j<=i) continue;          for(i=1; i<=nlstate;i++)
               for (age=bage; age<=fage; age ++){            prlim[i][i]=mobaverage[(int)age][i][ij];
                 if ((int)age %5==0){        }
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;      }
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;               
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;      /* This for computing probability of death (h=1 means
                   mu1=mu[i][(int) age]/stepm*YEARM ;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                   mu2=mu[j][(int) age]/stepm*YEARM;         as a weighted average of prlim.
                   /* Computing eigen value of matrix of covariance */      */
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));      for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                   if(first1==1){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                     first1=0;      }    
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);      /* end probability of death */
                   }  
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
                   /* Eigen vectors */      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
                   v21=sqrt(1.-v11*v11);        for(i=1; i<=nlstate;i++){
                   v12=-v21;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                   v22=v11;        }
                   /*printf(fignu*/      } 
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */      fprintf(ficresprobmorprev,"\n");
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */  
                   if(first==1){      fprintf(ficresvij,"%.0f ",age );
                     first=0;      for(i=1; i<=nlstate;i++)
                     fprintf(ficgp,"\nset parametric;set nolabel");        for(j=1; j<=nlstate;j++){
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                     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>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);      fprintf(ficresvij,"\n");
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);      free_matrix(gp,0,nhstepm,1,nlstate);
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);      free_matrix(gm,0,nhstepm,1,nlstate);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                     /*              fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    } /* End age */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    free_vector(gpp,nlstate+1,nlstate+ndeath);
                     */    free_vector(gmp,nlstate+1,nlstate+ndeath);
                     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",\    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
                   }else{    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
                     first=0;    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
                     /*  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    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(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",\    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);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    /*  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);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));  */
                   }/* if first */    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
                 } /* age mod 5 */  
               } /* end loop age */    free_vector(xp,1,npar);
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);    free_matrix(doldm,1,nlstate,1,nlstate);
               first=1;    free_matrix(dnewm,1,nlstate,1,npar);
             } /*l12 */    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           } /* k12 */    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         } /*l1 */    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       }/* k1 */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     } /* loop covariates */    fclose(ficresprobmorprev);
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    fclose(ficgp);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    fclose(fichtm);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  }  /* end varevsij */
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  /************ Variance of prevlim ******************/
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  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)
   }  {
   free_vector(xp,1,npar);    /* Variance of prevalence limit */
   fclose(ficresprob);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   fclose(ficresprobcov);    double **newm;
   fclose(ficresprobcor);    double **dnewm,**doldm;
   fclose(ficgp);    int i, j, nhstepm, hstepm;
   fclose(fichtm);    int k, cptcode;
 }    double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
 /******************* Printing html file ***********/    double age,agelim;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    int theta;
                   int lastpass, int stepm, int weightopt, char model[],\     
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
                   int popforecast, int estepm ,\    fprintf(ficresvpl,"# Age");
                   double jprev1, double mprev1,double anprev1, \    for(i=1; i<=nlstate;i++)
                   double jprev2, double mprev2,double anprev2){        fprintf(ficresvpl," %1d-%1d",i,i);
   int jj1, k1, i1, cpt;    fprintf(ficresvpl,"\n");
   /*char optionfilehtm[FILENAMELENGTH];*/  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    xp=vector(1,npar);
     printf("Problem with %s \n",optionfilehtm), exit(0);    dnewm=matrix(1,nlstate,1,npar);
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);    doldm=matrix(1,nlstate,1,nlstate);
   }    
     hstepm=1*YEARM; /* Every year of age */
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
  - 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    agelim = AGESUP;
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  - Life expectancies by age and initial health status (estepm=%2d months):      if (stepm >= YEARM) hstepm=1;
    <a href=\"e%s\">e%s</a> <br>\n</li>", \      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");      gm=vector(1,nlstate);
   
  m=cptcoveff;      for(theta=1; theta <=npar; theta++){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
  jj1=0;        }
  for(k1=1; k1<=m;k1++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    for(i1=1; i1<=ncodemax[k1];i1++){        for(i=1;i<=nlstate;i++)
      jj1++;          gp[i] = prlim[i][i];
      if (cptcovn > 0) {      
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for(i=1; i<=npar; i++) /* Computes gradient */
        for (cpt=1; cpt<=cptcoveff;cpt++)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        for(i=1;i<=nlstate;i++)
      }          gm[i] = prlim[i][i];
      /* Pij */  
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>        for(i=1;i<=nlstate;i++)
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
      /* Quasi-incidences */      } /* End theta */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>  
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      trgradg =matrix(1,nlstate,1,npar);
        /* Stable prevalence in each health state */  
        for(cpt=1; cpt<nlstate;cpt++){      for(j=1; j<=nlstate;j++)
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>        for(theta=1; theta <=npar; theta++)
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          trgradg[j][theta]=gradg[theta][j];
        }  
      for(cpt=1; cpt<=nlstate;cpt++) {      for(i=1;i<=nlstate;i++)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>        varpl[i][(int)age] =0.;
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
      }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      for(i=1;i<=nlstate;i++)
 health expectancies in states (1) and (2): e%s%d.png<br>        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
    } /* end i1 */      fprintf(ficresvpl,"%.0f ",age );
  }/* End k1 */      for(i=1; i<=nlstate;i++)
  fprintf(fichtm,"</ul>");        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n      free_vector(gm,1,nlstate);
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n      free_matrix(gradg,1,npar,1,nlstate);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      free_matrix(trgradg,1,nlstate,1,npar);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    } /* End age */
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n  
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    free_vector(xp,1,npar);
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    free_matrix(doldm,1,nlstate,1,npar);
  - 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);    free_matrix(dnewm,1,nlstate,1,nlstate);
   
  if(popforecast==1) fprintf(fichtm,"\n  }
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n  
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  /************ Variance of one-step probabilities  ******************/
         <br>",fileres,fileres,fileres,fileres);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
  else  {
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    int i, j=0,  i1, k1, l1, t, tj;
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
  m=cptcoveff;    int first=1, first1;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
  jj1=0;    double *xp;
  for(k1=1; k1<=m;k1++){    double *gp, *gm;
    for(i1=1; i1<=ncodemax[k1];i1++){    double **gradg, **trgradg;
      jj1++;    double **mu;
      if (cptcovn > 0) {    double age,agelim, cov[NCOVMAX];
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
        for (cpt=1; cpt<=cptcoveff;cpt++)    int theta;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    char fileresprob[FILENAMELENGTH];
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    char fileresprobcov[FILENAMELENGTH];
      }    char fileresprobcor[FILENAMELENGTH];
      for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    double ***varpij;
 interval) in state (%d): v%s%d%d.png <br>  
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      strcpy(fileresprob,"prob"); 
      }    strcat(fileresprob,fileres);
    } /* end i1 */    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
  }/* End k1 */      printf("Problem with resultfile: %s\n", fileresprob);
  fprintf(fichtm,"</ul>");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
 fclose(fichtm);    }
 }    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
 /******************* Gnuplot file **************/    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    }
   int ng;    strcpy(fileresprobcor,"probcor"); 
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    strcat(fileresprobcor,fileres);
     printf("Problem with file %s",optionfilegnuplot);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);      printf("Problem with resultfile: %s\n", fileresprobcor);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
 #ifdef windows    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficgp,"cd \"%s\" \n",pathc);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 #endif    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
 m=pow(2,cptcoveff);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
  /* 1eme*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   for (cpt=1; cpt<= nlstate ; cpt ++) {    
    for (k1=1; k1<= m ; k1 ++) {    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
 #ifdef windows    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    fprintf(ficresprobcov,"# Age");
      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);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
 #endif    fprintf(ficresprobcov,"# Age");
 #ifdef unix  
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    for(i=1; i<=nlstate;i++)
 #endif      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
 for (i=1; i<= nlstate ; i ++) {        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }  
 }   /* fprintf(ficresprob,"\n");
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficresprobcov,"\n");
     for (i=1; i<= nlstate ; i ++) {    fprintf(ficresprobcor,"\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");   */
   else fprintf(ficgp," \%%*lf (\%%*lf)");   xp=vector(1,npar);
 }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      for (i=1; i<= nlstate ; i ++) {    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    first=1;
 }      if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
 #ifdef unix      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");      exit(0);
 #endif    }
    }    else{
   }      fprintf(ficgp,"\n# Routine varprob");
   /*2 eme*/    }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   for (k1=1; k1<= m ; k1 ++) {      printf("Problem with html file: %s\n", optionfilehtm);
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      exit(0);
        }
     for (i=1; i<= nlstate+1 ; i ++) {    else{
       k=2*i;      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      fprintf(fichtm,"\n");
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
 }        fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    cov[1]=1;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    tj=cptcoveff;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
 }      j1=0;
       fprintf(ficgp,"\" t\"\" w l 0,");    for(t=1; t<=tj;t++){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(i1=1; i1<=ncodemax[t];i1++){ 
       for (j=1; j<= nlstate+1 ; j ++) {        j1++;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if  (cptcovn>0) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficresprob, "\n#********** Variable "); 
 }            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          fprintf(ficresprob, "**********\n#\n");
       else fprintf(ficgp,"\" t\"\" w l 0,");          fprintf(ficresprobcov, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprobcov, "**********\n#\n");
            
   /*3eme*/          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for (k1=1; k1<= m ; k1 ++) {          fprintf(ficgp, "**********\n#\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {          
       k=2+nlstate*(2*cpt-2);          
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          fprintf(ficresprobcor, "\n#********** Variable ");    
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          fprintf(ficresprobcor, "**********\n#");    
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        }
         
 */        for (age=bage; age<=fage; age ++){ 
       for (i=1; i< nlstate ; i ++) {          cov[2]=age;
         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);          for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       }          }
     }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }          for (k=1; k<=cptcovprod;k++)
              cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   /* CV preval stat */          
     for (k1=1; k1<= m ; k1 ++) {          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     for (cpt=1; cpt<nlstate ; cpt ++) {          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       k=3;          gp=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          gm=vector(1,(nlstate)*(nlstate+ndeath));
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      
           for(theta=1; theta <=npar; theta++){
       for (i=1; i< nlstate ; i ++)            for(i=1; i<=npar; i++)
         fprintf(ficgp,"+$%d",k+i+1);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            
                  pmij(pmmij,cov,ncovmodel,xp,nlstate);
       l=3+(nlstate+ndeath)*cpt;            
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            k=0;
       for (i=1; i< nlstate ; i ++) {            for(i=1; i<= (nlstate); i++){
         l=3+(nlstate+ndeath)*cpt;              for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficgp,"+$%d",l+i+1);                k=k+1;
       }                gp[k]=pmmij[i][j];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                }
     }            }
   }              
              for(i=1; i<=npar; i++)
   /* proba elementaires */              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
    for(i=1,jk=1; i <=nlstate; i++){      
     for(k=1; k <=(nlstate+ndeath); k++){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       if (k != i) {            k=0;
         for(j=1; j <=ncovmodel; j++){            for(i=1; i<=(nlstate); i++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              for(j=1; j<=(nlstate+ndeath);j++){
           jk++;                k=k+1;
           fprintf(ficgp,"\n");                gm[k]=pmmij[i][j];
         }              }
       }            }
     }       
    }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
    for(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);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
        if (ng==2)            for(theta=1; theta <=npar; theta++)
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");              trgradg[j][theta]=gradg[theta][j];
        else          
          fprintf(ficgp,"\nset title \"Probability\"\n");          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
        i=1;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
        for(k2=1; k2<=nlstate; k2++) {          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
          k3=i;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
          for(k=1; k<=(nlstate+ndeath); k++) {          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
            if (k != k2){  
              if(ng==2)          pmij(pmmij,cov,ncovmodel,x,nlstate);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          
              else          k=0;
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          for(i=1; i<=(nlstate); i++){
              ij=1;            for(j=1; j<=(nlstate+ndeath);j++){
              for(j=3; j <=ncovmodel; j++) {              k=k+1;
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              mu[k][(int) age]=pmmij[i][j];
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            }
                  ij++;          }
                }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                else            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              varpij[i][j][(int)age] = doldm[i][j];
              }  
              fprintf(ficgp,")/(1");          /*printf("\n%d ",(int)age);
                          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
              for(k1=1; k1 <=nlstate; k1++){              printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                ij=1;            }*/
                for(j=3; j <=ncovmodel; j++){  
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          fprintf(ficresprob,"\n%d ",(int)age);
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          fprintf(ficresprobcov,"\n%d ",(int)age);
                    ij++;          fprintf(ficresprobcor,"\n%d ",(int)age);
                  }  
                  else          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                fprintf(ficgp,")");            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
              }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);          }
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          i=0;
              i=i+ncovmodel;          for (k=1; k<=(nlstate);k++){
            }            for (l=1; l<=(nlstate+ndeath);l++){ 
          } /* end k */              i=i++;
        } /* end k2 */              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
      } /* end jk */              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
    } /* end ng */              for (j=1; j<=i;j++){
    fclose(ficgp);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
 }  /* end gnuplot */                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
 /*************** Moving average **************/          }/* end of loop for state */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        } /* end of loop for age */
   
   int i, cpt, cptcod;        /* Confidence intervalle of pij  */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        /*
       for (i=1; i<=nlstate;i++)          fprintf(ficgp,"\nset noparametric;unset label");
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           mobaverage[(int)agedeb][i][cptcod]=0.;          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
              fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       for (i=1; i<=nlstate;i++){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           for (cpt=0;cpt<=4;cpt++){        */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        first1=1;
         }        for (k2=1; k2<=(nlstate);k2++){
       }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     }            if(l2==k2) continue;
                j=(k2-1)*(nlstate+ndeath)+l2;
 }            for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
 /************** Forecasting ******************/                i=(k1-1)*(nlstate+ndeath)+l1;
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){                if(i<=j) continue;
                  for (age=bage; age<=fage; age ++){ 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                  if ((int)age %5==0){
   int *popage;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   double *popeffectif,*popcount;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   double ***p3mat;                    mu1=mu[i][(int) age]/stepm*YEARM ;
   char fileresf[FILENAMELENGTH];                    mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
  agelim=AGESUP;                    /* Computing eigen value of matrix of covariance */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                    /* Eigen vectors */
                      v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                      /*v21=sqrt(1.-v11*v11); *//* error */
   strcpy(fileresf,"f");                    v21=(lc1-v1)/cv12*v11;
   strcat(fileresf,fileres);                    v12=-v21;
   if((ficresf=fopen(fileresf,"w"))==NULL) {                    v22=v11;
     printf("Problem with forecast resultfile: %s\n", fileresf);                    tnalp=v21/v11;
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);                    if(first1==1){
   }                      first1=0;
   printf("Computing forecasting: result on file '%s' \n", fileresf);                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);                    }
                     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);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                    /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   if (mobilav==1) {                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    if(first==1){
     movingaverage(agedeb, fage, ageminpar, mobaverage);                      first=0;
   }                      fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   stepsize=(int) (stepm+YEARM-1)/YEARM;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   if (stepm<=12) stepsize=1;                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
                        fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   agelim=AGESUP;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                        fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   hstepm=1;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   hstepm=hstepm/stepm;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   yp1=modf(dateintmean,&yp);                      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",\
   anprojmean=yp;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   yp2=modf((yp1*12),&yp);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   mprojmean=yp;                    }else{
   yp1=modf((yp2*30.5),&yp);                      first=0;
   jprojmean=yp;                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   if(jprojmean==0) jprojmean=1;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   if(mprojmean==0) jprojmean=1;                      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",\
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   for(cptcov=1;cptcov<=i2;cptcov++){                    }/* if first */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                  } /* age mod 5 */
       k=k+1;                } /* end loop age */
       fprintf(ficresf,"\n#******");                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
       for(j=1;j<=cptcoveff;j++) {                first=1;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              } /*l12 */
       }            } /* k12 */
       fprintf(ficresf,"******\n");          } /*l1 */
       fprintf(ficresf,"# StartingAge FinalAge");        }/* k1 */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      } /* loop covariates */
          }
          free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
         fprintf(ficresf,"\n");    free_vector(xp,1,npar);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      fclose(ficresprob);
     fclose(ficresprobcov);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fclose(ficresprobcor);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fclose(ficgp);
           nhstepm = nhstepm/hstepm;    fclose(fichtm);
            }
           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);    /******************* Printing html file ***********/
          void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
           for (h=0; h<=nhstepm; h++){                    int lastpass, int stepm, int weightopt, char model[],\
             if (h==(int) (calagedate+YEARM*cpt)) {                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);                    int popforecast, int estepm ,\
             }                    double jprev1, double mprev1,double anprev1, \
             for(j=1; j<=nlstate+ndeath;j++) {                    double jprev2, double mprev2,double anprev2){
               kk1=0.;kk2=0;    int jj1, k1, i1, cpt;
               for(i=1; i<=nlstate;i++) {                  /*char optionfilehtm[FILENAMELENGTH];*/
                 if (mobilav==1)    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      printf("Problem with %s \n",optionfilehtm), exit(0);
                 else {      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    }
                 }  
                     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
               if (h==(int)(calagedate+12*cpt)){   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
                 fprintf(ficresf," %.3f", kk1);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
                           - Life expectancies by age and initial health status (estepm=%2d months): 
               }     <a href=\"e%s\">e%s</a> <br>\n</li>", \
             }    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
         }  
       }   m=cptcoveff;
     }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   }  
           jj1=0;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   fclose(ficresf);       jj1++;
 }       if (cptcovn > 0) {
 /************** Forecasting ******************/         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 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){         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   int *popage;       }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;       /* Pij */
   double *popeffectif,*popcount;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
   double ***p3mat,***tabpop,***tabpopprev;  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
   char filerespop[FILENAMELENGTH];       /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         /* Stable prevalence in each health state */
   agelim=AGESUP;         for(cpt=1; cpt<nlstate;cpt++){
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
    <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);         }
         for(cpt=1; cpt<=nlstate;cpt++) {
            fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   strcpy(filerespop,"pop");  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   strcat(filerespop,fileres);       }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {       fprintf(fichtm,"\n<br>- Total life expectancy by age and
     printf("Problem with forecast resultfile: %s\n", filerespop);  health expectancies in states (1) and (2): e%s%d.png<br>
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   }     } /* end i1 */
   printf("Computing forecasting: result on file '%s' \n", filerespop);   }/* End k1 */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);   fprintf(fichtm,"</ul>");
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   if (mobilav==1) {   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     movingaverage(agedeb, fage, ageminpar, mobaverage);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
   }   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
   stepsize=(int) (stepm+YEARM-1)/YEARM;   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
   if (stepm<=12) stepsize=1;   - 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);
    
   agelim=AGESUP;  /*  if(popforecast==1) fprintf(fichtm,"\n */
    /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   hstepm=1;  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   hstepm=hstepm/stepm;  /*      <br>",fileres,fileres,fileres,fileres); */
    /*  else  */
   if (popforecast==1) {  /*    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); */
     if((ficpop=fopen(popfile,"r"))==NULL) {  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       printf("Problem with population file : %s\n",popfile);exit(0);  
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);   m=cptcoveff;
     }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);   jj1=0;
     popcount=vector(0,AGESUP);   for(k1=1; k1<=m;k1++){
         for(i1=1; i1<=ncodemax[k1];i1++){
     i=1;         jj1++;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;       if (cptcovn > 0) {
             fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     imx=i;         for (cpt=1; cpt<=cptcoveff;cpt++) 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   for(cptcov=1;cptcov<=i2;cptcov++){       for(cpt=1; cpt<=nlstate;cpt++) {
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
       k=k+1;  interval) in state (%d): v%s%d%d.png <br>
       fprintf(ficrespop,"\n#******");  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
       for(j=1;j<=cptcoveff;j++) {       }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     } /* end i1 */
       }   }/* End k1 */
       fprintf(ficrespop,"******\n");   fprintf(fichtm,"</ul>");
       fprintf(ficrespop,"# Age");  fclose(fichtm);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  }
       if (popforecast==1)  fprintf(ficrespop," [Population]");  
        /******************* Gnuplot file **************/
       for (cpt=0; cpt<=0;cpt++) {  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
            int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    int ng;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           nhstepm = nhstepm/hstepm;      printf("Problem with file %s",optionfilegnuplot);
                fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
           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);      /*#ifdef windows */
              fprintf(ficgp,"cd \"%s\" \n",pathc);
           for (h=0; h<=nhstepm; h++){      /*#endif */
             if (h==(int) (calagedate+YEARM*cpt)) {  m=pow(2,cptcoveff);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    
             }   /* 1eme*/
             for(j=1; j<=nlstate+ndeath;j++) {    for (cpt=1; cpt<= nlstate ; cpt ++) {
               kk1=0.;kk2=0;     for (k1=1; k1<= m ; k1 ++) {
               for(i=1; i<=nlstate;i++) {                     fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
                 if (mobilav==1)       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);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {       for (i=1; i<= nlstate ; i ++) {
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                 }         else fprintf(ficgp," \%%*lf (\%%*lf)");
               }       }
               if (h==(int)(calagedate+12*cpt)){       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);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;       for (i=1; i<= nlstate ; i ++) {
                   /*fprintf(ficrespop," %.3f", kk1);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/         else fprintf(ficgp," \%%*lf (\%%*lf)");
               }       } 
             }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
             for(i=1; i<=nlstate;i++){       for (i=1; i<= nlstate ; i ++) {
               kk1=0.;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                 for(j=1; j<=nlstate;j++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];       }  
                 }       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];     }
             }    }
     /*2 eme*/
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    for (k1=1; k1<= m ; k1 ++) { 
           }      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
         }      
       }      for (i=1; i<= nlstate+1 ; i ++) {
          k=2*i;
   /******/        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            else fprintf(ficgp," \%%*lf (\%%*lf)");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        }   
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
           nhstepm = nhstepm/hstepm;        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);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (j=1; j<= nlstate+1 ; j ++) {
           oldm=oldms;savm=savms;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            else fprintf(ficgp," \%%*lf (\%%*lf)");
           for (h=0; h<=nhstepm; h++){        }   
             if (h==(int) (calagedate+YEARM*cpt)) {        fprintf(ficgp,"\" t\"\" w l 0,");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
             }        for (j=1; j<= nlstate+1 ; j ++) {
             for(j=1; j<=nlstate+ndeath;j++) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
               kk1=0.;kk2=0;          else fprintf(ficgp," \%%*lf (\%%*lf)");
               for(i=1; i<=nlstate;i++) {                      }   
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
               }        else fprintf(ficgp,"\" t\"\" w l 0,");
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      }
             }    }
           }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*3eme*/
         }    
       }    for (k1=1; k1<= m ; k1 ++) { 
    }      for (cpt=1; cpt<= nlstate ; cpt ++) {
   }        k=2+nlstate*(2*cpt-2);
          fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   if (popforecast==1) {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     free_ivector(popage,0,AGESUP);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     free_vector(popeffectif,0,AGESUP);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     free_vector(popcount,0,AGESUP);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        */
   fclose(ficrespop);        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);
           
 /***********************************************/        } 
 /**************** Main Program *****************/      }
 /***********************************************/    }
     
 int main(int argc, char *argv[])    /* CV preval stable (period) */
 {    for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        k=3;
   double agedeb, agefin,hf;        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        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);
         
   double fret;        for (i=1; i< nlstate ; i ++)
   double **xi,tmp,delta;          fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   double dum; /* Dummy variable */        
   double ***p3mat;        l=3+(nlstate+ndeath)*cpt;
   int *indx;        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
   char line[MAXLINE], linepar[MAXLINE];        for (i=1; i< nlstate ; i ++) {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];          l=3+(nlstate+ndeath)*cpt;
   int firstobs=1, lastobs=10;          fprintf(ficgp,"+$%d",l+i+1);
   int sdeb, sfin; /* Status at beginning and end */        }
   int c,  h , cpt,l;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   int ju,jl, mi;      } 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    }  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    
   int mobilav=0,popforecast=0;    /* proba elementaires */
   int hstepm, nhstepm;    for(i=1,jk=1; i <=nlstate; i++){
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
   double bage, fage, age, agelim, agebase;          for(j=1; j <=ncovmodel; j++){
   double ftolpl=FTOL;            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   double **prlim;            jk++; 
   double *severity;            fprintf(ficgp,"\n");
   double ***param; /* Matrix of parameters */          }
   double  *p;        }
   double **matcov; /* Matrix of covariance */      }
   double ***delti3; /* Scale */     }
   double *delti; /* Scale */  
   double ***eij, ***vareij;     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   double **varpl; /* Variances of prevalence limits by age */       for(jk=1; jk <=m; jk++) {
   double *epj, vepp;         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
   double kk1, kk2;         if (ng==2)
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           else
            fprintf(ficgp,"\nset title \"Probability\"\n");
   char *alph[]={"a","a","b","c","d","e"}, str[4];         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++) {
   char z[1]="c", occ;           k3=i;
 #include <sys/time.h>           for(k=1; k<=(nlstate+ndeath); k++) {
 #include <time.h>             if (k != k2){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];               if(ng==2)
                   fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   /* long total_usecs;               else
   struct timeval start_time, end_time;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 ij=1;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */               for(j=3; j <=ncovmodel; j++) {
   getcwd(pathcd, size);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   printf("\n%s",version);                   ij++;
   if(argc <=1){                 }
     printf("\nEnter the parameter file name: ");                 else
     scanf("%s",pathtot);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   }               }
   else{               fprintf(ficgp,")/(1");
     strcpy(pathtot,argv[1]);               
   }               for(k1=1; k1 <=nlstate; k1++){   
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   /*cygwin_split_path(pathtot,path,optionfile);                 ij=1;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/                 for(j=3; j <=ncovmodel; j++){
   /* cutv(path,optionfile,pathtot,'\\');*/                   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]]]);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);                     ij++;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                   }
   chdir(path);                   else
   replace(pathc,path);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
 /*-------- arguments in the command line --------*/                 fprintf(ficgp,")");
                }
   /* Log file */               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   strcat(filelog, optionfilefiname);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   strcat(filelog,".log");    /* */               i=i+ncovmodel;
   if((ficlog=fopen(filelog,"w"))==NULL)    {             }
     printf("Problem with logfile %s\n",filelog);           } /* end k */
     goto end;         } /* end k2 */
   }       } /* end jk */
   fprintf(ficlog,"Log filename:%s\n",filelog);     } /* end ng */
   fprintf(ficlog,"\n%s",version);     fclose(ficgp); 
   fprintf(ficlog,"\nEnter the parameter file name: ");  }  /* end gnuplot */
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   fflush(ficlog);  
   /*************** Moving average **************/
   /* */  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);    int i, cpt, cptcod;
   strcat(fileres,".txt");    /* Other files have txt extension */    int modcovmax =1;
     int mobilavrange, mob;
   /*---------arguments file --------*/    double age;
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
     printf("Problem with optionfile %s\n",optionfile);                             a covariate has 2 modalities */
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     goto end;  
   }    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
   strcpy(filereso,"o");      else mobilavrange=mobilav;
   strcat(filereso,fileres);      for (age=bage; age<=fage; age++)
   if((ficparo=fopen(filereso,"w"))==NULL) {        for (i=1; i<=nlstate;i++)
     printf("Problem with Output resultfile: %s\n", filereso);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     goto end;      /* 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. 
   /* Reads comments: lines beginning with '#' */      */ 
   while((c=getc(ficpar))=='#' && c!= EOF){      for (mob=3;mob <=mobilavrange;mob=mob+2){
     ungetc(c,ficpar);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     fgets(line, MAXLINE, ficpar);          for (i=1; i<=nlstate;i++){
     puts(line);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
     fputs(line,ficparo);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   }                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   ungetc(c,ficpar);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);                }
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);            }
 while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }/* end age */
     fgets(line, MAXLINE, ficpar);      }/* end mob */
     puts(line);    }else return -1;
     fputs(line,ficparo);    return 0;
   }  }/* End movingaverage */
   ungetc(c,ficpar);  
    
      /************** Forecasting ******************/
   covar=matrix(0,NCOVMAX,1,n);  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){
   cptcovn=0;    /* proj1, year, month, day of starting projection 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;       agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
   ncovmodel=2+cptcovn;       anproj2 year of en of projection (same day and month as proj1).
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    */
      int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   /* Read guess parameters */    int *popage;
   /* Reads comments: lines beginning with '#' */    double agec; /* generic age */
   while((c=getc(ficpar))=='#' && c!= EOF){    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     ungetc(c,ficpar);    double *popeffectif,*popcount;
     fgets(line, MAXLINE, ficpar);    double ***p3mat;
     puts(line);    double ***mobaverage;
     fputs(line,ficparo);    char fileresf[FILENAMELENGTH];
   }  
   ungetc(c,ficpar);    agelim=AGESUP;
      prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);   
     for(i=1; i <=nlstate; i++)    strcpy(fileresf,"f"); 
     for(j=1; j <=nlstate+ndeath-1; j++){    strcat(fileresf,fileres);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    if((ficresf=fopen(fileresf,"w"))==NULL) {
       fprintf(ficparo,"%1d%1d",i1,j1);      printf("Problem with forecast resultfile: %s\n", fileresf);
       if(mle==1)      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
         printf("%1d%1d",i,j);    }
       fprintf(ficlog,"%1d%1d",i,j);    printf("Computing forecasting: result on file '%s' \n", fileresf);
       for(k=1; k<=ncovmodel;k++){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
         fscanf(ficpar," %lf",&param[i][j][k]);  
         if(mle==1){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
           printf(" %lf",param[i][j][k]);  
           fprintf(ficlog," %lf",param[i][j][k]);    if (mobilav!=0) {
         }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         else      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," %lf",param[i][j][k]);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         fprintf(ficparo," %lf",param[i][j][k]);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }      }
       fscanf(ficpar,"\n");    }
       if(mle==1)  
         printf("\n");    stepsize=(int) (stepm+YEARM-1)/YEARM;
       fprintf(ficlog,"\n");    if (stepm<=12) stepsize=1;
       fprintf(ficparo,"\n");    if(estepm < stepm){
     }      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    else  hstepm=estepm;   
   
   p=param[1][1];    hstepm=hstepm/stepm; 
      yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   /* Reads comments: lines beginning with '#' */                                 fractional in yp1 */
   while((c=getc(ficpar))=='#' && c!= EOF){    anprojmean=yp;
     ungetc(c,ficpar);    yp2=modf((yp1*12),&yp);
     fgets(line, MAXLINE, ficpar);    mprojmean=yp;
     puts(line);    yp1=modf((yp2*30.5),&yp);
     fputs(line,ficparo);    jprojmean=yp;
   }    if(jprojmean==0) jprojmean=1;
   ungetc(c,ficpar);    if(mprojmean==0) jprojmean=1;
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    i1=cptcoveff;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    if (cptcovn < 1){i1=1;}
   for(i=1; i <=nlstate; i++){    
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
       fscanf(ficpar,"%1d%1d",&i1,&j1);    
       printf("%1d%1d",i,j);    fprintf(ficresf,"#****** Routine prevforecast **\n");
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){  /*            if (h==(int)(YEARM*yearp)){ */
         fscanf(ficpar,"%le",&delti3[i][j][k]);    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
         printf(" %le",delti3[i][j][k]);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         fprintf(ficparo," %le",delti3[i][j][k]);        k=k+1;
       }        fprintf(ficresf,"\n#******");
       fscanf(ficpar,"\n");        for(j=1;j<=cptcoveff;j++) {
       printf("\n");          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(ficparo,"\n");        }
     }        fprintf(ficresf,"******\n");
   }        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   delti=delti3[1][1];        for(j=1; j<=nlstate+ndeath;j++){ 
            for(i=1; i<=nlstate;i++)              
   /* Reads comments: lines beginning with '#' */            fprintf(ficresf," p%d%d",i,j);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresf," p.%d",j);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     puts(line);          fprintf(ficresf,"\n");
     fputs(line,ficparo);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   }  
   ungetc(c,ficpar);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
              nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
   matcov=matrix(1,npar,1,npar);            nhstepm = nhstepm/hstepm; 
   for(i=1; i <=npar; i++){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fscanf(ficpar,"%s",&str);            oldm=oldms;savm=savms;
     if(mle==1)            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
       printf("%s",str);          
     fprintf(ficlog,"%s",str);            for (h=0; h<=nhstepm; h++){
     fprintf(ficparo,"%s",str);              if (h*hstepm/YEARM*stepm ==yearp) {
     for(j=1; j <=i; j++){                fprintf(ficresf,"\n");
       fscanf(ficpar," %le",&matcov[i][j]);                for(j=1;j<=cptcoveff;j++) 
       if(mle==1){                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         printf(" %.5le",matcov[i][j]);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
         fprintf(ficlog," %.5le",matcov[i][j]);              } 
       }              for(j=1; j<=nlstate+ndeath;j++) {
       else                ppij=0.;
         fprintf(ficlog," %.5le",matcov[i][j]);                for(i=1; i<=nlstate;i++) {
       fprintf(ficparo," %.5le",matcov[i][j]);                  if (mobilav==1) 
     }                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
     fscanf(ficpar,"\n");                  else {
     if(mle==1)                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
       printf("\n");                  }
     fprintf(ficlog,"\n");                  if (h*hstepm/YEARM*stepm== yearp) {
     fprintf(ficparo,"\n");                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
   }                  }
   for(i=1; i <=npar; i++)                } /* end i */
     for(j=i+1;j<=npar;j++)                if (h*hstepm/YEARM*stepm==yearp) {
       matcov[i][j]=matcov[j][i];                  fprintf(ficresf," %.3f", ppij);
                    }
   if(mle==1)              }/* end j */
     printf("\n");            } /* end h */
   fprintf(ficlog,"\n");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
     /*-------- Rewriting paramater file ----------*/      } /* end cptcod */
      strcpy(rfileres,"r");    /* "Rparameterfile */    } /* end  cptcov */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/         
      strcat(rfileres,".");    /* */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  
     if((ficres =fopen(rfileres,"w"))==NULL) {    fclose(ficresf);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  }
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;  
     }  /************** Forecasting *****not tested NB*************/
     fprintf(ficres,"#%s\n",version);  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){
        
     /*-------- data file ----------*/    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     if((fic=fopen(datafile,"r"))==NULL)    {    int *popage;
       printf("Problem with datafile: %s\n", datafile);goto end;    double calagedatem, agelim, kk1, kk2;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;    double *popeffectif,*popcount;
     }    double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     n= lastobs;    char filerespop[FILENAMELENGTH];
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     num=ivector(1,n);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     moisnais=vector(1,n);    agelim=AGESUP;
     annais=vector(1,n);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     moisdc=vector(1,n);    
     andc=vector(1,n);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     agedc=vector(1,n);    
     cod=ivector(1,n);    
     weight=vector(1,n);    strcpy(filerespop,"pop"); 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    strcat(filerespop,fileres);
     mint=matrix(1,maxwav,1,n);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     anint=matrix(1,maxwav,1,n);      printf("Problem with forecast resultfile: %s\n", filerespop);
     s=imatrix(1,maxwav+1,1,n);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     adl=imatrix(1,maxwav+1,1,n);        }
     tab=ivector(1,NCOVMAX);    printf("Computing forecasting: result on file '%s' \n", filerespop);
     ncodemax=ivector(1,8);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     i=1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {    if (mobilav!=0) {
              mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for (j=maxwav;j>=1;j--){      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           strcpy(line,stra);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           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);    }
         }  
            stepsize=(int) (stepm+YEARM-1)/YEARM;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    if (stepm<=12) stepsize=1;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    
     agelim=AGESUP;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=1;
     hstepm=hstepm/stepm; 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    
         for (j=ncovcol;j>=1;j--){    if (popforecast==1) {
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      if((ficpop=fopen(popfile,"r"))==NULL) {
         }        printf("Problem with population file : %s\n",popfile);exit(0);
         num[i]=atol(stra);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
              } 
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      popage=ivector(0,AGESUP);
           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;}*/      popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
         i=i+1;      
       }      i=1;   
     }      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
     /* printf("ii=%d", ij);     
        scanf("%d",i);*/      imx=i;
   imx=i-1; /* Number of individuals */      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   /* for (i=1; i<=imx; i++){  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        k=k+1;
     }*/        fprintf(ficrespop,"\n#******");
    /*  for (i=1; i<=imx; i++){        for(j=1;j<=cptcoveff;j++) {
      if (s[4][i]==9)  s[4][i]=-1;          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/        }
          fprintf(ficrespop,"******\n");
          fprintf(ficrespop,"# Age");
   /* Calculation of the number of parameter from char model*/        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */        if (popforecast==1)  fprintf(ficrespop," [Population]");
   Tprod=ivector(1,15);        
   Tvaraff=ivector(1,15);        for (cpt=0; cpt<=0;cpt++) { 
   Tvard=imatrix(1,15,1,2);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   Tage=ivector(1,15);                
              for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   if (strlen(model) >1){            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     j=0, j1=0, k1=1, k2=1;            nhstepm = nhstepm/hstepm; 
     j=nbocc(model,'+');            
     j1=nbocc(model,'*');            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     cptcovn=j+1;            oldm=oldms;savm=savms;
     cptcovprod=j1;            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
              
     strcpy(modelsav,model);            for (h=0; h<=nhstepm; h++){
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){              if (h==(int) (calagedatem+YEARM*cpt)) {
       printf("Error. Non available option model=%s ",model);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       fprintf(ficlog,"Error. Non available option model=%s ",model);              } 
       goto end;              for(j=1; j<=nlstate+ndeath;j++) {
     }                kk1=0.;kk2=0;
                    for(i=1; i<=nlstate;i++) {              
     for(i=(j+1); i>=1;i--){                  if (mobilav==1) 
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */                  else {
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
       /*scanf("%d",i);*/                  }
       if (strchr(strb,'*')) {  /* Model includes a product */                }
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/                if (h==(int)(calagedatem+12*cpt)){
         if (strcmp(strc,"age")==0) { /* Vn*age */                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
           cptcovprod--;                    /*fprintf(ficrespop," %.3f", kk1);
           cutv(strb,stre,strd,'V');                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/                }
           cptcovage++;              }
             Tage[cptcovage]=i;              for(i=1; i<=nlstate;i++){
             /*printf("stre=%s ", stre);*/                kk1=0.;
         }                  for(j=1; j<=nlstate;j++){
         else if (strcmp(strd,"age")==0) { /* or age*Vn */                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
           cptcovprod--;                  }
           cutv(strb,stre,strc,'V');                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
           Tvar[i]=atoi(stre);              }
           cptcovage++;  
           Tage[cptcovage]=i;              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
         }                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
         else {  /* Age is not in the model */            }
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           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];        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (k=1; k<=lastobs;k++)          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           k1++;            nhstepm = nhstepm/hstepm; 
           k2=k2+2;            
         }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }            oldm=oldms;savm=savms;
       else { /* no more sum */            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            for (h=0; h<=nhstepm; h++){
        /*  scanf("%d",i);*/              if (h==(int) (calagedatem+YEARM*cpt)) {
       cutv(strd,strc,strb,'V');                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       Tvar[i]=atoi(strc);              } 
       }              for(j=1; j<=nlstate+ndeath;j++) {
       strcpy(modelsav,stra);                  kk1=0.;kk2=0;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                for(i=1; i<=nlstate;i++) {              
         scanf("%d",i);*/                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
     } /* end of loop + */                }
   } /* end model */                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
                }
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            }
   printf("cptcovprod=%d ", cptcovprod);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);          }
   scanf("%d ",i);*/        }
     fclose(fic);     } 
     }
     /*  if(mle==1){*/   
     if (weightopt != 1) { /* Maximisation without weights*/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }    if (popforecast==1) {
     /*-calculation of age at interview from date of interview and age at death -*/      free_ivector(popage,0,AGESUP);
     agev=matrix(1,maxwav,1,imx);      free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     for (i=1; i<=imx; i++) {    }
       for(m=2; (m<= maxwav); m++) {    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
          anint[m][i]=9999;    fclose(ficrespop);
          s[m][i]=-1;  } /* End of popforecast */
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  /***********************************************/
       }  /**************** Main Program *****************/
     }  /***********************************************/
   
     for (i=1; i<=imx; i++)  {  int main(int argc, char *argv[])
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  {
       for(m=1; (m<= maxwav); m++){    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
         if(s[m][i] >0){    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
           if (s[m][i] >= nlstate+1) {    double agedeb, agefin,hf;
             if(agedc[i]>0)    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
               if(moisdc[i]!=99 && andc[i]!=9999)  
                 agev[m][i]=agedc[i];    double fret;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    double **xi,tmp,delta;
            else {  
               if (andc[i]!=9999){    double dum; /* Dummy variable */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    double ***p3mat;
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);    double ***mobaverage;
               agev[m][i]=-1;    int *indx;
               }    char line[MAXLINE], linepar[MAXLINE];
             }    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
           }    int firstobs=1, lastobs=10;
           else if(s[m][i] !=9){ /* Should no more exist */    int sdeb, sfin; /* Status at beginning and end */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    int c,  h , cpt,l;
             if(mint[m][i]==99 || anint[m][i]==9999)    int ju,jl, mi;
               agev[m][i]=1;    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
             else if(agev[m][i] <agemin){    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
               agemin=agev[m][i];    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    int mobilav=0,popforecast=0;
             }    int hstepm, nhstepm;
             else if(agev[m][i] >agemax){    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
               agemax=agev[m][i];    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }    double bage, fage, age, agelim, agebase;
             /*agev[m][i]=anint[m][i]-annais[i];*/    double ftolpl=FTOL;
             /*   agev[m][i] = age[i]+2*m;*/    double **prlim;
           }    double *severity;
           else { /* =9 */    double ***param; /* Matrix of parameters */
             agev[m][i]=1;    double  *p;
             s[m][i]=-1;    double **matcov; /* Matrix of covariance */
           }    double ***delti3; /* Scale */
         }    double *delti; /* Scale */
         else /*= 0 Unknown */    double ***eij, ***vareij;
           agev[m][i]=1;    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;
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){    char *alph[]={"a","a","b","c","d","e"}, str[4];
         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);      char z[1]="c", occ;
           goto end;  #include <sys/time.h>
         }  #include <time.h>
       }    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     }   
     /* long total_usecs;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       struct timeval start_time, end_time;
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     free_vector(severity,1,maxwav);    getcwd(pathcd, size);
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);    printf("\n%s\n%s",version,fullversion);
     free_vector(annais,1,n);    if(argc <=1){
     /* free_matrix(mint,1,maxwav,1,n);      printf("\nEnter the parameter file name: ");
        free_matrix(anint,1,maxwav,1,n);*/      scanf("%s",pathtot);
     free_vector(moisdc,1,n);    }
     free_vector(andc,1,n);    else{
       strcpy(pathtot,argv[1]);
        }
     wav=ivector(1,imx);    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    /*cygwin_split_path(pathtot,path,optionfile);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
        /* cutv(path,optionfile,pathtot,'\\');*/
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
       Tcode=ivector(1,100);    replace(pathc,path);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;    /*-------- arguments in the command line --------*/
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
          /* Log file */
    codtab=imatrix(1,100,1,10);    strcat(filelog, optionfilefiname);
    h=0;    strcat(filelog,".log");    /* */
    m=pow(2,cptcoveff);    if((ficlog=fopen(filelog,"w"))==NULL)    {
        printf("Problem with logfile %s\n",filelog);
    for(k=1;k<=cptcoveff; k++){      goto end;
      for(i=1; i <=(m/pow(2,k));i++){    }
        for(j=1; j <= ncodemax[k]; j++){    fprintf(ficlog,"Log filename:%s\n",filelog);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    fprintf(ficlog,"\n%s",version);
            h++;    fprintf(ficlog,"\nEnter the parameter file name: ");
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    fflush(ficlog);
          }  
        }    /* */
      }    strcpy(fileres,"r");
    }    strcat(fileres, optionfilefiname);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    strcat(fileres,".txt");    /* Other files have txt extension */
       codtab[1][2]=1;codtab[2][2]=2; */  
    /* for(i=1; i <=m ;i++){    /*---------arguments file --------*/
       for(k=1; k <=cptcovn; k++){  
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    if((ficpar=fopen(optionfile,"r"))==NULL)    {
       }      printf("Problem with optionfile %s\n",optionfile);
       printf("\n");      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       }      goto end;
       scanf("%d",i);*/    }
      
    /* Calculates basic frequencies. Computes observed prevalence at single age    strcpy(filereso,"o");
        and prints on file fileres'p'. */    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);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      goto end;
     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 */    /* Reads comments: lines beginning with '#' */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    while((c=getc(ficpar))=='#' && c!= EOF){
            ungetc(c,ficpar);
     /* For Powell, parameters are in a vector p[] starting at p[1]      fgets(line, MAXLINE, ficpar);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      puts(line);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      fputs(line,ficparo);
     }
     if(mle==1){    ungetc(c,ficpar);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
        printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     /*--------- results files --------------*/    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(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);    while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
    jk=1;      puts(line);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fputs(line,ficparo);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    }
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    ungetc(c,ficpar);
    for(i=1,jk=1; i <=nlstate; i++){    
      for(k=1; k <=(nlstate+ndeath); k++){     
        if (k != i)    covar=matrix(0,NCOVMAX,1,n); 
          {    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
            printf("%d%d ",i,k);    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
            fprintf(ficlog,"%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
            for(j=1; j <=ncovmodel; j++){    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
              printf("%f ",p[jk]);    
              fprintf(ficlog,"%f ",p[jk]);    /* Read guess parameters */
              fprintf(ficres,"%f ",p[jk]);    /* Reads comments: lines beginning with '#' */
              jk++;    while((c=getc(ficpar))=='#' && c!= EOF){
            }      ungetc(c,ficpar);
            printf("\n");      fgets(line, MAXLINE, ficpar);
            fprintf(ficlog,"\n");      puts(line);
            fprintf(ficres,"\n");      fputs(line,ficparo);
          }    }
      }    ungetc(c,ficpar);
    }    
    if(mle==1){    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
      /* Computing hessian and covariance matrix */    for(i=1; i <=nlstate; i++)
      ftolhess=ftol; /* Usually correct */      for(j=1; j <=nlstate+ndeath-1; j++){
      hesscov(matcov, p, npar, delti, ftolhess, func);        fscanf(ficpar,"%1d%1d",&i1,&j1);
    }        fprintf(ficparo,"%1d%1d",i1,j1);
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        if(mle==1)
    printf("# Scales (for hessian or gradient estimation)\n");          printf("%1d%1d",i,j);
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");        fprintf(ficlog,"%1d%1d",i,j);
    for(i=1,jk=1; i <=nlstate; i++){        for(k=1; k<=ncovmodel;k++){
      for(j=1; j <=nlstate+ndeath; j++){          fscanf(ficpar," %lf",&param[i][j][k]);
        if (j!=i) {          if(mle==1){
          fprintf(ficres,"%1d%1d",i,j);            printf(" %lf",param[i][j][k]);
          printf("%1d%1d",i,j);            fprintf(ficlog," %lf",param[i][j][k]);
          fprintf(ficlog,"%1d%1d",i,j);          }
          for(k=1; k<=ncovmodel;k++){          else
            printf(" %.5e",delti[jk]);            fprintf(ficlog," %lf",param[i][j][k]);
            fprintf(ficlog," %.5e",delti[jk]);          fprintf(ficparo," %lf",param[i][j][k]);
            fprintf(ficres," %.5e",delti[jk]);        }
            jk++;        fscanf(ficpar,"\n");
          }        if(mle==1)
          printf("\n");          printf("\n");
          fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
          fprintf(ficres,"\n");        fprintf(ficparo,"\n");
        }      }
      }    
    }    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
      
    k=1;    p=param[1][1];
    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    
    if(mle==1)    /* Reads comments: lines beginning with '#' */
      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");    while((c=getc(ficpar))=='#' && c!= EOF){
    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");      ungetc(c,ficpar);
    for(i=1;i<=npar;i++){      fgets(line, MAXLINE, ficpar);
      /*  if (k>nlstate) k=1;      puts(line);
          i1=(i-1)/(ncovmodel*nlstate)+1;      fputs(line,ficparo);
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    }
          printf("%s%d%d",alph[k],i1,tab[i]);*/    ungetc(c,ficpar);
      fprintf(ficres,"%3d",i);  
      if(mle==1)    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
        printf("%3d",i);    /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
      fprintf(ficlog,"%3d",i);    for(i=1; i <=nlstate; i++){
      for(j=1; j<=i;j++){      for(j=1; j <=nlstate+ndeath-1; j++){
        fprintf(ficres," %.5e",matcov[i][j]);        fscanf(ficpar,"%1d%1d",&i1,&j1);
        if(mle==1)        printf("%1d%1d",i,j);
          printf(" %.5e",matcov[i][j]);        fprintf(ficparo,"%1d%1d",i1,j1);
        fprintf(ficlog," %.5e",matcov[i][j]);        for(k=1; k<=ncovmodel;k++){
      }          fscanf(ficpar,"%le",&delti3[i][j][k]);
      fprintf(ficres,"\n");          printf(" %le",delti3[i][j][k]);
      if(mle==1)          fprintf(ficparo," %le",delti3[i][j][k]);
        printf("\n");        }
      fprintf(ficlog,"\n");        fscanf(ficpar,"\n");
      k++;        printf("\n");
    }        fprintf(ficparo,"\n");
          }
    while((c=getc(ficpar))=='#' && c!= EOF){    }
      ungetc(c,ficpar);    delti=delti3[1][1];
      fgets(line, MAXLINE, ficpar);  
      puts(line);  
      fputs(line,ficparo);    /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
    }    
    ungetc(c,ficpar);    /* Reads comments: lines beginning with '#' */
    estepm=0;    while((c=getc(ficpar))=='#' && c!= EOF){
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      ungetc(c,ficpar);
    if (estepm==0 || estepm < stepm) estepm=stepm;      fgets(line, MAXLINE, ficpar);
    if (fage <= 2) {      puts(line);
      bage = ageminpar;      fputs(line,ficparo);
      fage = agemaxpar;    }
    }    ungetc(c,ficpar);
        
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    matcov=matrix(1,npar,1,npar);
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    for(i=1; i <=npar; i++){
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fscanf(ficpar,"%s",&str);
          if(mle==1)
    while((c=getc(ficpar))=='#' && c!= EOF){        printf("%s",str);
      ungetc(c,ficpar);      fprintf(ficlog,"%s",str);
      fgets(line, MAXLINE, ficpar);      fprintf(ficparo,"%s",str);
      puts(line);      for(j=1; j <=i; j++){
      fputs(line,ficparo);        fscanf(ficpar," %le",&matcov[i][j]);
    }        if(mle==1){
    ungetc(c,ficpar);          printf(" %.5le",matcov[i][j]);
            fprintf(ficlog," %.5le",matcov[i][j]);
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        }
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        else
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(ficlog," %.5le",matcov[i][j]);
            fprintf(ficparo," %.5le",matcov[i][j]);
    while((c=getc(ficpar))=='#' && c!= EOF){      }
      ungetc(c,ficpar);      fscanf(ficpar,"\n");
      fgets(line, MAXLINE, ficpar);      if(mle==1)
      puts(line);        printf("\n");
      fputs(line,ficparo);      fprintf(ficlog,"\n");
    }      fprintf(ficparo,"\n");
    ungetc(c,ficpar);    }
      for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        matcov[i][j]=matcov[j][i];
    dateprev2=anprev2+mprev2/12.+jprev2/365.;     
     if(mle==1)
   fscanf(ficpar,"pop_based=%d\n",&popbased);      printf("\n");
   fprintf(ficparo,"pop_based=%d\n",popbased);      fprintf(ficlog,"\n");
   fprintf(ficres,"pop_based=%d\n",popbased);    
    
   while((c=getc(ficpar))=='#' && c!= EOF){    /*-------- Rewriting paramater file ----------*/
     ungetc(c,ficpar);    strcpy(rfileres,"r");    /* "Rparameterfile */
     fgets(line, MAXLINE, ficpar);    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     puts(line);    strcat(rfileres,".");    /* */
     fputs(line,ficparo);    strcat(rfileres,optionfilext);    /* Other files have txt extension */
   }    if((ficres =fopen(rfileres,"w"))==NULL) {
   ungetc(c,ficpar);      printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);    }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    fprintf(ficres,"#%s\n",version);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
 while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with datafile: %s\n", datafile);goto end;
     ungetc(c,ficpar);      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     fgets(line, MAXLINE, ficpar);    }
     puts(line);  
     fputs(line,ficparo);    n= lastobs;
   }    severity = vector(1,maxwav);
   ungetc(c,ficpar);    outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    moisnais=vector(1,n);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    annais=vector(1,n);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    moisdc=vector(1,n);
     andc=vector(1,n);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    agedc=vector(1,n);
     cod=ivector(1,n);
 /*------------ gnuplot -------------*/    weight=vector(1,n);
   strcpy(optionfilegnuplot,optionfilefiname);    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
   strcat(optionfilegnuplot,".gp");    mint=matrix(1,maxwav,1,n);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    anint=matrix(1,maxwav,1,n);
     printf("Problem with file %s",optionfilegnuplot);    s=imatrix(1,maxwav+1,1,n);
   }    tab=ivector(1,NCOVMAX);
   fclose(ficgp);    ncodemax=ivector(1,8);
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);  
 /*--------- index.htm --------*/    i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
   strcpy(optionfilehtm,optionfile);      if ((i >= firstobs) && (i <=lastobs)) {
   strcat(optionfilehtm,".htm");          
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        for (j=maxwav;j>=1;j--){
     printf("Problem with %s \n",optionfilehtm), exit(0);          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);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        }
 \n          
 Total number of observations=%d <br>\n        cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li><h4>Parameter files</h4>\n        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
  - Log file of the run: <a href=\"%s\">%s</a><br>\n  
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
   fclose(fichtm);        for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);        } 
          num[i]=atol(stra);
 /*------------ free_vector  -------------*/          
  chdir(path);        /*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;}*/
  free_ivector(wav,1,imx);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        i=i+1;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        }
  free_ivector(num,1,n);    }
  free_vector(agedc,1,n);    /* printf("ii=%d", ij);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/       scanf("%d",i);*/
  fclose(ficparo);    imx=i-1; /* Number of individuals */
  fclose(ficres);  
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
   /*--------------- Prevalence limit --------------*/      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;
   strcpy(filerespl,"pl");      }*/
   strcat(filerespl,fileres);     /*  for (i=1; i<=imx; i++){
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       if (s[4][i]==9)  s[4][i]=-1; 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;       printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;    
   }   for (i=1; i<=imx; i++)
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);   
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);     /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
   fprintf(ficrespl,"#Prevalence limit\n");       else weight[i]=1;*/
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    /* Calculation of the number of parameter from char model*/
   fprintf(ficrespl,"\n");    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
      Tprod=ivector(1,15); 
   prlim=matrix(1,nlstate,1,nlstate);    Tvaraff=ivector(1,15); 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    Tvard=imatrix(1,15,1,2);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    Tage=ivector(1,15);      
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (strlen(model) >1){ /* If there is at least 1 covariate */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      j=0, j1=0, k1=1, k2=1;
   k=0;      j=nbocc(model,'+'); /* j=Number of '+' */
   agebase=ageminpar;      j1=nbocc(model,'*'); /* j1=Number of '*' */
   agelim=agemaxpar;      cptcovn=j+1; 
   ftolpl=1.e-10;      cptcovprod=j1; /*Number of products */
   i1=cptcoveff;      
   if (cptcovn < 1){i1=1;}      strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
   for(cptcov=1;cptcov<=i1;cptcov++){        printf("Error. Non available option model=%s ",model);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficlog,"Error. Non available option model=%s ",model);
         k=k+1;        goto end;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      }
         fprintf(ficrespl,"\n#******");      
         printf("\n#******");      /* This loop fills the array Tvar from the string 'model'.*/
         fprintf(ficlog,"\n#******");  
         for(j=1;j<=cptcoveff;j++) {      for(i=(j+1); i>=1;i--){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         }        /*scanf("%d",i);*/
         fprintf(ficrespl,"******\n");        if (strchr(strb,'*')) {  /* Model includes a product */
         printf("******\n");          cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
         fprintf(ficlog,"******\n");          if (strcmp(strc,"age")==0) { /* Vn*age */
                    cptcovprod--;
         for (age=agebase; age<=agelim; age++){            cutv(strb,stre,strd,'V');
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
           fprintf(ficrespl,"%.0f",age );            cptcovage++;
           for(i=1; i<=nlstate;i++)              Tage[cptcovage]=i;
           fprintf(ficrespl," %.5f", prlim[i][i]);              /*printf("stre=%s ", stre);*/
           fprintf(ficrespl,"\n");          }
         }          else if (strcmp(strd,"age")==0) { /* or age*Vn */
       }            cptcovprod--;
     }            cutv(strb,stre,strc,'V');
   fclose(ficrespl);            Tvar[i]=atoi(stre);
             cptcovage++;
   /*------------- h Pij x at various ages ------------*/            Tage[cptcovage]=i;
            }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          else {  /* Age is not in the model */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            Tvar[i]=ncovcol+k1;
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
   }            Tprod[k1]=i;
   printf("Computing pij: result on file '%s' \n", filerespij);            Tvard[k1][1]=atoi(strc); /* m*/
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);            Tvard[k1][2]=atoi(stre); /* n */
              Tvar[cptcovn+k2]=Tvard[k1][1];
   stepsize=(int) (stepm+YEARM-1)/YEARM;            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
   /*if (stepm<=24) stepsize=2;*/            for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
   agelim=AGESUP;            k1++;
   hstepm=stepsize*YEARM; /* Every year of age */            k2=k2+2;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          }
         }
   /* hstepm=1;   aff par mois*/        else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
   k=0;         /*  scanf("%d",i);*/
   for(cptcov=1;cptcov<=i1;cptcov++){        cutv(strd,strc,strb,'V');
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        Tvar[i]=atoi(strc);
       k=k+1;        }
         fprintf(ficrespij,"\n#****** ");        strcpy(modelsav,stra);  
         for(j=1;j<=cptcoveff;j++)        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          scanf("%d",i);*/
         fprintf(ficrespij,"******\n");      } /* end of loop + */
            } /* end model */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
           /*      nhstepm=nhstepm*YEARM; aff par mois*/    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      scanf("%d ",i);
           fprintf(ficrespij,"# Age");    fclose(fic);*/
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)      /*  if(mle==1){*/
               fprintf(ficrespij," %1d-%1d",i,j);    if (weightopt != 1) { /* Maximisation without weights*/
           fprintf(ficrespij,"\n");      for(i=1;i<=n;i++) weight[i]=1.0;
            for (h=0; h<=nhstepm; h++){    }
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      /*-calculation of age at interview from date of interview and age at death -*/
             for(i=1; i<=nlstate;i++)    agev=matrix(1,maxwav,1,imx);
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    for (i=1; i<=imx; i++) {
             fprintf(ficrespij,"\n");      for(m=2; (m<= maxwav); m++) {
              }        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          anint[m][i]=9999;
           fprintf(ficrespij,"\n");          s[m][i]=-1;
         }        }
     }        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
   }          printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          s[m][i]=-1;
         }
   fclose(ficrespij);        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
   /*---------- Forecasting ------------------*/          s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
   if((stepm == 1) && (strcmp(model,".")==0)){        }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      }
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    }
   }  
   else{    for (i=1; i<=imx; i++)  {
     erreur=108;      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);      for(m=firstpass; (m<= lastpass); m++){
     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);        if(s[m][i] >0){
   }          if (s[m][i] >= nlstate+1) {
              if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
   /*---------- Health expectancies and variances ------------*/                agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
   strcpy(filerest,"t");              else {
   strcat(filerest,fileres);                if ((int)andc[i]!=9999){
   if((ficrest=fopen(filerest,"w"))==NULL) {                  printf("Warning negative age at death: %d line:%d\n",num[i],i);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                  fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;                  agev[m][i]=-1;
   }                }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);              }
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);          }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
   strcpy(filerese,"e");                                   month */
   strcat(filerese,fileres);            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
   if((ficreseij=fopen(filerese,"w"))==NULL) {            if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);              agev[m][i]=1;
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);            else if(agev[m][i] <agemin){ 
   }              agemin=agev[m][i];
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);              /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);            }
             else if(agev[m][i] >agemax){
   strcpy(fileresv,"v");              agemax=agev[m][i];
   strcat(fileresv,fileres);              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
   if((ficresvij=fopen(fileresv,"w"))==NULL) {            }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);            /*agev[m][i]=anint[m][i]-annais[i];*/
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);            /*     agev[m][i] = age[i]+2*m;*/
   }          }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          else { /* =9 */
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);            agev[m][i]=1;
   calagedate=-1;            s[m][i]=-1;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          }
         }
   k=0;        else /*= 0 Unknown */
   for(cptcov=1;cptcov<=i1;cptcov++){          agev[m][i]=1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }
       k=k+1;      
       fprintf(ficrest,"\n#****** ");    }
       for(j=1;j<=cptcoveff;j++)    for (i=1; i<=imx; i++)  {
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(m=firstpass; (m<=lastpass); m++){
       fprintf(ficrest,"******\n");        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(ficreseij,"\n#****** ");          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);     
       for(j=1;j<=cptcoveff;j++)          goto end;
         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++)    /*for (i=1; i<=imx; i++){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (m=firstpass; (m<lastpass); m++){
       fprintf(ficresvij,"******\n");       printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  }*/
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    
      printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
       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);    free_vector(severity,1,maxwav);
       if(popbased==1){    free_imatrix(outcome,1,maxwav+1,1,n);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);    free_vector(moisnais,1,n);
        }    free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
         free_matrix(anint,1,maxwav,1,n);*/
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    free_vector(moisdc,1,n);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    free_vector(andc,1,n);
       fprintf(ficrest,"\n");  
      
       epj=vector(1,nlstate+1);    wav=ivector(1,imx);
       for(age=bage; age <=fage ;age++){    dh=imatrix(1,lastpass-firstpass+1,1,imx);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    bh=imatrix(1,lastpass-firstpass+1,1,imx);
         if (popbased==1) {    mw=imatrix(1,lastpass-firstpass+1,1,imx);
           for(i=1; i<=nlstate;i++)     
             prlim[i][i]=probs[(int)age][i][k];    /* Concatenates waves */
         }    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
          
         fprintf(ficrest," %4.0f",age);    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    Tcode=ivector(1,100);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    ncodemax[1]=1;
           }    if (cptcovn > 0) tricode(Tvar,nbcode,imx);
           epj[nlstate+1] +=epj[j];        
         }    codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
         for(i=1, vepp=0.;i <=nlstate;i++)    h=0;
           for(j=1;j <=nlstate;j++)    m=pow(2,cptcoveff);
             vepp += vareij[i][j][(int)age];   
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    for(k=1;k<=cptcoveff; k++){
         for(j=1;j <=nlstate;j++){      for(i=1; i <=(m/pow(2,k));i++){
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));        for(j=1; j <= ncodemax[k]; j++){
         }          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
         fprintf(ficrest,"\n");            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]);*/
   }          } 
 free_matrix(mint,1,maxwav,1,n);        }
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      }
     free_vector(weight,1,n);    } 
   fclose(ficreseij);    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
   fclose(ficresvij);       codtab[1][2]=1;codtab[2][2]=2; */
   fclose(ficrest);    /* for(i=1; i <=m ;i++){ 
   fclose(ficpar);       for(k=1; k <=cptcovn; k++){
   free_vector(epj,1,nlstate+1);       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
         }
   /*------- Variance limit prevalence------*/         printf("\n");
        }
   strcpy(fileresvpl,"vpl");       scanf("%d",i);*/
   strcat(fileresvpl,fileres);      
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    /* Calculates basic frequencies. Computes observed prevalence at single age
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);       and prints on file fileres'p'. */
     exit(0);    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
   k=0;      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
   for(cptcov=1;cptcov<=i1;cptcov++){      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       k=k+1;      
       fprintf(ficresvpl,"\n#****** ");     
       for(j=1;j<=cptcoveff;j++)    /* For Powell, parameters are in a vector p[] starting at p[1]
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
       fprintf(ficresvpl,"******\n");    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
        
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    if(mle>=1){ /* Could be 1 or 2 */
       oldm=oldms;savm=savms;      mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    }
     }      
  }    /*--------- 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);
   fclose(ficresvpl);    
   
   /*---------- End : free ----------------*/    jk=1;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
      printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    for(i=1,jk=1; i <=nlstate; i++){
        for(k=1; k <=(nlstate+ndeath); k++){
          if (k != i) 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          {
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            printf("%d%d ",i,k);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            fprintf(ficlog,"%d%d ",i,k);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            fprintf(ficres,"%1d%1d ",i,k);
              for(j=1; j <=ncovmodel; j++){
   free_matrix(matcov,1,npar,1,npar);              printf("%f ",p[jk]);
   free_vector(delti,1,npar);              fprintf(ficlog,"%f ",p[jk]);
   free_matrix(agev,1,maxwav,1,imx);              fprintf(ficres,"%f ",p[jk]);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);              jk++; 
             }
   fprintf(fichtm,"\n</body>");            printf("\n");
   fclose(fichtm);            fprintf(ficlog,"\n");
   fclose(ficgp);            fprintf(ficres,"\n");
            }
       }
   if(erreur >0){    }
     printf("End of Imach with error or warning %d\n",erreur);    if(mle!=0){
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);      /* Computing hessian and covariance matrix */
   }else{      ftolhess=ftol; /* Usually correct */
    printf("End of Imach\n");      hesscov(matcov, p, npar, delti, ftolhess, func);
    fprintf(ficlog,"End of Imach\n");    }
   }    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
   printf("See log file on %s\n",filelog);    printf("# Scales (for hessian or gradient estimation)\n");
   fclose(ficlog);    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    for(i=1,jk=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath; j++){
   /* 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);*/        if (j!=i) {
   /*printf("Total time was %d uSec.\n", total_usecs);*/          fprintf(ficres,"%1d%1d",i,j);
   /*------ End -----------*/          printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
  end:            printf(" %.5e",delti[jk]);
 #ifdef windows            fprintf(ficlog," %.5e",delti[jk]);
   /* chdir(pathcd);*/            fprintf(ficres," %.5e",delti[jk]);
 #endif            jk++;
  /*system("wgnuplot graph.plt");*/          }
  /*system("../gp37mgw/wgnuplot graph.plt");*/          printf("\n");
  /*system("cd ../gp37mgw");*/          fprintf(ficlog,"\n");
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          fprintf(ficres,"\n");
  strcpy(plotcmd,GNUPLOTPROGRAM);        }
  strcat(plotcmd," ");      }
  strcat(plotcmd,optionfilegnuplot);    }
  system(plotcmd);     
     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");
 #ifdef windows    if(mle==1)
   while (z[0] != 'q') {      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");
     /* chdir(path); */    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");
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    for(i=1,k=1;i<=npar;i++){
     scanf("%s",z);      /*  if (k>nlstate) k=1;
     if (z[0] == 'c') system("./imach");          i1=(i-1)/(ncovmodel*nlstate)+1; 
     else if (z[0] == 'e') system(optionfilehtm);          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
     else if (z[0] == 'g') system(plotcmd);          printf("%s%d%d",alph[k],i1,tab[i]);
     else if (z[0] == 'q') exit(0);      */
   }      fprintf(ficres,"%3d",i);
 #endif      if(mle==1)
 }        printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.50  
changed lines
  Added in v.1.84


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