Diff for /imach/src/imach.c between versions 1.50 and 1.80

version 1.50, 2002/06/26 23:25:02 version 1.80, 2003/06/05 15:34:14
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    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    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    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    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    '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    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "gnuplot"    read datafile
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    concatwav
 #define FILENAMELENGTH 80    if (mle >= 1)
 /*#define DEBUG*/      mlikeli
 #define windows    print results files
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    if mle==1 
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */        begin-prev-date,...
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open gnuplot file
     open html file
 #define NINTERVMAX 8    stable prevalence
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */     for age prevalim()
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    h Pij x
 #define NCOVMAX 8 /* Maximum number of covariates */    variance of p varprob
 #define MAXN 20000    forecasting if prevfcast==1 prevforecast call prevalence()
 #define YEARM 12. /* Number of months per year */    health expectancies
 #define AGESUP 130    Variance-covariance of DFLE
 #define AGEBASE 40    prevalence()
 #ifdef windows     movingaverage()
 #define DIRSEPARATOR '\\'    varevsij() 
 #define ODIRSEPARATOR '/'    if popbased==1 varevsij(,popbased)
 #else    total life expectancies
 #define DIRSEPARATOR '/'    Variance of stable prevalence
 #define ODIRSEPARATOR '\\'   end
 #endif  */
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";  
 int erreur; /* Error number */  
 int nvar;   
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  #include <math.h>
 int npar=NPARMAX;  #include <stdio.h>
 int nlstate=2; /* Number of live states */  #include <stdlib.h>
 int ndeath=1; /* Number of dead states */  #include <unistd.h>
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 int *wav; /* Number of waves for this individuual 0 is possible */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 int maxwav; /* Maxim number of waves */  #define FILENAMELENGTH 80
 int jmin, jmax; /* min, max spacing between 2 waves */  /*#define DEBUG*/
 int mle, weightopt;  #define windows
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficlog;  #define NINTERVMAX 8
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 FILE *ficresprobmorprev;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 FILE *fichtm; /* Html File */  #define NCOVMAX 8 /* Maximum number of covariates */
 FILE *ficreseij;  #define MAXN 20000
 char filerese[FILENAMELENGTH];  #define YEARM 12. /* Number of months per year */
 FILE  *ficresvij;  #define AGESUP 130
 char fileresv[FILENAMELENGTH];  #define AGEBASE 40
 FILE  *ficresvpl;  #ifdef windows
 char fileresvpl[FILENAMELENGTH];  #define DIRSEPARATOR '\\'
 char title[MAXLINE];  #define ODIRSEPARATOR '/'
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  #else
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  #endif
 char filelog[FILENAMELENGTH]; /* Log file */  
 char filerest[FILENAMELENGTH];  /* $Id$ */
 char fileregp[FILENAMELENGTH];  /* $Log$
 char popfile[FILENAMELENGTH];   * Revision 1.80  2003/06/05 15:34:14  brouard
    * Trying to add the true revision is the program and log
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];   *
   /* Revision 1.79  2003/06/05 15:17:23  brouard
 #define NR_END 1  /* *** empty log message ***
 #define FREE_ARG char*  /* */
 #define FTOL 1.0e-10  /* $Revision$ */
   /* $Date$ */
 #define NRANSI  /* $State$ */
 #define ITMAX 200  
   char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 #define TOL 2.0e-4  int erreur; /* Error number */
   int nvar;
 #define CGOLD 0.3819660  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #define ZEPS 1.0e-10  int npar=NPARMAX;
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
 #define GOLD 1.618034  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #define GLIMIT 100.0  int popbased=0;
 #define TINY 1.0e-20  
   int *wav; /* Number of waves for this individuual 0 is possible */
 static double maxarg1,maxarg2;  int maxwav; /* Maxim number of waves */
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  int jmin, jmax; /* min, max spacing between 2 waves */
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  int mle, weightopt;
    int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #define rint(a) floor(a+0.5)  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 static double sqrarg;  double jmean; /* Mean space between 2 waves */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 int imx;  FILE *ficlog, *ficrespow;
 int stepm;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 /* Stepm, step in month: minimum step interpolation*/  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
 int estepm;  FILE *ficreseij;
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 int m,nb;  char fileresv[FILENAMELENGTH];
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  FILE  *ficresvpl;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  char fileresvpl[FILENAMELENGTH];
 double **pmmij, ***probs, ***mobaverage;  char title[MAXLINE];
 double dateintmean=0;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 double *weight;  
 int **s; /* Status */  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 double *agedc, **covar, idx;  char filelog[FILENAMELENGTH]; /* Log file */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  char popfile[FILENAMELENGTH];
 double ftolhess; /* Tolerance for computing hessian */  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define NR_END 1
 {  #define FREE_ARG char*
    char *s;                             /* pointer */  #define FTOL 1.0e-10
    int  l1, l2;                         /* length counters */  
   #define NRANSI 
    l1 = strlen( path );                 /* length of path */  #define ITMAX 200 
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  #define TOL 2.0e-4 
    if ( s == NULL ) {                   /* no directory, so use current */  
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  #define CGOLD 0.3819660 
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  #define ZEPS 1.0e-10 
 #if     defined(__bsd__)                /* get current working directory */  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       extern char       *getwd( );  
   #define GOLD 1.618034 
       if ( getwd( dirc ) == NULL ) {  #define GLIMIT 100.0 
 #else  #define TINY 1.0e-20 
       extern char       *getcwd( );  
   static double maxarg1,maxarg2;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 #endif  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
          return( GLOCK_ERROR_GETCWD );    
       }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       strcpy( name, path );             /* we've got it */  #define rint(a) floor(a+0.5)
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  static double sqrarg;
       l2 = strlen( s );                 /* length of filename */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  int imx; 
       dirc[l1-l2] = 0;                  /* add zero */  int stepm;
    }  /* Stepm, step in month: minimum step interpolation*/
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows  int estepm;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int m,nb;
 #endif  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    s = strrchr( name, '.' );            /* find last / */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    s++;  double **pmmij, ***probs;
    strcpy(ext,s);                       /* save extension */  double dateintmean=0;
    l1= strlen( name);  
    l2= strlen( s)+1;  double *weight;
    strncpy( finame, name, l1-l2);  int **s; /* Status */
    finame[l1-l2]= 0;  double *agedc, **covar, idx;
    return( 0 );                         /* we're done */  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 }  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
 /******************************************/  
   /**************** split *************************/
 void replace(char *s, char*t)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
   int i;    char  *ss;                            /* pointer */
   int lg=20;    int   l1, l2;                         /* length counters */
   i=0;  
   lg=strlen(t);    l1 = strlen(path );                   /* length of path */
   for(i=0; i<= lg; i++) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     (s[i] = t[i]);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if (t[i]== '\\') s[i]='/';    if ( ss == NULL ) {                   /* no directory, so use current */
   }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* get current working directory */
 int nbocc(char *s, char occ)      /*    extern  char* getcwd ( char *buf , int len);*/
 {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   int i,j=0;        return( GLOCK_ERROR_GETCWD );
   int lg=20;      }
   i=0;      strcpy( name, path );               /* we've got it */
   lg=strlen(s);    } else {                              /* strip direcotry from path */
   for(i=0; i<= lg; i++) {      ss++;                               /* after this, the filename */
   if  (s[i] == occ ) j++;      l2 = strlen( ss );                  /* length of filename */
   }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   return j;      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 void cutv(char *u,char *v, char*t, char occ)    }
 {    l1 = strlen( dirc );                  /* length of directory */
   /* cuts string t into u and v where u is ended by char occ excluding it  #ifdef windows
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
      gives u="abcedf" and v="ghi2j" */  #else
   int i,lg,j,p=0;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   i=0;  #endif
   for(j=0; j<=strlen(t)-1; j++) {    ss = strrchr( name, '.' );            /* find last / */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    ss++;
   }    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
   lg=strlen(t);    l2= strlen(ss)+1;
   for(j=0; j<p; j++) {    strncpy( finame, name, l1-l2);
     (u[j] = t[j]);    finame[l1-l2]= 0;
   }    return( 0 );                          /* we're done */
      u[p]='\0';  }
   
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  /******************************************/
   }  
 }  void replace(char *s, char*t)
   {
 /********************** nrerror ********************/    int i;
     int lg=20;
 void nrerror(char error_text[])    i=0;
 {    lg=strlen(t);
   fprintf(stderr,"ERREUR ...\n");    for(i=0; i<= lg; i++) {
   fprintf(stderr,"%s\n",error_text);      (s[i] = t[i]);
   exit(1);      if (t[i]== '\\') s[i]='/';
 }    }
 /*********************** vector *******************/  }
 double *vector(int nl, int nh)  
 {  int nbocc(char *s, char occ)
   double *v;  {
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    int i,j=0;
   if (!v) nrerror("allocation failure in vector");    int lg=20;
   return v-nl+NR_END;    i=0;
 }    lg=strlen(s);
     for(i=0; i<= lg; i++) {
 /************************ free vector ******************/    if  (s[i] == occ ) j++;
 void free_vector(double*v, int nl, int nh)    }
 {    return j;
   free((FREE_ARG)(v+nl-NR_END));  }
 }  
   void cutv(char *u,char *v, char*t, char occ)
 /************************ivector *******************************/  {
 int *ivector(long nl,long nh)    /* cuts string t into u and v where u is ended by char occ excluding it
 {       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   int *v;       gives u="abcedf" and v="ghi2j" */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    int i,lg,j,p=0;
   if (!v) nrerror("allocation failure in ivector");    i=0;
   return v-nl+NR_END;    for(j=0; j<=strlen(t)-1; j++) {
 }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    lg=strlen(t);
 {    for(j=0; j<p; j++) {
   free((FREE_ARG)(v+nl-NR_END));      (u[j] = t[j]);
 }    }
        u[p]='\0';
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)     for(j=0; j<= lg; j++) {
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */      if (j>=(p+1))(v[j-p-1] = t[j]);
 {    }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  }
   int **m;  
    /********************** nrerror ********************/
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  void nrerror(char error_text[])
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    fprintf(stderr,"ERREUR ...\n");
   m -= nrl;    fprintf(stderr,"%s\n",error_text);
      exit(EXIT_FAILURE);
    }
   /* allocate rows and set pointers to them */  /*********************** vector *******************/
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  double *vector(int nl, int nh)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  {
   m[nrl] += NR_END;    double *v;
   m[nrl] -= ncl;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
      if (!v) nrerror("allocation failure in vector");
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    return v-nl+NR_END;
    }
   /* return pointer to array of pointers to rows */  
   return m;  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /****************** free_imatrix *************************/    free((FREE_ARG)(v+nl-NR_END));
 void free_imatrix(m,nrl,nrh,ncl,nch)  }
       int **m;  
       long nch,ncl,nrh,nrl;  /************************ivector *******************************/
      /* free an int matrix allocated by imatrix() */  char *cvector(long nl,long nh)
 {  {
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    char *v;
   free((FREE_ARG) (m+nrl-NR_END));    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
 }    if (!v) nrerror("allocation failure in cvector");
     return v-nl+NR_END;
 /******************* matrix *******************************/  }
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  /******************free ivector **************************/
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  void free_cvector(char *v, long nl, long nh)
   double **m;  {
     free((FREE_ARG)(v+nl-NR_END));
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /************************ivector *******************************/
   m -= nrl;  int *ivector(long nl,long nh)
   {
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    int *v;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m[nrl] += NR_END;    if (!v) nrerror("allocation failure in ivector");
   m[nrl] -= ncl;    return v-nl+NR_END;
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  /******************free ivector **************************/
 }  void free_ivector(int *v, long nl, long nh)
   {
 /*************************free matrix ************************/    free((FREE_ARG)(v+nl-NR_END));
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  }
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /******************* imatrix *******************************/
   free((FREE_ARG)(m+nrl-NR_END));  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
 /******************* ma3x *******************************/    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    int **m; 
 {    
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    /* allocate pointers to rows */ 
   double ***m;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m += NR_END; 
   if (!m) nrerror("allocation failure 1 in matrix()");    m -= nrl; 
   m += NR_END;    
   m -= nrl;    
     /* allocate rows and set pointers to them */ 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m[nrl] += NR_END;    m[nrl] += NR_END; 
   m[nrl] -= ncl;    m[nrl] -= ncl; 
     
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    /* return pointer to array of pointers to rows */ 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    return m; 
   m[nrl][ncl] += NR_END;  } 
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  /****************** free_imatrix *************************/
     m[nrl][j]=m[nrl][j-1]+nlay;  void free_imatrix(m,nrl,nrh,ncl,nch)
          int **m;
   for (i=nrl+1; i<=nrh; i++) {        long nch,ncl,nrh,nrl; 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;       /* free an int matrix allocated by imatrix() */ 
     for (j=ncl+1; j<=nch; j++)  { 
       m[i][j]=m[i][j-1]+nlay;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   }    free((FREE_ARG) (m+nrl-NR_END)); 
   return m;  } 
 }  
   /******************* matrix *******************************/
 /*************************free ma3x ************************/  double **matrix(long nrl, long nrh, long ncl, long nch)
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  {
 {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    double **m;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /***************** f1dim *************************/    m -= nrl;
 extern int ncom;  
 extern double *pcom,*xicom;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 extern double (*nrfunc)(double []);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      m[nrl] += NR_END;
 double f1dim(double x)    m[nrl] -= ncl;
 {  
   int j;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double f;    return m;
   double *xt;    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
       */
   xt=vector(1,ncom);  }
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  /*************************free matrix ************************/
   free_vector(xt,1,ncom);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   return f;  {
 }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 /*****************brent *************************/  }
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  /******************* ma3x *******************************/
   int iter;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   double a,b,d,etemp;  {
   double fu,fv,fw,fx;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   double ftemp;    double ***m;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      if (!m) nrerror("allocation failure 1 in matrix()");
   a=(ax < cx ? ax : cx);    m += NR_END;
   b=(ax > cx ? ax : cx);    m -= nrl;
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for (iter=1;iter<=ITMAX;iter++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     xm=0.5*(a+b);    m[nrl] += NR_END;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    m[nrl] -= ncl;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     fprintf(ficlog,".");fflush(ficlog);  
 #ifdef DEBUG    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     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 (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     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);    m[nrl][ncl] += NR_END;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    m[nrl][ncl] -= nll;
 #endif    for (j=ncl+1; j<=nch; j++) 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      m[nrl][j]=m[nrl][j-1]+nlay;
       *xmin=x;    
       return fx;    for (i=nrl+1; i<=nrh; i++) {
     }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     ftemp=fu;      for (j=ncl+1; j<=nch; j++) 
     if (fabs(e) > tol1) {        m[i][j]=m[i][j-1]+nlay;
       r=(x-w)*(fx-fv);    }
       q=(x-v)*(fx-fw);    return m; 
       p=(x-v)*q-(x-w)*r;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       q=2.0*(q-r);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       if (q > 0.0) p = -p;    */
       q=fabs(q);  }
       etemp=e;  
       e=d;  /*************************free ma3x ************************/
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  {
       else {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         d=p/q;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         u=x+d;    free((FREE_ARG)(m+nrl-NR_END));
         if (u-a < tol2 || b-u < tol2)  }
           d=SIGN(tol1,xm-x);  
       }  /***************** f1dim *************************/
     } else {  extern int ncom; 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  extern double *pcom,*xicom;
     }  extern double (*nrfunc)(double []); 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));   
     fu=(*f)(u);  double f1dim(double x) 
     if (fu <= fx) {  { 
       if (u >= x) a=x; else b=x;    int j; 
       SHFT(v,w,x,u)    double f;
         SHFT(fv,fw,fx,fu)    double *xt; 
         } else {   
           if (u < x) a=u; else b=u;    xt=vector(1,ncom); 
           if (fu <= fw || w == x) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
             v=w;    f=(*nrfunc)(xt); 
             w=u;    free_vector(xt,1,ncom); 
             fv=fw;    return f; 
             fw=fu;  } 
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  /*****************brent *************************/
             fv=fu;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
           }  { 
         }    int iter; 
   }    double a,b,d,etemp;
   nrerror("Too many iterations in brent");    double fu,fv,fw,fx;
   *xmin=x;    double ftemp;
   return fx;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
 }    double e=0.0; 
    
 /****************** mnbrak ***********************/    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    x=w=v=bx; 
             double (*func)(double))    fw=fv=fx=(*f)(x); 
 {    for (iter=1;iter<=ITMAX;iter++) { 
   double ulim,u,r,q, dum;      xm=0.5*(a+b); 
   double fu;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
        /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   *fa=(*func)(*ax);      printf(".");fflush(stdout);
   *fb=(*func)(*bx);      fprintf(ficlog,".");fflush(ficlog);
   if (*fb > *fa) {  #ifdef DEBUG
     SHFT(dum,*ax,*bx,dum)      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);
       SHFT(dum,*fb,*fa,dum)      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)))) { */
   *cx=(*bx)+GOLD*(*bx-*ax);  #endif
   *fc=(*func)(*cx);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   while (*fb > *fc) {        *xmin=x; 
     r=(*bx-*ax)*(*fb-*fc);        return fx; 
     q=(*bx-*cx)*(*fb-*fa);      } 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      ftemp=fu;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      if (fabs(e) > tol1) { 
     ulim=(*bx)+GLIMIT*(*cx-*bx);        r=(x-w)*(fx-fv); 
     if ((*bx-u)*(u-*cx) > 0.0) {        q=(x-v)*(fx-fw); 
       fu=(*func)(u);        p=(x-v)*q-(x-w)*r; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {        q=2.0*(q-r); 
       fu=(*func)(u);        if (q > 0.0) p = -p; 
       if (fu < *fc) {        q=fabs(q); 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        etemp=e; 
           SHFT(*fb,*fc,fu,(*func)(u))        e=d; 
           }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       u=ulim;        else { 
       fu=(*func)(u);          d=p/q; 
     } else {          u=x+d; 
       u=(*cx)+GOLD*(*cx-*bx);          if (u-a < tol2 || b-u < tol2) 
       fu=(*func)(u);            d=SIGN(tol1,xm-x); 
     }        } 
     SHFT(*ax,*bx,*cx,u)      } else { 
       SHFT(*fa,*fb,*fc,fu)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }      } 
 }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
 /*************** linmin ************************/      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
 int ncom;        SHFT(v,w,x,u) 
 double *pcom,*xicom;          SHFT(fv,fw,fx,fu) 
 double (*nrfunc)(double []);          } else { 
              if (u < x) a=u; else b=u; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))            if (fu <= fw || w == x) { 
 {              v=w; 
   double brent(double ax, double bx, double cx,              w=u; 
                double (*f)(double), double tol, double *xmin);              fv=fw; 
   double f1dim(double x);              fw=fu; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,            } else if (fu <= fv || v == x || v == w) { 
               double *fc, double (*func)(double));              v=u; 
   int j;              fv=fu; 
   double xx,xmin,bx,ax;            } 
   double fx,fb,fa;          } 
      } 
   ncom=n;    nrerror("Too many iterations in brent"); 
   pcom=vector(1,n);    *xmin=x; 
   xicom=vector(1,n);    return fx; 
   nrfunc=func;  } 
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  /****************** mnbrak ***********************/
     xicom[j]=xi[j];  
   }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   ax=0.0;              double (*func)(double)) 
   xx=1.0;  { 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double ulim,u,r,q, dum;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    double fu; 
 #ifdef DEBUG   
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    *fa=(*func)(*ax); 
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    *fb=(*func)(*bx); 
 #endif    if (*fb > *fa) { 
   for (j=1;j<=n;j++) {      SHFT(dum,*ax,*bx,dum) 
     xi[j] *= xmin;        SHFT(dum,*fb,*fa,dum) 
     p[j] += xi[j];        } 
   }    *cx=(*bx)+GOLD*(*bx-*ax); 
   free_vector(xicom,1,n);    *fc=(*func)(*cx); 
   free_vector(pcom,1,n);    while (*fb > *fc) { 
 }      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 /*************** powell ************************/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
             double (*func)(double []))      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 {      if ((*bx-u)*(u-*cx) > 0.0) { 
   void linmin(double p[], double xi[], int n, double *fret,        fu=(*func)(u); 
               double (*func)(double []));      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   int i,ibig,j;        fu=(*func)(u); 
   double del,t,*pt,*ptt,*xit;        if (fu < *fc) { 
   double fp,fptt;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double *xits;            SHFT(*fb,*fc,fu,(*func)(u)) 
   pt=vector(1,n);            } 
   ptt=vector(1,n);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   xit=vector(1,n);        u=ulim; 
   xits=vector(1,n);        fu=(*func)(u); 
   *fret=(*func)(p);      } else { 
   for (j=1;j<=n;j++) pt[j]=p[j];        u=(*cx)+GOLD*(*cx-*bx); 
   for (*iter=1;;++(*iter)) {        fu=(*func)(u); 
     fp=(*fret);      } 
     ibig=0;      SHFT(*ax,*bx,*cx,u) 
     del=0.0;        SHFT(*fa,*fb,*fc,fu) 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);        } 
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  } 
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  /*************** linmin ************************/
     fprintf(ficlog," %d %.12f",i, p[i]);  
     printf("\n");  int ncom; 
     fprintf(ficlog,"\n");  double *pcom,*xicom;
     for (i=1;i<=n;i++) {  double (*nrfunc)(double []); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];   
       fptt=(*fret);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 #ifdef DEBUG  { 
       printf("fret=%lf \n",*fret);    double brent(double ax, double bx, double cx, 
       fprintf(ficlog,"fret=%lf \n",*fret);                 double (*f)(double), double tol, double *xmin); 
 #endif    double f1dim(double x); 
       printf("%d",i);fflush(stdout);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       fprintf(ficlog,"%d",i);fflush(ficlog);                double *fc, double (*func)(double)); 
       linmin(p,xit,n,fret,func);    int j; 
       if (fabs(fptt-(*fret)) > del) {    double xx,xmin,bx,ax; 
         del=fabs(fptt-(*fret));    double fx,fb,fa;
         ibig=i;   
       }    ncom=n; 
 #ifdef DEBUG    pcom=vector(1,n); 
       printf("%d %.12e",i,(*fret));    xicom=vector(1,n); 
       fprintf(ficlog,"%d %.12e",i,(*fret));    nrfunc=func; 
       for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      pcom[j]=p[j]; 
         printf(" x(%d)=%.12e",j,xit[j]);      xicom[j]=xi[j]; 
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);    } 
       }    ax=0.0; 
       for(j=1;j<=n;j++) {    xx=1.0; 
         printf(" p=%.12e",p[j]);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         fprintf(ficlog," p=%.12e",p[j]);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       }  #ifdef DEBUG
       printf("\n");    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       fprintf(ficlog,"\n");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #endif  #endif
     }    for (j=1;j<=n;j++) { 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      xi[j] *= xmin; 
 #ifdef DEBUG      p[j] += xi[j]; 
       int k[2],l;    } 
       k[0]=1;    free_vector(xicom,1,n); 
       k[1]=-1;    free_vector(pcom,1,n); 
       printf("Max: %.12e",(*func)(p));  } 
       fprintf(ficlog,"Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++) {  /*************** powell ************************/
         printf(" %.12e",p[j]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         fprintf(ficlog," %.12e",p[j]);              double (*func)(double [])) 
       }  { 
       printf("\n");    void linmin(double p[], double xi[], int n, double *fret, 
       fprintf(ficlog,"\n");                double (*func)(double [])); 
       for(l=0;l<=1;l++) {    int i,ibig,j; 
         for (j=1;j<=n;j++) {    double del,t,*pt,*ptt,*xit;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    double fp,fptt;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    double *xits;
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    pt=vector(1,n); 
         }    ptt=vector(1,n); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    xit=vector(1,n); 
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    xits=vector(1,n); 
       }    *fret=(*func)(p); 
 #endif    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
       free_vector(xit,1,n);      ibig=0; 
       free_vector(xits,1,n);      del=0.0; 
       free_vector(ptt,1,n);      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       free_vector(pt,1,n);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       return;      fprintf(ficrespow,"%d %.12f",*iter,*fret);
     }      for (i=1;i<=n;i++) {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        printf(" %d %.12f",i, p[i]);
     for (j=1;j<=n;j++) {        fprintf(ficlog," %d %.12lf",i, p[i]);
       ptt[j]=2.0*p[j]-pt[j];        fprintf(ficrespow," %.12lf", p[i]);
       xit[j]=p[j]-pt[j];      }
       pt[j]=p[j];      printf("\n");
     }      fprintf(ficlog,"\n");
     fptt=(*func)(ptt);      fprintf(ficrespow,"\n");
     if (fptt < fp) {      for (i=1;i<=n;i++) { 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       if (t < 0.0) {        fptt=(*fret); 
         linmin(p,xit,n,fret,func);  #ifdef DEBUG
         for (j=1;j<=n;j++) {        printf("fret=%lf \n",*fret);
           xi[j][ibig]=xi[j][n];        fprintf(ficlog,"fret=%lf \n",*fret);
           xi[j][n]=xit[j];  #endif
         }        printf("%d",i);fflush(stdout);
 #ifdef DEBUG        fprintf(ficlog,"%d",i);fflush(ficlog);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        linmin(p,xit,n,fret,func); 
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        if (fabs(fptt-(*fret)) > del) { 
         for(j=1;j<=n;j++){          del=fabs(fptt-(*fret)); 
           printf(" %.12e",xit[j]);          ibig=i; 
           fprintf(ficlog," %.12e",xit[j]);        } 
         }  #ifdef DEBUG
         printf("\n");        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"\n");        fprintf(ficlog,"%d %.12e",i,(*fret));
 #endif        for (j=1;j<=n;j++) {
       }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     }          printf(" x(%d)=%.12e",j,xit[j]);
   }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
 }        }
         for(j=1;j<=n;j++) {
 /**** Prevalence limit ****************/          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        }
 {        printf("\n");
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        fprintf(ficlog,"\n");
      matrix by transitions matrix until convergence is reached */  #endif
       } 
   int i, ii,j,k;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double min, max, maxmin, maxmax,sumnew=0.;  #ifdef DEBUG
   double **matprod2();        int k[2],l;
   double **out, cov[NCOVMAX], **pmij();        k[0]=1;
   double **newm;        k[1]=-1;
   double agefin, delaymax=50 ; /* Max number of years to converge */        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   for (ii=1;ii<=nlstate+ndeath;ii++)        for (j=1;j<=n;j++) {
     for (j=1;j<=nlstate+ndeath;j++){          printf(" %.12e",p[j]);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);          fprintf(ficlog," %.12e",p[j]);
     }        }
         printf("\n");
    cov[1]=1.;        fprintf(ficlog,"\n");
          for(l=0;l<=1;l++) {
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */          for (j=1;j<=n;j++) {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     newm=savm;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     /* Covariates have to be included here again */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
      cov[2]=agefin;          }
            printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for (k=1; k<=cptcovn;k++) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        }
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  #endif
       }  
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)        free_vector(xit,1,n); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        free_vector(pt,1,n); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        return; 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      } 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
     savm=oldm;        ptt[j]=2.0*p[j]-pt[j]; 
     oldm=newm;        xit[j]=p[j]-pt[j]; 
     maxmax=0.;        pt[j]=p[j]; 
     for(j=1;j<=nlstate;j++){      } 
       min=1.;      fptt=(*func)(ptt); 
       max=0.;      if (fptt < fp) { 
       for(i=1; i<=nlstate; i++) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         sumnew=0;        if (t < 0.0) { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          linmin(p,xit,n,fret,func); 
         prlim[i][j]= newm[i][j]/(1-sumnew);          for (j=1;j<=n;j++) { 
         max=FMAX(max,prlim[i][j]);            xi[j][ibig]=xi[j][n]; 
         min=FMIN(min,prlim[i][j]);            xi[j][n]=xit[j]; 
       }          }
       maxmin=max-min;  #ifdef DEBUG
       maxmax=FMAX(maxmax,maxmin);          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);
     if(maxmax < ftolpl){          for(j=1;j<=n;j++){
       return prlim;            printf(" %.12e",xit[j]);
     }            fprintf(ficlog," %.12e",xit[j]);
   }          }
 }          printf("\n");
           fprintf(ficlog,"\n");
 /*************** transition probabilities ***************/  #endif
         }
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      } 
 {    } 
   double s1, s2;  } 
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;  /**** Prevalence limit (stable prevalence)  ****************/
   
     for(i=1; i<= nlstate; i++){  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for(j=1; j<i;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         /*s2 += param[i][j][nc]*cov[nc];*/       matrix by transitions matrix until convergence is reached */
         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);*/    int i, ii,j,k;
       }    double min, max, maxmin, maxmax,sumnew=0.;
       ps[i][j]=s2;    double **matprod2();
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
     for(j=i+1; j<=nlstate+ndeath;j++){    double agefin, delaymax=50 ; /* Max number of years to converge */
       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];    for (ii=1;ii<=nlstate+ndeath;ii++)
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      for (j=1;j<=nlstate+ndeath;j++){
       }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       ps[i][j]=s2;      }
     }  
   }     cov[1]=1.;
     /*ps[3][2]=1;*/   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(i=1; i<= nlstate; i++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
      s1=0;      newm=savm;
     for(j=1; j<i; j++)      /* Covariates have to be included here again */
       s1+=exp(ps[i][j]);       cov[2]=agefin;
     for(j=i+1; j<=nlstate+ndeath; j++)    
       s1+=exp(ps[i][j]);        for (k=1; k<=cptcovn;k++) {
     ps[i][i]=1./(s1+1.);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for(j=1; j<i; j++)          /*      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]]);*/
       ps[i][j]= exp(ps[i][j])*ps[i][i];        }
     for(j=i+1; j<=nlstate+ndeath; j++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       ps[i][j]= exp(ps[i][j])*ps[i][i];        for (k=1; k<=cptcovprod;k++)
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   } /* end i */  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for(jj=1; jj<= nlstate+ndeath; jj++){        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       ps[ii][jj]=0;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       ps[ii][ii]=1;  
     }      savm=oldm;
   }      oldm=newm;
       maxmax=0.;
       for(j=1;j<=nlstate;j++){
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        min=1.;
     for(jj=1; jj<= nlstate+ndeath; jj++){        max=0.;
      printf("%lf ",ps[ii][jj]);        for(i=1; i<=nlstate; i++) {
    }          sumnew=0;
     printf("\n ");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     }          prlim[i][j]= newm[i][j]/(1-sumnew);
     printf("\n ");printf("%lf ",cov[2]);*/          max=FMAX(max,prlim[i][j]);
 /*          min=FMIN(min,prlim[i][j]);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        }
   goto end;*/        maxmin=max-min;
     return ps;        maxmax=FMAX(maxmax,maxmin);
 }      }
       if(maxmax < ftolpl){
 /**************** Product of 2 matrices ******************/        return prlim;
       }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    }
 {  }
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /*************** transition probabilities ***************/ 
   /* in, b, out are matrice of pointers which should have been initialized  
      before: only the contents of out is modified. The function returns  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      a pointer to pointers identical to out */  {
   long i, j, k;    double s1, s2;
   for(i=nrl; i<= nrh; i++)    /*double t34;*/
     for(k=ncolol; k<=ncoloh; k++)    int i,j,j1, nc, ii, jj;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
   return out;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 }          /*s2 += param[i][j][nc]*cov[nc];*/
           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 /************* Higher Matrix Product ***************/        }
         ps[i][j]=s2;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 {      }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      for(j=i+1; j<=nlstate+ndeath;j++){
      duration (i.e. until        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
      (typically every 2 years instead of every month which is too big).        }
      Model is determined by parameters x and covariates have to be        ps[i][j]=s2;
      included manually here.      }
     }
      */      /*ps[3][2]=1;*/
   
   int i, j, d, h, k;    for(i=1; i<= nlstate; i++){
   double **out, cov[NCOVMAX];       s1=0;
   double **newm;      for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
   /* Hstepm could be zero and should return the unit matrix */      for(j=i+1; j<=nlstate+ndeath; j++)
   for (i=1;i<=nlstate+ndeath;i++)        s1+=exp(ps[i][j]);
     for (j=1;j<=nlstate+ndeath;j++){      ps[i][i]=1./(s1+1.);
       oldm[i][j]=(i==j ? 1.0 : 0.0);      for(j=1; j<i; j++)
       po[i][j][0]=(i==j ? 1.0 : 0.0);        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(h=1; h <=nhstepm; h++){      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     for(d=1; d <=hstepm; d++){    } /* end i */
       newm=savm;  
       /* Covariates have to be included here again */    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       cov[1]=1.;      for(jj=1; jj<= nlstate+ndeath; jj++){
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        ps[ii][jj]=0;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        ps[ii][ii]=1;
       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("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/       printf("%lf ",ps[ii][jj]);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/     }
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      printf("\n ");
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      }
       savm=oldm;      printf("\n ");printf("%lf ",cov[2]);*/
       oldm=newm;  /*
     }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     for(i=1; i<=nlstate+ndeath; i++)    goto end;*/
       for(j=1;j<=nlstate+ndeath;j++) {      return ps;
         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]);  
          */  /**************** Product of 2 matrices ******************/
       }  
   } /* end h */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   return po;  {
 }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
 /*************** log-likelihood *************/       before: only the contents of out is modified. The function returns
 double func( double *x)       a pointer to pointers identical to out */
 {    long i, j, k;
   int i, ii, j, k, mi, d, kk;    for(i=nrl; i<= nrh; i++)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      for(k=ncolol; k<=ncoloh; k++)
   double **out;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   double sw; /* Sum of weights */          out[i][k] +=in[i][j]*b[j][k];
   double lli; /* Individual log likelihood */  
   long ipmx;    return out;
   /*extern weight */  }
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  /************* Higher Matrix Product ***************/
     printf(" %d\n",s[4][i]);  
   */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   cov[1]=1.;  {
     /* Computes the transition matrix starting at age 'age' over 
   for(k=1; k<=nlstate; k++) ll[k]=0.;       'nhstepm*hstepm*stepm' months (i.e. until
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];       nhstepm*hstepm matrices. 
     for(mi=1; mi<= wav[i]-1; mi++){       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       for (ii=1;ii<=nlstate+ndeath;ii++)       (typically every 2 years instead of every month which is too big 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);       for the memory).
       for(d=0; d<dh[mi][i]; d++){       Model is determined by parameters x and covariates have to be 
         newm=savm;       included manually here. 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {       */
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }    int i, j, d, h, k;
            double **out, cov[NCOVMAX];
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    double **newm;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;    /* Hstepm could be zero and should return the unit matrix */
         oldm=newm;    for (i=1;i<=nlstate+ndeath;i++)
              for (j=1;j<=nlstate+ndeath;j++){
                oldm[i][j]=(i==j ? 1.0 : 0.0);
       } /* end mult */        po[i][j][0]=(i==j ? 1.0 : 0.0);
            }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    for(h=1; h <=nhstepm; h++){
       ipmx +=1;      for(d=1; d <=hstepm; d++){
       sw += weight[i];        newm=savm;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        /* Covariates have to be included here again */
     } /* end of wave */        cov[1]=1.;
   } /* end of individual */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        for (k=1; k<=cptcovage;k++)
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        for (k=1; k<=cptcovprod;k++)
   return -l;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 }  
   
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 /*********** Maximum Likelihood Estimation ***************/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))                     pmij(pmmij,cov,ncovmodel,x,nlstate));
 {        savm=oldm;
   int i,j, iter;        oldm=newm;
   double **xi,*delti;      }
   double fret;      for(i=1; i<=nlstate+ndeath; i++)
   xi=matrix(1,npar,1,npar);        for(j=1;j<=nlstate+ndeath;j++) {
   for (i=1;i<=npar;i++)          po[i][j][h]=newm[i][j];
     for (j=1;j<=npar;j++)          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       xi[i][j]=(i==j ? 1.0 : 0.0);           */
   printf("Powell\n");  fprintf(ficlog,"Powell\n");        }
   powell(p,xi,npar,ftol,&iter,&fret,func);    } /* end h */
     return po;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  }
   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));  
   /*************** log-likelihood *************/
 }  double func( double *x)
   {
 /**** Computes Hessian and covariance matrix ***/    int i, ii, j, k, mi, d, kk;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    double l, ll[NLSTATEMAX], cov[NCOVMAX];
 {    double **out;
   double  **a,**y,*x,pd;    double sw; /* Sum of weights */
   double **hess;    double lli; /* Individual log likelihood */
   int i, j,jk;    int s1, s2;
   int *indx;    double bbh, survp;
     long ipmx;
   double hessii(double p[], double delta, int theta, double delti[]);    /*extern weight */
   double hessij(double p[], double delti[], int i, int j);    /* We are differentiating ll according to initial status */
   void lubksb(double **a, int npar, int *indx, double b[]) ;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   void ludcmp(double **a, int npar, int *indx, double *d) ;    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   hess=matrix(1,npar,1,npar);    */
     cov[1]=1.;
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    for(k=1; k<=nlstate; k++) ll[k]=0.;
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);    if(mle==1){
     fprintf(ficlog,"%d",i);fflush(ficlog);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     hess[i][i]=hessii(p,ftolhess,i,delti);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     /*printf(" %f ",p[i]);*/        for(mi=1; mi<= wav[i]-1; mi++){
     /*printf(" %lf ",hess[i][i]);*/          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=1;j<=npar;j++)  {            }
       if (j>i) {          for(d=0; d<dh[mi][i]; d++){
         printf(".%d%d",i,j);fflush(stdout);            newm=savm;
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         hess[i][j]=hessij(p,delti,i,j);            for (kk=1; kk<=cptcovage;kk++) {
         hess[j][i]=hess[i][j];                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         /*printf(" %lf ",hess[i][j]);*/            }
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   printf("\n");            oldm=newm;
   fprintf(ficlog,"\n");          } /* end mult */
         
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");          /* 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 
   a=matrix(1,npar,1,npar);           * (in months) between two waves is not a multiple of stepm, we rounded to 
   y=matrix(1,npar,1,npar);           * the nearest (and in case of equal distance, to the lowest) interval but now
   x=vector(1,npar);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   indx=ivector(1,npar);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   for (i=1;i<=npar;i++)           * probability in order to take into account the bias as a fraction of the way
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   ludcmp(a,npar,indx,&pd);           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
   for (j=1;j<=npar;j++) {           * For stepm > 1 the results are less biased than in previous versions. 
     for (i=1;i<=npar;i++) x[i]=0;           */
     x[j]=1;          s1=s[mw[mi][i]][i];
     lubksb(a,npar,indx,x);          s2=s[mw[mi+1][i]][i];
     for (i=1;i<=npar;i++){          bbh=(double)bh[mi][i]/(double)stepm; 
       matcov[i][j]=x[i];          /* bias is positive if real duration
     }           * is higher than the multiple of stepm and negative otherwise.
   }           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   printf("\n#Hessian matrix#\n");          if( s2 > nlstate){ 
   fprintf(ficlog,"\n#Hessian matrix#\n");            /* 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++) {               step unit time, which is also the differences between probability to die before dh 
       printf("%.3e ",hess[i][j]);               and probability to die before dh-stepm . 
       fprintf(ficlog,"%.3e ",hess[i][j]);               In version up to 0.92 likelihood was computed
     }          as if date of death was unknown. Death was treated as any other
     printf("\n");          health state: the date of the interview describes the actual state
     fprintf(ficlog,"\n");          and not the date of a change in health state. The former idea was
   }          to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
   /* Recompute Inverse */          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
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          contribution is smaller and very dependent of the step unit
   ludcmp(a,npar,indx,&pd);          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
   /*  printf("\n#Hessian matrix recomputed#\n");          interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
   for (j=1;j<=npar;j++) {          Jackson for correcting this bug.  Former versions increased
     for (i=1;i<=npar;i++) x[i]=0;          mortality artificially. The bad side is that we add another loop
     x[j]=1;          which slows down the processing. The difference can be up to 10%
     lubksb(a,npar,indx,x);          lower mortality.
     for (i=1;i<=npar;i++){            */
       y[i][j]=x[i];            lli=log(out[s1][s2] - savm[s1][s2]);
       printf("%.3e ",y[i][j]);          }else{
       fprintf(ficlog,"%.3e ",y[i][j]);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     printf("\n");          } 
     fprintf(ficlog,"\n");          /*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); */
           ipmx +=1;
   free_matrix(a,1,npar,1,npar);          sw += weight[i];
   free_matrix(y,1,npar,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_vector(x,1,npar);        } /* end of wave */
   free_ivector(indx,1,npar);      } /* end of individual */
   free_matrix(hess,1,npar,1,npar);    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         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++)
 /*************** hessian matrix ****************/            for (j=1;j<=nlstate+ndeath;j++){
 double hessii( double x[], double delta, int theta, double delti[])              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i;            }
   int l=1, lmax=20;          for(d=0; d<=dh[mi][i]; d++){
   double k1,k2;            newm=savm;
   double p2[NPARMAX+1];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double res;            for (kk=1; kk<=cptcovage;kk++) {
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double fx;            }
   int k=0,kmax=10;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double l1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   fx=func(x);            oldm=newm;
   for (i=1;i<=npar;i++) p2[i]=x[i];          } /* end mult */
   for(l=0 ; l <=lmax; l++){        
     l1=pow(10,l);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     delts=delt;          /* But now since version 0.9 we anticipate for bias and large stepm.
     for(k=1 ; k <kmax; k=k+1){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       delt = delta*(l1*k);           * (in months) between two waves is not a multiple of stepm, we rounded to 
       p2[theta]=x[theta] +delt;           * the nearest (and in case of equal distance, to the lowest) interval but now
       k1=func(p2)-fx;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       p2[theta]=x[theta]-delt;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       k2=func(p2)-fx;           * probability in order to take into account the bias as a fraction of the way
       /*res= (k1-2.0*fx+k2)/delt/delt; */           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */           * -stepm/2 to stepm/2 .
                 * For stepm=1 the results are the same as for previous versions of Imach.
 #ifdef DEBUG           * For stepm > 1 the results are less biased than in previous versions. 
       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);          s1=s[mw[mi][i]][i];
 #endif          s2=s[mw[mi+1][i]][i];
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          bbh=(double)bh[mi][i]/(double)stepm; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /* bias is positive if real duration
         k=kmax;           * is higher than the multiple of stepm and negative otherwise.
       }           */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          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 */
         k=kmax; l=lmax*10.;          /* 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 */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         delts=delt;          /*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); */
     }          ipmx +=1;
   }          sw += weight[i];
   delti[theta]=delts;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   return res;        } /* end of wave */
        } /* end of individual */
 }    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 double hessij( double x[], double delti[], int thetai,int thetaj)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {        for(mi=1; mi<= wav[i]-1; mi++){
   int i;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int l=1, l1, lmax=20;            for (j=1;j<=nlstate+ndeath;j++){
   double k1,k2,k3,k4,res,fx;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double p2[NPARMAX+1];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int k;            }
           for(d=0; d<dh[mi][i]; d++){
   fx=func(x);            newm=savm;
   for (k=1; k<=2; k++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for (i=1;i<=npar;i++) p2[i]=x[i];            for (kk=1; kk<=cptcovage;kk++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            }
     k1=func(p2)-fx;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     p2[thetai]=x[thetai]+delti[thetai]/k;            savm=oldm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            oldm=newm;
     k2=func(p2)-fx;          } /* end mult */
          
     p2[thetai]=x[thetai]-delti[thetai]/k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /* But now since version 0.9 we anticipate for bias and large stepm.
     k3=func(p2)-fx;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             * (in months) between two waves is not a multiple of stepm, we rounded to 
     p2[thetai]=x[thetai]-delti[thetai]/k;           * the nearest (and in case of equal distance, to the lowest) interval but now
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     k4=func(p2)-fx;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */           * probability in order to take into account the bias as a fraction of the way
 #ifdef DEBUG           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     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);           * -stepm/2 to stepm/2 .
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);           * For stepm=1 the results are the same as for previous versions of Imach.
 #endif           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
   return res;          s1=s[mw[mi][i]][i];
 }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
 /************** Inverse of matrix **************/          /* bias is positive if real duration
 void ludcmp(double **a, int n, int *indx, double *d)           * is higher than the multiple of stepm and negative otherwise.
 {           */
   int i,imax,j,k;          /* 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 */
   double big,dum,sum,temp;          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 */
   double *vv;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            /*if(lli ==000.0)*/
   vv=vector(1,n);          /*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); */
   *d=1.0;          ipmx +=1;
   for (i=1;i<=n;i++) {          sw += weight[i];
     big=0.0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (j=1;j<=n;j++)        } /* end of wave */
       if ((temp=fabs(a[i][j])) > big) big=temp;      } /* end of individual */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    }else{  /* ml=4 no inter-extrapolation */
     vv[i]=1.0/big;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (j=1;j<=n;j++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1;i<j;i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       sum=a[i][j];            for (j=1;j<=nlstate+ndeath;j++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       a[i][j]=sum;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
     big=0.0;          for(d=0; d<dh[mi][i]; d++){
     for (i=j;i<=n;i++) {            newm=savm;
       sum=a[i][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (k=1;k<j;k++)            for (kk=1; kk<=cptcovage;kk++) {
         sum -= a[i][k]*a[k][j];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       a[i][j]=sum;            }
       if ( (dum=vv[i]*fabs(sum)) >= big) {          
         big=dum;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         imax=i;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
     }            oldm=newm;
     if (j != imax) {          } /* end mult */
       for (k=1;k<=n;k++) {        
         dum=a[imax][k];          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         a[imax][k]=a[j][k];          ipmx +=1;
         a[j][k]=dum;          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       *d = -(*d);        } /* end of wave */
       vv[imax]=vv[j];      } /* end of individual */
     }    } /* End of if */
     indx[j]=imax;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     if (a[j][j] == 0.0) a[j][j]=TINY;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     if (j != n) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       dum=1.0/(a[j][j]);    return -l;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  }
     }  
   }  
   free_vector(vv,1,n);  /* Doesn't work */  /*********** Maximum Likelihood Estimation ***************/
 ;  
 }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
 void lubksb(double **a, int n, int *indx, double b[])    int i,j, iter;
 {    double **xi;
   int i,ii=0,ip,j;    double fret;
   double sum;    char filerespow[FILENAMELENGTH];
      xi=matrix(1,npar,1,npar);
   for (i=1;i<=n;i++) {    for (i=1;i<=npar;i++)
     ip=indx[i];      for (j=1;j<=npar;j++)
     sum=b[ip];        xi[i][j]=(i==j ? 1.0 : 0.0);
     b[ip]=b[i];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     if (ii)    strcpy(filerespow,"pow"); 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    strcat(filerespow,fileres);
     else if (sum) ii=i;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     b[i]=sum;      printf("Problem with resultfile: %s\n", filerespow);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   for (i=n;i>=1;i--) {    }
     sum=b[i];    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    for (i=1;i<=nlstate;i++)
     b[i]=sum/a[i][i];      for(j=1;j<=nlstate+ndeath;j++)
   }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 }    fprintf(ficrespow,"\n");
     powell(p,xi,npar,ftol,&iter,&fret,func);
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    fclose(ficrespow);
 {  /* Some frequencies */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
      fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   int first;  
   double ***freq; /* Frequencies */  }
   double *pp;  
   double pos, k2, dateintsum=0,k2cpt=0;  /**** Computes Hessian and covariance matrix ***/
   FILE *ficresp;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   char fileresp[FILENAMELENGTH];  {
      double  **a,**y,*x,pd;
   pp=vector(1,nlstate);    double **hess;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i, j,jk;
   strcpy(fileresp,"p");    int *indx;
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double hessii(double p[], double delta, int theta, double delti[]);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double hessij(double p[], double delti[], int i, int j);
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     exit(0);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    hess=matrix(1,npar,1,npar);
   j1=0;  
      printf("\nCalculation of the hessian matrix. Wait...\n");
   j=cptcoveff;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
   first=1;      fprintf(ficlog,"%d",i);fflush(ficlog);
       hess[i][i]=hessii(p,ftolhess,i,delti);
   for(k1=1; k1<=j;k1++){      /*printf(" %f ",p[i]);*/
     for(i1=1; i1<=ncodemax[k1];i1++){      /*printf(" %lf ",hess[i][i]);*/
       j1++;    }
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    
         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++)          if (j>i) { 
           for(m=agemin; m <= agemax+3; m++)          printf(".%d%d",i,j);fflush(stdout);
             freq[i][jk][m]=0;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                hess[i][j]=hessij(p,delti,i,j);
       dateintsum=0;          hess[j][i]=hess[i][j];    
       k2cpt=0;          /*printf(" %lf ",hess[i][j]);*/
       for (i=1; i<=imx; i++) {        }
         bool=1;      }
         if  (cptcovn>0) {    }
           for (z1=1; z1<=cptcoveff; z1++)    printf("\n");
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    fprintf(ficlog,"\n");
               bool=0;  
         }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         if (bool==1) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           for(m=firstpass; m<=lastpass; m++){    
             k2=anint[m][i]+(mint[m][i]/12.);    a=matrix(1,npar,1,npar);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    y=matrix(1,npar,1,npar);
               if(agev[m][i]==0) agev[m][i]=agemax+1;    x=vector(1,npar);
               if(agev[m][i]==1) agev[m][i]=agemax+2;    indx=ivector(1,npar);
               if (m<lastpass) {    for (i=1;i<=npar;i++)
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    ludcmp(a,npar,indx,&pd);
               }  
                  for (j=1;j<=npar;j++) {
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      for (i=1;i<=npar;i++) x[i]=0;
                 dateintsum=dateintsum+k2;      x[j]=1;
                 k2cpt++;      lubksb(a,npar,indx,x);
               }      for (i=1;i<=npar;i++){ 
             }        matcov[i][j]=x[i];
           }      }
         }    }
       }  
            printf("\n#Hessian matrix#\n");
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
       if  (cptcovn>0) {      for (j=1;j<=npar;j++) { 
         fprintf(ficresp, "\n#********** Variable ");        printf("%.3e ",hess[i][j]);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        fprintf(ficlog,"%.3e ",hess[i][j]);
         fprintf(ficresp, "**********\n#");      }
       }      printf("\n");
       for(i=1; i<=nlstate;i++)      fprintf(ficlog,"\n");
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    }
       fprintf(ficresp, "\n");  
          /* Recompute Inverse */
       for(i=(int)agemin; i <= (int)agemax+3; i++){    for (i=1;i<=npar;i++)
         if(i==(int)agemax+3){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           fprintf(ficlog,"Total");    ludcmp(a,npar,indx,&pd);
         }else{  
           if(first==1){    /*  printf("\n#Hessian matrix recomputed#\n");
             first=0;  
             printf("See log file for details...\n");    for (j=1;j<=npar;j++) {
           }      for (i=1;i<=npar;i++) x[i]=0;
           fprintf(ficlog,"Age %d", i);      x[j]=1;
         }      lubksb(a,npar,indx,x);
         for(jk=1; jk <=nlstate ; jk++){      for (i=1;i<=npar;i++){ 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        y[i][j]=x[i];
             pp[jk] += freq[jk][m][i];        printf("%.3e ",y[i][j]);
         }        fprintf(ficlog,"%.3e ",y[i][j]);
         for(jk=1; jk <=nlstate ; jk++){      }
           for(m=-1, pos=0; m <=0 ; m++)      printf("\n");
             pos += freq[jk][m][i];      fprintf(ficlog,"\n");
           if(pp[jk]>=1.e-10){    }
             if(first==1){    */
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
             }    free_matrix(a,1,npar,1,npar);
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    free_matrix(y,1,npar,1,npar);
           }else{    free_vector(x,1,npar);
             if(first==1)    free_ivector(indx,1,npar);
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    free_matrix(hess,1,npar,1,npar);
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
           }  
         }  }
   
         for(jk=1; jk <=nlstate ; jk++){  /*************** hessian matrix ****************/
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  double hessii( double x[], double delta, int theta, double delti[])
             pp[jk] += freq[jk][m][i];  {
         }    int i;
     int l=1, lmax=20;
         for(jk=1,pos=0; jk <=nlstate ; jk++)    double k1,k2;
           pos += pp[jk];    double p2[NPARMAX+1];
         for(jk=1; jk <=nlstate ; jk++){    double res;
           if(pos>=1.e-5){    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
             if(first==1)    double fx;
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    int k=0,kmax=10;
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    double l1;
           }else{  
             if(first==1)    fx=func(x);
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for (i=1;i<=npar;i++) p2[i]=x[i];
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for(l=0 ; l <=lmax; l++){
           }      l1=pow(10,l);
           if( i <= (int) agemax){      delts=delt;
             if(pos>=1.e-5){      for(k=1 ; k <kmax; k=k+1){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        delt = delta*(l1*k);
               probs[i][jk][j1]= pp[jk]/pos;        p2[theta]=x[theta] +delt;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        k1=func(p2)-fx;
             }        p2[theta]=x[theta]-delt;
             else        k2=func(p2)-fx;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        /*res= (k1-2.0*fx+k2)/delt/delt; */
           }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         }        
          #ifdef DEBUG
         for(jk=-1; jk <=nlstate+ndeath; jk++)        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           for(m=-1; m <=nlstate+ndeath; m++)        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);
             if(freq[jk][m][i] !=0 ) {  #endif
             if(first==1)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);          k=kmax;
             }        }
         if(i <= (int) agemax)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           fprintf(ficresp,"\n");          k=kmax; l=lmax*10.;
         if(first==1)        }
           printf("Others in log...\n");        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         fprintf(ficlog,"\n");          delts=delt;
       }        }
     }      }
   }    }
   dateintmean=dateintsum/k2cpt;    delti[theta]=delts;
      return res; 
   fclose(ficresp);    
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  }
   free_vector(pp,1,nlstate);  
    double hessij( double x[], double delti[], int thetai,int thetaj)
   /* End of Freq */  {
 }    int i;
     int l=1, l1, lmax=20;
 /************ Prevalence ********************/    double k1,k2,k3,k4,res,fx;
 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)    double p2[NPARMAX+1];
 {  /* Some frequencies */    int k;
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    fx=func(x);
   double ***freq; /* Frequencies */    for (k=1; k<=2; k++) {
   double *pp;      for (i=1;i<=npar;i++) p2[i]=x[i];
   double pos, k2;      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   pp=vector(1,nlstate);      k1=func(p2)-fx;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    
        p2[thetai]=x[thetai]+delti[thetai]/k;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   j1=0;      k2=func(p2)-fx;
      
   j=cptcoveff;      p2[thetai]=x[thetai]-delti[thetai]/k;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k3=func(p2)-fx;
   for(k1=1; k1<=j;k1++){    
     for(i1=1; i1<=ncodemax[k1];i1++){      p2[thetai]=x[thetai]-delti[thetai]/k;
       j1++;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
            k4=func(p2)-fx;
       for (i=-1; i<=nlstate+ndeath; i++)        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         for (jk=-1; jk<=nlstate+ndeath; jk++)    #ifdef DEBUG
           for(m=agemin; m <= agemax+3; m++)      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);
             freq[i][jk][m]=0;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
        #endif
       for (i=1; i<=imx; i++) {    }
         bool=1;    return res;
         if  (cptcovn>0) {  }
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  /************** Inverse of matrix **************/
               bool=0;  void ludcmp(double **a, int n, int *indx, double *d) 
         }  { 
         if (bool==1) {    int i,imax,j,k; 
           for(m=firstpass; m<=lastpass; m++){    double big,dum,sum,temp; 
             k2=anint[m][i]+(mint[m][i]/12.);    double *vv; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {   
               if(agev[m][i]==0) agev[m][i]=agemax+1;    vv=vector(1,n); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    *d=1.0; 
               if (m<lastpass) {    for (i=1;i<=n;i++) { 
                 if (calagedate>0)      big=0.0; 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      for (j=1;j<=n;j++) 
                 else        if ((temp=fabs(a[i][j])) > big) big=temp; 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      vv[i]=1.0/big; 
               }    } 
             }    for (j=1;j<=n;j++) { 
           }      for (i=1;i<j;i++) { 
         }        sum=a[i][j]; 
       }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){        a[i][j]=sum; 
         for(jk=1; jk <=nlstate ; jk++){      } 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      big=0.0; 
             pp[jk] += freq[jk][m][i];      for (i=j;i<=n;i++) { 
         }        sum=a[i][j]; 
         for(jk=1; jk <=nlstate ; jk++){        for (k=1;k<j;k++) 
           for(m=-1, pos=0; m <=0 ; m++)          sum -= a[i][k]*a[k][j]; 
             pos += freq[jk][m][i];        a[i][j]=sum; 
         }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
                  big=dum; 
         for(jk=1; jk <=nlstate ; jk++){          imax=i; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        } 
             pp[jk] += freq[jk][m][i];      } 
         }      if (j != imax) { 
                for (k=1;k<=n;k++) { 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          dum=a[imax][k]; 
                  a[imax][k]=a[j][k]; 
         for(jk=1; jk <=nlstate ; jk++){              a[j][k]=dum; 
           if( i <= (int) agemax){        } 
             if(pos>=1.e-5){        *d = -(*d); 
               probs[i][jk][j1]= pp[jk]/pos;        vv[imax]=vv[j]; 
             }      } 
           }      indx[j]=imax; 
         }/* end jk */      if (a[j][j] == 0.0) a[j][j]=TINY; 
       }/* end i */      if (j != n) { 
     } /* end i1 */        dum=1.0/(a[j][j]); 
   } /* end k1 */        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
      } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    free_vector(vv,1,n);  /* Doesn't work */
   free_vector(pp,1,nlstate);  ;
    } 
 }  /* End of Freq */  
   void lubksb(double **a, int n, int *indx, double b[]) 
 /************* Waves Concatenation ***************/  { 
     int i,ii=0,ip,j; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    double sum; 
 {   
   /* 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).      ip=indx[i]; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      sum=b[ip]; 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      b[ip]=b[i]; 
      and mw[mi+1][i]. dh depends on stepm.      if (ii) 
      */        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
   int i, mi, m;      b[i]=sum; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    } 
      double sum=0., jmean=0.;*/    for (i=n;i>=1;i--) { 
   int first;      sum=b[i]; 
   int j, k=0,jk, ju, jl;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   double sum=0.;      b[i]=sum/a[i][i]; 
   first=0;    } 
   jmin=1e+5;  } 
   jmax=-1;  
   jmean=0.;  /************ Frequencies ********************/
   for(i=1; i<=imx; i++){  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
     mi=0;  {  /* Some frequencies */
     m=firstpass;    
     while(s[m][i] <= nlstate){    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       if(s[m][i]>=1)    int first;
         mw[++mi][i]=m;    double ***freq; /* Frequencies */
       if(m >=lastpass)    double *pp, **prop;
         break;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       else    FILE *ficresp;
         m++;    char fileresp[FILENAMELENGTH];
     }/* end while */    
     if (s[m][i] > nlstate){    pp=vector(1,nlstate);
       mi++;     /* Death is another wave */    prop=matrix(1,nlstate,iagemin,iagemax+3);
       /* if(mi==0)  never been interviewed correctly before death */    strcpy(fileresp,"p");
          /* Only death is a correct wave */    strcat(fileresp,fileres);
       mw[mi][i]=m;    if((ficresp=fopen(fileresp,"w"))==NULL) {
     }      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     wav[i]=mi;      exit(0);
     if(mi==0){    }
       if(first==0){    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);    j1=0;
         first=1;    
       }    j=cptcoveff;
       if(first==1){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);  
       }    first=1;
     } /* end mi==0 */  
   }    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   for(i=1; i<=imx; i++){        j1++;
     for(mi=1; mi<wav[i];mi++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       if (stepm <=0)          scanf("%d", i);*/
         dh[mi][i]=1;        for (i=-1; i<=nlstate+ndeath; i++)  
       else{          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         if (s[mw[mi+1][i]][i] > nlstate) {            for(m=iagemin; m <= iagemax+3; m++)
           if (agedc[i] < 2*AGESUP) {              freq[i][jk][m]=0;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */      for (i=1; i<=nlstate; i++)  
           k=k+1;        for(m=iagemin; m <= iagemax+3; m++)
           if (j >= jmax) jmax=j;          prop[i][m]=0;
           if (j <= jmin) jmin=j;        
           sum=sum+j;        dateintsum=0;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        k2cpt=0;
           }        for (i=1; i<=imx; i++) {
         }          bool=1;
         else{          if  (cptcovn>0) {
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            for (z1=1; z1<=cptcoveff; z1++) 
           k=k+1;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           if (j >= jmax) jmax=j;                bool=0;
           else if (j <= jmin)jmin=j;          }
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          if (bool==1){
           sum=sum+j;            for(m=firstpass; m<=lastpass; m++){
         }              k2=anint[m][i]+(mint[m][i]/12.);
         jk= j/stepm;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
         jl= j -jk*stepm;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         ju= j -(jk+1)*stepm;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         if(jl <= -ju)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
           dh[mi][i]=jk;                if (m<lastpass) {
         else                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           dh[mi][i]=jk+1;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         if(dh[mi][i]==0)                }
           dh[mi][i]=1; /* At least one step */                
       }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     }                  dateintsum=dateintsum+k2;
   }                  k2cpt++;
   jmean=sum/k;                }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);              }
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            }
  }          }
         }
 /*********** Tricode ****************************/         
 void tricode(int *Tvar, int **nbcode, int imx)        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 {  
   int Ndum[20],ij=1, k, j, i;        if  (cptcovn>0) {
   int cptcode=0;          fprintf(ficresp, "\n#********** Variable "); 
   cptcoveff=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresp, "**********\n#");
   for (k=0; k<19; k++) Ndum[k]=0;        }
   for (k=1; k<=7; k++) ncodemax[k]=0;        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        fprintf(ficresp, "\n");
     for (i=1; i<=imx; i++) {        
       ij=(int)(covar[Tvar[j]][i]);        for(i=iagemin; i <= iagemax+3; i++){
       Ndum[ij]++;          if(i==iagemax+3){
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            fprintf(ficlog,"Total");
       if (ij > cptcode) cptcode=ij;          }else{
     }            if(first==1){
               first=0;
     for (i=0; i<=cptcode; i++) {              printf("See log file for details...\n");
       if(Ndum[i]!=0) ncodemax[j]++;            }
     }            fprintf(ficlog,"Age %d", i);
     ij=1;          }
           for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for (i=1; i<=ncodemax[j]; i++) {              pp[jk] += freq[jk][m][i]; 
       for (k=0; k<=19; k++) {          }
         if (Ndum[k] != 0) {          for(jk=1; jk <=nlstate ; jk++){
           nbcode[Tvar[j]][ij]=k;            for(m=-1, pos=0; m <=0 ; m++)
                        pos += freq[jk][m][i];
           ij++;            if(pp[jk]>=1.e-10){
         }              if(first==1){
         if (ij > ncodemax[j]) break;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       }                }
     }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }              }else{
               if(first==1)
  for (k=0; k<19; k++) Ndum[k]=0;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  for (i=1; i<=ncovmodel-2; i++) {            }
    ij=Tvar[i];          }
    Ndum[ij]++;  
  }          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
  ij=1;              pp[jk] += freq[jk][m][i];
  for (i=1; i<=10; i++) {          }       
    if((Ndum[i]!=0) && (i<=ncovcol)){          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
      Tvaraff[ij]=i;            pos += pp[jk];
      ij++;            posprop += prop[jk][i];
    }          }
  }          for(jk=1; jk <=nlstate ; jk++){
              if(pos>=1.e-5){
  cptcoveff=ij-1;              if(first==1)
 }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 /*********** Health Expectancies ****************/            }else{
               if(first==1)
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 {            }
   /* Health expectancies */            if( i <= iagemax){
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;              if(pos>=1.e-5){
   double age, agelim, hf;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   double ***p3mat,***varhe;                probs[i][jk][j1]= pp[jk]/pos;
   double **dnewm,**doldm;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   double *xp;              }
   double **gp, **gm;              else
   double ***gradg, ***trgradg;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   int theta;            }
           }
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          
   xp=vector(1,npar);          for(jk=-1; jk <=nlstate+ndeath; jk++)
   dnewm=matrix(1,nlstate*2,1,npar);            for(m=-1; m <=nlstate+ndeath; m++)
   doldm=matrix(1,nlstate*2,1,nlstate*2);              if(freq[jk][m][i] !=0 ) {
                if(first==1)
   fprintf(ficreseij,"# Health expectancies\n");                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficreseij,"# Age");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   for(i=1; i<=nlstate;i++)              }
     for(j=1; j<=nlstate;j++)          if(i <= iagemax)
       fprintf(ficreseij," %1d-%1d (SE)",i,j);            fprintf(ficresp,"\n");
   fprintf(ficreseij,"\n");          if(first==1)
             printf("Others in log...\n");
   if(estepm < stepm){          fprintf(ficlog,"\n");
     printf ("Problem %d lower than %d\n",estepm, stepm);        }
   }      }
   else  hstepm=estepm;      }
   /* We compute the life expectancy from trapezoids spaced every estepm months    dateintmean=dateintsum/k2cpt; 
    * This is mainly to measure the difference between two models: for example   
    * if stepm=24 months pijx are given only every 2 years and by summing them    fclose(ficresp);
    * we are calculating an estimate of the Life Expectancy assuming a linear    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
    * progression inbetween and thus overestimating or underestimating according    free_vector(pp,1,nlstate);
    * to the curvature of the survival function. If, for the same date, we    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    /* End of Freq */
    * to compare the new estimate of Life expectancy with the same linear  }
    * hypothesis. A more precise result, taking into account a more precise  
    * curvature will be obtained if estepm is as small as stepm. */  /************ Prevalence ********************/
   void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   /* For example we decided to compute the life expectancy with the smallest unit */  {  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
      nhstepm is the number of hstepm from age to agelim       in each health status at the date of interview (if between dateprev1 and dateprev2).
      nstepm is the number of stepm from age to agelin.       We still use firstpass and lastpass as another selection.
      Look at hpijx to understand the reason of that which relies in memory size    */
      and note for a fixed period like estepm months */   
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
      survival function given by stepm (the optimization length). Unfortunately it    double ***freq; /* Frequencies */
      means that if the survival funtion is printed only each two years of age and if    double *pp, **prop;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    double pos,posprop; 
      results. So we changed our mind and took the option of the best precision.    double  y2; /* in fractional years */
   */    int iagemin, iagemax;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
     iagemin= (int) agemin;
   agelim=AGESUP;    iagemax= (int) agemax;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /*pp=vector(1,nlstate);*/
     /* nhstepm age range expressed in number of stepm */    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    j1=0;
     /* if (stepm >= YEARM) hstepm=1;*/    
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    j=cptcoveff;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    
     gp=matrix(0,nhstepm,1,nlstate*2);    for(k1=1; k1<=j;k1++){
     gm=matrix(0,nhstepm,1,nlstate*2);      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        for (i=1; i<=nlstate; i++)  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            for(m=iagemin; m <= iagemax+3; m++)
              prop[i][m]=0.0;
        
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
     /* Computing Variances of health expectancies */          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
      for(theta=1; theta <=npar; theta++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for(i=1; i<=npar; i++){                bool=0;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          } 
       }          if (bool==1) { 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       cptj=0;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       for(j=1; j<= nlstate; j++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         for(i=1; i<=nlstate; i++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           cptj=cptj+1;                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); 
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;                  /*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]]);*/
           }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         }                  prop[s[m][i]][iagemax+3] += weight[i]; 
       }                } 
                    }
                  } /* end selection of waves */
       for(i=1; i<=npar; i++)          }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          for(i=iagemin; i <= iagemax+3; i++){  
                
       cptj=0;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       for(j=1; j<= nlstate; j++){            posprop += prop[jk][i]; 
         for(i=1;i<=nlstate;i++){          } 
           cptj=cptj+1;  
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          for(jk=1; jk <=nlstate ; jk++){     
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;            if( i <=  iagemax){ 
           }              if(posprop>=1.e-5){ 
         }                probs[i][jk][j1]= prop[jk][i]/posprop;
       }              } 
       for(j=1; j<= nlstate*2; j++)            } 
         for(h=0; h<=nhstepm-1; h++){          }/* end jk */ 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        }/* end i */ 
         }      } /* end i1 */
      }    } /* end k1 */
        
 /* End theta */    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
      for(h=0; h<=nhstepm-1; h++)  
       for(j=1; j<=nlstate*2;j++)  /************* Waves Concatenation ***************/
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];  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.
      for(i=1;i<=nlstate*2;i++)       Death is a valid wave (if date is known).
       for(j=1;j<=nlstate*2;j++)       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         varhe[i][j][(int)age] =0.;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
      printf("%d|",(int)age);fflush(stdout);       */
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);  
      for(h=0;h<=nhstepm-1;h++){    int i, mi, m;
       for(k=0;k<=nhstepm-1;k++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);       double sum=0., jmean=0.;*/
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    int first;
         for(i=1;i<=nlstate*2;i++)    int j, k=0,jk, ju, jl;
           for(j=1;j<=nlstate*2;j++)    double sum=0.;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    first=0;
       }    jmin=1e+5;
     }    jmax=-1;
     /* Computing expectancies */    jmean=0.;
     for(i=1; i<=nlstate;i++)    for(i=1; i<=imx; i++){
       for(j=1; j<=nlstate;j++)      mi=0;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      m=firstpass;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      while(s[m][i] <= nlstate){
                  if(s[m][i]>=1)
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/          mw[++mi][i]=m;
         if(m >=lastpass)
         }          break;
         else
     fprintf(ficreseij,"%3.0f",age );          m++;
     cptj=0;      }/* end while */
     for(i=1; i<=nlstate;i++)      if (s[m][i] > nlstate){
       for(j=1; j<=nlstate;j++){        mi++;     /* Death is another wave */
         cptj++;        /* if(mi==0)  never been interviewed correctly before death */
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );           /* Only death is a correct wave */
       }        mw[mi][i]=m;
     fprintf(ficreseij,"\n");      }
      
     free_matrix(gm,0,nhstepm,1,nlstate*2);      wav[i]=mi;
     free_matrix(gp,0,nhstepm,1,nlstate*2);      if(mi==0){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        if(first==0){
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          first=1;
   }        }
   printf("\n");        if(first==1){
   fprintf(ficlog,"\n");          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
         }
   free_vector(xp,1,npar);      } /* end mi==0 */
   free_matrix(dnewm,1,nlstate*2,1,npar);    } /* End individuals */
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    for(i=1; i<=imx; i++){
 }      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
 /************ Variance ******************/          dh[mi][i]=1;
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased)        else{
 {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   /* Variance of health expectancies */            if (agedc[i] < 2*AGESUP) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   /* double **newm;*/            if(j==0) j=1;  /* Survives at least one month after exam */
   double **dnewm,**doldm;            k=k+1;
   double **dnewmp,**doldmp;            if (j >= jmax) jmax=j;
   int i, j, nhstepm, hstepm, h, nstepm ;            if (j <= jmin) jmin=j;
   int k, cptcode;            sum=sum+j;
   double *xp;            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   double **gp, **gm;  /* for var eij */            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   double ***gradg, ***trgradg; /*for var eij */            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]);
   double **gradgp, **trgradgp; /* for var p point j */            }
   double *gpp, *gmp; /* for var p point j */          }
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */          else{
   double ***p3mat;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   double age,agelim, hf;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   int theta;            k=k+1;
   char digit[4];            if (j >= jmax) jmax=j;
   char digitp[16];            else if (j <= jmin)jmin=j;
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   char fileresprobmorprev[FILENAMELENGTH];            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0)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]);
   if(popbased==1)            sum=sum+j;
     strcpy(digitp,"-populbased-");          }
   else          jk= j/stepm;
     strcpy(digitp,"-stablbased-");          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
   strcpy(fileresprobmorprev,"prmorprev");          if(mle <=1){ 
   sprintf(digit,"%-d",ij);            if(jl==0){
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/              dh[mi][i]=jk;
   strcat(fileresprobmorprev,digit); /* Tvar to be done */              bh[mi][i]=0;
   strcat(fileresprobmorprev,digitp); /* Popbased or not */            }else{ /* We want a negative bias in order to only have interpolation ie
   strcat(fileresprobmorprev,fileres);                    * at the price of an extra matrix product in likelihood */
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {              dh[mi][i]=jk+1;
     printf("Problem with resultfile: %s\n", fileresprobmorprev);              bh[mi][i]=ju;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);            }
   }          }else{
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);            if(jl <= -ju){
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);              dh[mi][i]=jk;
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");              bh[mi][i]=jl;       /* bias is positive if real duration
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);                                   * is higher than the multiple of stepm and negative otherwise.
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){                                   */
     fprintf(ficresprobmorprev," p.%-d SE",j);            }
     for(i=1; i<=nlstate;i++)            else{
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);              dh[mi][i]=jk+1;
   }                bh[mi][i]=ju;
   fprintf(ficresprobmorprev,"\n");            }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            if(dh[mi][i]==0){
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);              dh[mi][i]=1; /* At least one step */
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);              bh[mi][i]=ju; /* At least one step */
     exit(0);              /*  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);*/
   }            }
   else{          }
     fprintf(ficgp,"\n# Routine varevsij");        } /* end if mle */
   }      } /* end wave */
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    }
     printf("Problem with html file: %s\n", optionfilehtm);    jmean=sum/k;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    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);
   }   }
   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");  /*********** Tricode ****************************/
   }  void tricode(int *Tvar, int **nbcode, int imx)
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  {
     
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");    int Ndum[20],ij=1, k, j, i, maxncov=19;
   fprintf(ficresvij,"# Age");    int cptcode=0;
   for(i=1; i<=nlstate;i++)    cptcoveff=0; 
     for(j=1; j<=nlstate;j++)   
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    for (k=0; k<maxncov; k++) Ndum[k]=0;
   fprintf(ficresvij,"\n");    for (k=1; k<=7; k++) ncodemax[k]=0;
   
   xp=vector(1,npar);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   dnewm=matrix(1,nlstate,1,npar);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   doldm=matrix(1,nlstate,1,nlstate);                                 modality*/ 
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   gpp=vector(nlstate+1,nlstate+ndeath);                                         Tvar[j]. If V=sex and male is 0 and 
   gmp=vector(nlstate+1,nlstate+ndeath);                                         female is 1, then  cptcode=1.*/
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/      }
    
   if(estepm < stepm){      for (i=0; i<=cptcode; i++) {
     printf ("Problem %d lower than %d\n",estepm, stepm);        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 */
   }      }
   else  hstepm=estepm;    
   /* For example we decided to compute the life expectancy with the smallest unit */      ij=1; 
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (i=1; i<=ncodemax[j]; i++) {
      nhstepm is the number of hstepm from age to agelim        for (k=0; k<= maxncov; k++) {
      nstepm is the number of stepm from age to agelin.          if (Ndum[k] != 0) {
      Look at hpijx to understand the reason of that which relies in memory size            nbcode[Tvar[j]][ij]=k; 
      and note for a fixed period like k years */            /* 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; */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            
      survival function given by stepm (the optimization length). Unfortunately it            ij++;
      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 (ij > ncodemax[j]) break; 
      results. So we changed our mind and took the option of the best precision.        }  
   */      } 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    }  
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */   for (k=0; k< maxncov; k++) Ndum[k]=0;
     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 */   for (i=1; i<=ncovmodel-2; i++) { 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);     ij=Tvar[i];
     gp=matrix(0,nhstepm,1,nlstate);     Ndum[ij]++;
     gm=matrix(0,nhstepm,1,nlstate);   }
   
    ij=1;
     for(theta=1; theta <=npar; theta++){   for (i=1; i<= maxncov; i++) {
       for(i=1; i<=npar; i++){ /* Computes gradient */     if((Ndum[i]!=0) && (i<=ncovcol)){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);       Tvaraff[ij]=i; /*For printing */
       }       ij++;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);       }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);   }
    
       if (popbased==1) {   cptcoveff=ij-1; /*Number of simple covariates*/
         for(i=1; i<=nlstate;i++)  }
           prlim[i][i]=probs[(int)age][i][ij];  
       }  /*********** Health Expectancies ****************/
    
       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(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  {
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    /* Health expectancies */
         }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       }    double age, agelim, hf;
       /* This for computing forces of mortality (h=1)as a weighted average */    double ***p3mat,***varhe;
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    double **dnewm,**doldm;
         for(i=1; i<= nlstate; i++)    double *xp;
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    double **gp, **gm;
       }        double ***gradg, ***trgradg;
       /* end force of mortality */    int theta;
   
       for(i=1; i<=npar; i++) /* Computes gradient */    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    xp=vector(1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      dnewm=matrix(1,nlstate*nlstate,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      
       if (popbased==1) {    fprintf(ficreseij,"# Health expectancies\n");
         for(i=1; i<=nlstate;i++)    fprintf(ficreseij,"# Age");
           prlim[i][i]=probs[(int)age][i][ij];    for(i=1; i<=nlstate;i++)
       }      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
       for(j=1; j<= nlstate; j++){    fprintf(ficreseij,"\n");
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    if(estepm < stepm){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      printf ("Problem %d lower than %d\n",estepm, stepm);
         }    }
       }    else  hstepm=estepm;   
       /* This for computing force of mortality (h=1)as a weighted average */    /* We compute the life expectancy from trapezoids spaced every estepm months
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){     * This is mainly to measure the difference between two models: for example
         for(i=1; i<= nlstate; i++)     * if stepm=24 months pijx are given only every 2 years and by summing them
           gmp[j] += prlim[i][i]*p3mat[i][j][1];     * we are calculating an estimate of the Life Expectancy assuming a linear 
       }         * progression in between and thus overestimating or underestimating according
       /* end force of mortality */     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
       for(j=1; j<= nlstate; j++) /* vareij */     * to compare the new estimate of Life expectancy with the same linear 
         for(h=0; h<=nhstepm; h++){     * hypothesis. A more precise result, taking into account a more precise
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];     * curvature will be obtained if estepm is as small as stepm. */
         }  
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */    /* For example we decided to compute the life expectancy with the smallest unit */
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       }       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
     } /* End theta */       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
     for(h=0; h<=nhstepm; h++) /* veij */       means that if the survival funtion is printed only each two years of age and if
       for(j=1; j<=nlstate;j++)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for(theta=1; theta <=npar; theta++)       results. So we changed our mind and took the option of the best precision.
           trgradg[h][j][theta]=gradg[h][theta][j];    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */  
       for(theta=1; theta <=npar; theta++)    agelim=AGESUP;
         trgradgp[j][theta]=gradgp[theta][j];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* nhstepm age range expressed in number of stepm */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     for(i=1;i<=nlstate;i++)      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       for(j=1;j<=nlstate;j++)      /* if (stepm >= YEARM) hstepm=1;*/
         vareij[i][j][(int)age] =0.;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(h=0;h<=nhstepm;h++){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       for(k=0;k<=nhstepm;k++){      gp=matrix(0,nhstepm,1,nlstate*nlstate);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           for(j=1;j<=nlstate;j++)         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       }   
     }  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     /* pptj */  
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);      /* Computing Variances of health expectancies */
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);  
     for(j=nlstate+1;j<=nlstate+ndeath;j++)       for(theta=1; theta <=npar; theta++){
       for(i=nlstate+1;i<=nlstate+ndeath;i++)        for(i=1; i<=npar; i++){ 
         varppt[j][i]=doldmp[j][i];          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     /* end ppptj */        }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    
          cptj=0;
     if (popbased==1) {        for(j=1; j<= nlstate; j++){
       for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate; i++){
         prlim[i][i]=probs[(int)age][i][ij];            cptj=cptj+1;
     }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
                  gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     /* 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<= nlstate; i++)        }
         gmp[j] += prlim[i][i]*p3mat[i][j][1];       
     }           
     /* end force of mortality */        for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){        
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));        cptj=0;
       for(i=1; i<=nlstate;i++){        for(j=1; j<= nlstate; j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);          for(i=1;i<=nlstate;i++){
       }            cptj=cptj+1;
     }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     fprintf(ficresprobmorprev,"\n");  
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     fprintf(ficresvij,"%.0f ",age );            }
     for(i=1; i<=nlstate;i++)          }
       for(j=1; j<=nlstate;j++){        }
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);        for(j=1; j<= nlstate*nlstate; j++)
       }          for(h=0; h<=nhstepm-1; h++){
     fprintf(ficresvij,"\n");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     free_matrix(gp,0,nhstepm,1,nlstate);          }
     free_matrix(gm,0,nhstepm,1,nlstate);       } 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);     
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  /* End theta */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   free_vector(gpp,nlstate+1,nlstate+ndeath);  
   free_vector(gmp,nlstate+1,nlstate+ndeath);       for(h=0; h<=nhstepm-1; h++)
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);        for(j=1; j<=nlstate*nlstate;j++)
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/          for(theta=1; theta <=npar; theta++)
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");            trgradg[h][j][theta]=gradg[h][theta][j];
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */       
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");  
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);       for(i=1;i<=nlstate*nlstate;i++)
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);        for(j=1;j<=nlstate*nlstate;j++)
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);          varhe[i][j][(int)age] =0.;
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);  
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months 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);       printf("%d|",(int)age);fflush(stdout);
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
   free_vector(xp,1,npar);        for(k=0;k<=nhstepm-1;k++){
   free_matrix(doldm,1,nlstate,1,nlstate);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   free_matrix(dnewm,1,nlstate,1,npar);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          for(i=1;i<=nlstate*nlstate;i++)
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);            for(j=1;j<=nlstate*nlstate;j++)
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   fclose(ficresprobmorprev);        }
   fclose(ficgp);      }
   fclose(fichtm);      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
 }        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 /************ Variance of prevlim ******************/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)            
 {  /* if((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]);*/
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          }
   double **newm;  
   double **dnewm,**doldm;      fprintf(ficreseij,"%3.0f",age );
   int i, j, nhstepm, hstepm;      cptj=0;
   int k, cptcode;      for(i=1; i<=nlstate;i++)
   double *xp;        for(j=1; j<=nlstate;j++){
   double *gp, *gm;          cptj++;
   double **gradg, **trgradg;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   double age,agelim;        }
   int theta;      fprintf(ficreseij,"\n");
         
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   fprintf(ficresvpl,"# Age");      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   for(i=1; i<=nlstate;i++)      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       fprintf(ficresvpl," %1d-%1d",i,i);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   fprintf(ficresvpl,"\n");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }
   xp=vector(1,npar);    printf("\n");
   dnewm=matrix(1,nlstate,1,npar);    fprintf(ficlog,"\n");
   doldm=matrix(1,nlstate,1,nlstate);  
      free_vector(xp,1,npar);
   hstepm=1*YEARM; /* Every year of age */    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   agelim = AGESUP;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   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;  /************ Variance ******************/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  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)
     gradg=matrix(1,npar,1,nlstate);  {
     gp=vector(1,nlstate);    /* Variance of health expectancies */
     gm=vector(1,nlstate);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     for(theta=1; theta <=npar; theta++){    double **dnewm,**doldm;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double **dnewmp,**doldmp;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int i, j, nhstepm, hstepm, h, nstepm ;
       }    int k, cptcode;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double *xp;
       for(i=1;i<=nlstate;i++)    double **gp, **gm;  /* for var eij */
         gp[i] = prlim[i][i];    double ***gradg, ***trgradg; /*for var eij */
        double **gradgp, **trgradgp; /* for var p point j */
       for(i=1; i<=npar; i++) /* Computes gradient */    double *gpp, *gmp; /* for var p point j */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double ***p3mat;
       for(i=1;i<=nlstate;i++)    double age,agelim, hf;
         gm[i] = prlim[i][i];    double ***mobaverage;
     int theta;
       for(i=1;i<=nlstate;i++)    char digit[4];
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    char digitp[25];
     } /* End theta */  
     char fileresprobmorprev[FILENAMELENGTH];
     trgradg =matrix(1,nlstate,1,npar);  
     if(popbased==1){
     for(j=1; j<=nlstate;j++)      if(mobilav!=0)
       for(theta=1; theta <=npar; theta++)        strcpy(digitp,"-populbased-mobilav-");
         trgradg[j][theta]=gradg[theta][j];      else strcpy(digitp,"-populbased-nomobil-");
     }
     for(i=1;i<=nlstate;i++)    else 
       varpl[i][(int)age] =0.;      strcpy(digitp,"-stablbased-");
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    if (mobilav!=0) {
     for(i=1;i<=nlstate;i++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     fprintf(ficresvpl,"%.0f ",age );        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     for(i=1; i<=nlstate;i++)      }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    }
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);    strcpy(fileresprobmorprev,"prmorprev"); 
     free_vector(gm,1,nlstate);    sprintf(digit,"%-d",ij);
     free_matrix(gradg,1,npar,1,nlstate);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     free_matrix(trgradg,1,nlstate,1,npar);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   } /* End age */    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
   free_vector(xp,1,npar);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   free_matrix(doldm,1,nlstate,1,npar);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   free_matrix(dnewm,1,nlstate,1,nlstate);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
 }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 /************ Variance of one-step probabilities  ******************/    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);
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   int i, j=0,  i1, k1, l1, t, tj;      fprintf(ficresprobmorprev," p.%-d SE",j);
   int k2, l2, j1,  z1;      for(i=1; i<=nlstate;i++)
   int k=0,l, cptcode;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   int first=1, first1;    }  
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;    fprintf(ficresprobmorprev,"\n");
   double **dnewm,**doldm;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   double *xp;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   double *gp, *gm;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   double **gradg, **trgradg;      exit(0);
   double **mu;    }
   double age,agelim, cov[NCOVMAX];    else{
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */      fprintf(ficgp,"\n# Routine varevsij");
   int theta;    }
   char fileresprob[FILENAMELENGTH];    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   char fileresprobcov[FILENAMELENGTH];      printf("Problem with html file: %s\n", optionfilehtm);
   char fileresprobcor[FILENAMELENGTH];      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
       exit(0);
   double ***varpij;    }
     else{
   strcpy(fileresprob,"prob");      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");
   strcat(fileresprob,fileres);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    }
     printf("Problem with resultfile: %s\n", fileresprob);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);  
   }    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");
   strcpy(fileresprobcov,"probcov");    fprintf(ficresvij,"# Age");
   strcat(fileresprobcov,fileres);    for(i=1; i<=nlstate;i++)
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {      for(j=1; j<=nlstate;j++)
     printf("Problem with resultfile: %s\n", fileresprobcov);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    fprintf(ficresvij,"\n");
   }  
   strcpy(fileresprobcor,"probcor");    xp=vector(1,npar);
   strcat(fileresprobcor,fileres);    dnewm=matrix(1,nlstate,1,npar);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    doldm=matrix(1,nlstate,1,nlstate);
     printf("Problem with resultfile: %s\n", fileresprobcor);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    gpp=vector(nlstate+1,nlstate+ndeath);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    gmp=vector(nlstate+1,nlstate+ndeath);
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    }
   fprintf(ficresprob,"# Age");    else  hstepm=estepm;   
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    /* For example we decided to compute the life expectancy with the smallest unit */
   fprintf(ficresprobcov,"# Age");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");       nhstepm is the number of hstepm from age to agelim 
   fprintf(ficresprobcov,"# Age");       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
   for(i=1; i<=nlstate;i++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     for(j=1; j<=(nlstate+ndeath);j++){       survival function given by stepm (the optimization length). Unfortunately it
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);       means that if the survival funtion is printed every two years of age and if
       fprintf(ficresprobcov," p%1d-%1d ",i,j);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fprintf(ficresprobcor," p%1d-%1d ",i,j);       results. So we changed our mind and took the option of the best precision.
     }      */
   fprintf(ficresprob,"\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fprintf(ficresprobcov,"\n");    agelim = AGESUP;
   fprintf(ficresprobcor,"\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   xp=vector(1,npar);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);      gp=matrix(0,nhstepm,1,nlstate);
   first=1;      gm=matrix(0,nhstepm,1,nlstate);
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);  
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);      for(theta=1; theta <=npar; theta++){
     exit(0);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   else{        }
     fprintf(ficgp,"\n# Routine varprob");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  
     printf("Problem with html file: %s\n", optionfilehtm);        if (popbased==1) {
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);          if(mobilav ==0){
     exit(0);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=probs[(int)age][i][ij];
   else{          }else{ /* mobilav */ 
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");            for(i=1; i<=nlstate;i++)
     fprintf(fichtm,"\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");        }
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");    
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
   cov[1]=1;        }
   tj=cptcoveff;        /* This for computing probability of death (h=1 means
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}           computed over hstepm matrices product = hstepm*stepm months) 
   j1=0;           as a weighted average of prlim.
   for(t=1; t<=tj;t++){        */
     for(i1=1; i1<=ncodemax[t];i1++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       j1++;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
                  gpp[j] += prlim[i][i]*p3mat[i][j][1];
       if  (cptcovn>0) {        }    
         fprintf(ficresprob, "\n#********** Variable ");        /* end probability of death */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresprob, "**********\n#");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         fprintf(ficresprobcov, "\n#********** Variable ");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficresprobcov, "**********\n#");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           
         fprintf(ficgp, "\n#********** Variable ");        if (popbased==1) {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          if(mobilav ==0){
         fprintf(ficgp, "**********\n#");            for(i=1; i<=nlstate;i++)
                      prlim[i][i]=probs[(int)age][i][ij];
                  }else{ /* mobilav */ 
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");            for(i=1; i<=nlstate;i++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              prlim[i][i]=mobaverage[(int)age][i][ij];
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");          }
                }
         fprintf(ficresprobcor, "\n#********** Variable ");      
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for(j=1; j<= nlstate; j++){
         fprintf(ficgp, "**********\n#");              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 (age=bage; age<=fage; age ++){          }
         cov[2]=age;        }
         for (k=1; k<=cptcovn;k++) {        /* This for computing probability of death (h=1 means
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];           computed over hstepm matrices product = hstepm*stepm months) 
         }           as a weighted average of prlim.
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        */
         for (k=1; k<=cptcovprod;k++)        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          for(i=1,gmp[j]=0.; i<= nlstate; i++)
                   gmp[j] += prlim[i][i]*p3mat[i][j][1];
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));        }    
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);        /* end probability of death */
         gp=vector(1,(nlstate)*(nlstate+ndeath));  
         gm=vector(1,(nlstate)*(nlstate+ndeath));        for(j=1; j<= nlstate; j++) /* vareij */
              for(h=0; h<=nhstepm; h++){
         for(theta=1; theta <=npar; theta++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           for(i=1; i<=npar; i++)          }
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  
                  for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                  }
           k=0;  
           for(i=1; i<= (nlstate); i++){      } /* End theta */
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
               gp[k]=pmmij[i][j];  
             }      for(h=0; h<=nhstepm; h++) /* veij */
           }        for(j=1; j<=nlstate;j++)
                    for(theta=1; theta <=npar; theta++)
           for(i=1; i<=npar; i++)            trgradg[h][j][theta]=gradg[h][theta][j];
             xp[i] = x[i] - (i==theta ?delti[theta]:0);  
          for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        for(theta=1; theta <=npar; theta++)
           k=0;          trgradgp[j][theta]=gradgp[theta][j];
           for(i=1; i<=(nlstate); i++){    
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               gm[k]=pmmij[i][j];      for(i=1;i<=nlstate;i++)
             }        for(j=1;j<=nlstate;j++)
           }          vareij[i][j][(int)age] =0.;
        
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)      for(h=0;h<=nhstepm;h++){
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          for(k=0;k<=nhstepm;k++){
         }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)          for(i=1;i<=nlstate;i++)
           for(theta=1; theta <=npar; theta++)            for(j=1;j<=nlstate;j++)
             trgradg[j][theta]=gradg[theta][j];              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                }
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);      }
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);    
              /* pptj */
         pmij(pmmij,cov,ncovmodel,x,nlstate);      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);
         k=0;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=1; i<=(nlstate); i++){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           for(j=1; j<=(nlstate+ndeath);j++){          varppt[j][i]=doldmp[j][i];
             k=k+1;      /* end ppptj */
             mu[k][(int) age]=pmmij[i][j];      /*  x centered again */
           }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)   
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)      if (popbased==1) {
             varpij[i][j][(int)age] = doldm[i][j];        if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
         /*printf("\n%d ",(int)age);            prlim[i][i]=probs[(int)age][i][ij];
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){        }else{ /* mobilav */ 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          for(i=1; i<=nlstate;i++)
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            prlim[i][i]=mobaverage[(int)age][i][ij];
      }*/        }
       }
         fprintf(ficresprob,"\n%d ",(int)age);               
         fprintf(ficresprobcov,"\n%d ",(int)age);      /* This for computing probability of death (h=1 means
         fprintf(ficresprobcor,"\n%d ",(int)age);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)      */
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);      }    
         }      /* end probability of death */
         i=0;  
         for (k=1; k<=(nlstate);k++){      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           for (l=1; l<=(nlstate+ndeath);l++){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
             i=i++;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);        for(i=1; i<=nlstate;i++){
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
             for (j=1; j<=i;j++){        }
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);      } 
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));      fprintf(ficresprobmorprev,"\n");
             }  
           }      fprintf(ficresvij,"%.0f ",age );
         }/* end of loop for state */      for(i=1; i<=nlstate;i++)
       } /* end of loop for age */        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       /* Confidence intervalle of pij  */        }
       /*      fprintf(ficresvij,"\n");
       fprintf(ficgp,"\nset noparametric;unset label");      free_matrix(gp,0,nhstepm,1,nlstate);
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");      free_matrix(gm,0,nhstepm,1,nlstate);
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       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);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);    } /* End age */
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);    free_vector(gpp,nlstate+1,nlstate+ndeath);
       */    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       first1=1;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       for (k1=1; k1<=(nlstate);k1++){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
         for (l1=1; l1<=(nlstate+ndeath);l1++){    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           if(l1==k1) continue;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           i=(k1-1)*(nlstate+ndeath)+l1;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
           for (k2=1; k2<=(nlstate);k2++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
             for (l2=1; l2<=(nlstate+ndeath);l2++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
               if(l2==k2) continue;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
               j=(k2-1)*(nlstate+ndeath)+l2;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
               if(j<=i) continue;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
               for (age=bage; age<=fage; age ++){    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
                 if ((int)age %5==0){    /*  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);
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;  */
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;  
                   mu1=mu[i][(int) age]/stepm*YEARM ;    free_vector(xp,1,npar);
                   mu2=mu[j][(int) age]/stepm*YEARM;    free_matrix(doldm,1,nlstate,1,nlstate);
                   /* Computing eigen value of matrix of covariance */    free_matrix(dnewm,1,nlstate,1,npar);
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                   if(first1==1){    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                     first1=0;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);    fclose(ficresprobmorprev);
                   }    fclose(ficgp);
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);    fclose(fichtm);
                   /* Eigen vectors */  }  
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));  
                   v21=sqrt(1.-v11*v11);  /************ Variance of prevlim ******************/
                   v12=-v21;  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)
                   v22=v11;  {
                   /*printf(fignu*/    /* Variance of prevalence limit */
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */    double **newm;
                   if(first==1){    double **dnewm,**doldm;
                     first=0;    int i, j, nhstepm, hstepm;
                     fprintf(ficgp,"\nset parametric;set nolabel");    int k, cptcode;
                     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);    double *xp;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    double *gp, *gm;
                     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);    double **gradg, **trgradg;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);    double age,agelim;
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);    int theta;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);     
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
                     /*              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\"",\    fprintf(ficresvpl,"# Age");
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    for(i=1; i<=nlstate;i++)
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);        fprintf(ficresvpl," %1d-%1d",i,i);
                     */    fprintf(ficresvpl,"\n");
                     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",\  
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    xp=vector(1,npar);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));    dnewm=matrix(1,nlstate,1,npar);
                   }else{    doldm=matrix(1,nlstate,1,nlstate);
                     first=0;    
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    hstepm=1*YEARM; /* Every year of age */
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                     /*    agelim = AGESUP;
                     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\"",\    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);      if (stepm >= YEARM) hstepm=1;
                     */      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                     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",\      gradg=matrix(1,npar,1,nlstate);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      gp=vector(1,nlstate);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));      gm=vector(1,nlstate);
                   }/* if first */  
                 } /* age mod 5 */      for(theta=1; theta <=npar; theta++){
               } /* end loop age */        for(i=1; i<=npar; i++){ /* Computes gradient */
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
               first=1;        }
             } /*l12 */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           } /* k12 */        for(i=1;i<=nlstate;i++)
         } /*l1 */          gp[i] = prlim[i][i];
       }/* k1 */      
     } /* loop covariates */        for(i=1; i<=npar; i++) /* Computes gradient */
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        for(i=1;i<=nlstate;i++)
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);          gm[i] = prlim[i][i];
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for(i=1;i<=nlstate;i++)
   }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   free_vector(xp,1,npar);      } /* End theta */
   fclose(ficresprob);  
   fclose(ficresprobcov);      trgradg =matrix(1,nlstate,1,npar);
   fclose(ficresprobcor);  
   fclose(ficgp);      for(j=1; j<=nlstate;j++)
   fclose(fichtm);        for(theta=1; theta <=npar; theta++)
 }          trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
 /******************* Printing html file ***********/        varpl[i][(int)age] =0.;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   int lastpass, int stepm, int weightopt, char model[],\      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\      for(i=1;i<=nlstate;i++)
                   int popforecast, int estepm ,\        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
                   double jprev1, double mprev1,double anprev1, \  
                   double jprev2, double mprev2,double anprev2){      fprintf(ficresvpl,"%.0f ",age );
   int jj1, k1, i1, cpt;      for(i=1; i<=nlstate;i++)
   /*char optionfilehtm[FILENAMELENGTH];*/        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {      fprintf(ficresvpl,"\n");
     printf("Problem with %s \n",optionfilehtm), exit(0);      free_vector(gp,1,nlstate);
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);      free_vector(gm,1,nlstate);
   }      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n    } /* End age */
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n  
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    free_vector(xp,1,npar);
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    free_matrix(doldm,1,nlstate,1,npar);
  - Life expectancies by age and initial health status (estepm=%2d months):    free_matrix(dnewm,1,nlstate,1,nlstate);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  }
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
  m=cptcoveff;  {
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
  jj1=0;    int k=0,l, cptcode;
  for(k1=1; k1<=m;k1++){    int first=1, first1;
    for(i1=1; i1<=ncodemax[k1];i1++){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      jj1++;    double **dnewm,**doldm;
      if (cptcovn > 0) {    double *xp;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double *gp, *gm;
        for (cpt=1; cpt<=cptcoveff;cpt++)    double **gradg, **trgradg;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double **mu;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double age,agelim, cov[NCOVMAX];
      }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
      /* Pij */    int theta;
      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>    char fileresprob[FILENAMELENGTH];
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        char fileresprobcov[FILENAMELENGTH];
      /* Quasi-incidences */    char fileresprobcor[FILENAMELENGTH];
      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);    double ***varpij;
        /* Stable prevalence in each health state */  
        for(cpt=1; cpt<nlstate;cpt++){    strcpy(fileresprob,"prob"); 
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    strcat(fileresprob,fileres);
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        }      printf("Problem with resultfile: %s\n", fileresprob);
      for(cpt=1; cpt<=nlstate;cpt++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    }
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    strcpy(fileresprobcov,"probcov"); 
      }    strcat(fileresprobcov,fileres);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 health expectancies in states (1) and (2): e%s%d.png<br>      printf("Problem with resultfile: %s\n", fileresprobcov);
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
    } /* end i1 */    }
  }/* End k1 */    strcpy(fileresprobcor,"probcor"); 
  fprintf(fichtm,"</ul>");    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    }
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     
  if(popforecast==1) fprintf(fichtm,"\n    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    fprintf(ficresprob,"# Age");
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
         <br>",fileres,fileres,fileres,fileres);    fprintf(ficresprobcov,"# Age");
  else    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    fprintf(ficresprobcov,"# Age");
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");  
   
  m=cptcoveff;    for(i=1; i<=nlstate;i++)
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
  jj1=0;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
  for(k1=1; k1<=m;k1++){        fprintf(ficresprobcor," p%1d-%1d ",i,j);
    for(i1=1; i1<=ncodemax[k1];i1++){      }  
      jj1++;   /* fprintf(ficresprob,"\n");
      if (cptcovn > 0) {    fprintf(ficresprobcov,"\n");
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    fprintf(ficresprobcor,"\n");
        for (cpt=1; cpt<=cptcoveff;cpt++)   */
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);   xp=vector(1,npar);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      for(cpt=1; cpt<=nlstate;cpt++) {    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
 interval) in state (%d): v%s%d%d.png <br>    first=1;
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
      }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
    } /* end i1 */      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
  }/* End k1 */      exit(0);
  fprintf(fichtm,"</ul>");    }
 fclose(fichtm);    else{
 }      fprintf(ficgp,"\n# Routine varprob");
     }
 /******************* Gnuplot file **************/    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      exit(0);
   int ng;    }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    else{
     printf("Problem with file %s",optionfilegnuplot);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);      fprintf(fichtm,"\n");
   }  
       fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
 #ifdef windows      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(ficgp,"cd \"%s\" \n",pathc);      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");
 #endif  
 m=pow(2,cptcoveff);    }
    
  /* 1eme*/    cov[1]=1;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    tj=cptcoveff;
    for (k1=1; k1<= m ; k1 ++) {    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
 #ifdef windows    for(t=1; t<=tj;t++){
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      for(i1=1; i1<=ncodemax[t];i1++){ 
      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);        j1++;
 #endif        if  (cptcovn>0) {
 #ifdef unix          fprintf(ficresprob, "\n#********** Variable "); 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          fprintf(ficresprob, "**********\n#\n");
 #endif          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 for (i=1; i<= nlstate ; i ++) {          fprintf(ficresprobcov, "**********\n#\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficgp, "\n#********** Variable "); 
 }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficgp, "**********\n#\n");
     for (i=1; i<= nlstate ; i ++) {          
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
 }          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
      for (i=1; i<= nlstate ; i ++) {          
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficresprobcor, "\n#********** Variable ");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }            fprintf(ficresprobcor, "**********\n#");    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        }
 #ifdef unix        
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");        for (age=bage; age<=fage; age ++){ 
 #endif          cov[2]=age;
    }          for (k=1; k<=cptcovn;k++) {
   }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   /*2 eme*/          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for (k1=1; k1<= m ; k1 ++) {          for (k=1; k<=cptcovprod;k++)
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);          
              gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     for (i=1; i<= nlstate+1 ; i ++) {          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       k=2*i;          gp=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          gm=vector(1,(nlstate)*(nlstate+ndeath));
       for (j=1; j<= nlstate+1 ; j ++) {      
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(theta=1; theta <=npar; theta++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1; i<=npar; i++)
 }                xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     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 ++) {            k=0;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(i=1; i<= (nlstate); i++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");              for(j=1; j<=(nlstate+ndeath);j++){
 }                  k=k+1;
       fprintf(ficgp,"\" t\"\" w l 0,");                gp[k]=pmmij[i][j];
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              }
       for (j=1; j<= nlstate+1 ; j ++) {            }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1; i<=npar; i++)
 }                xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      
       else fprintf(ficgp,"\" t\"\" w l 0,");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     }            k=0;
   }            for(i=1; i<=(nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
   /*3eme*/                k=k+1;
                 gm[k]=pmmij[i][j];
   for (k1=1; k1<= m ; k1 ++) {              }
     for (cpt=1; cpt<= nlstate ; cpt ++) {            }
       k=2+nlstate*(2*cpt-2);       
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            for(theta=1; theta <=npar; theta++)
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");              trgradg[j][theta]=gradg[theta][j];
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
 */          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       for (i=1; i< nlstate ; i ++) {          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         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);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       }          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     }  
   }          pmij(pmmij,cov,ncovmodel,x,nlstate);
            
   /* CV preval stat */          k=0;
     for (k1=1; k1<= m ; k1 ++) {          for(i=1; i<=(nlstate); i++){
     for (cpt=1; cpt<nlstate ; cpt ++) {            for(j=1; j<=(nlstate+ndeath);j++){
       k=3;              k=k+1;
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);              mu[k][(int) age]=pmmij[i][j];
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);            }
           }
       for (i=1; i< nlstate ; i ++)          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         fprintf(ficgp,"+$%d",k+i+1);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              varpij[i][j][(int)age] = doldm[i][j];
        
       l=3+(nlstate+ndeath)*cpt;          /*printf("\n%d ",(int)age);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       for (i=1; i< nlstate ; i ++) {            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         l=3+(nlstate+ndeath)*cpt;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         fprintf(ficgp,"+$%d",l+i+1);            }*/
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            fprintf(ficresprob,"\n%d ",(int)age);
     }          fprintf(ficresprobcov,"\n%d ",(int)age);
   }            fprintf(ficresprobcor,"\n%d ",(int)age);
    
   /* proba elementaires */          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
    for(i=1,jk=1; i <=nlstate; i++){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     for(k=1; k <=(nlstate+ndeath); k++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       if (k != i) {            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
         for(j=1; j <=ncovmodel; j++){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          }
           jk++;          i=0;
           fprintf(ficgp,"\n");          for (k=1; k<=(nlstate);k++){
         }            for (l=1; l<=(nlstate+ndeath);l++){ 
       }              i=i++;
     }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
    }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
      for(jk=1; jk <=m; jk++) {                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);              }
        if (ng==2)            }
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          }/* end of loop for state */
        else        } /* end of loop for age */
          fprintf(ficgp,"\nset title \"Probability\"\n");  
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        /* Confidence intervalle of pij  */
        i=1;        /*
        for(k2=1; k2<=nlstate; k2++) {          fprintf(ficgp,"\nset noparametric;unset label");
          k3=i;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
          for(k=1; k<=(nlstate+ndeath); k++) {          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
            if (k != k2){          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
              if(ng==2)          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
              else          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        */
              ij=1;  
              for(j=3; j <=ncovmodel; j++) {        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        first1=1;
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for (k2=1; k2<=(nlstate);k2++){
                  ij++;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                }            if(l2==k2) continue;
                else            j=(k2-1)*(nlstate+ndeath)+l2;
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            for (k1=1; k1<=(nlstate);k1++){
              }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
              fprintf(ficgp,")/(1");                if(l1==k1) continue;
                              i=(k1-1)*(nlstate+ndeath)+l1;
              for(k1=1; k1 <=nlstate; k1++){                  if(i<=j) continue;
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                for (age=bage; age<=fage; age ++){ 
                ij=1;                  if ((int)age %5==0){
                for(j=3; j <=ncovmodel; j++){                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                    ij++;                    mu1=mu[i][(int) age]/stepm*YEARM ;
                  }                    mu2=mu[j][(int) age]/stepm*YEARM;
                  else                    c12=cv12/sqrt(v1*v2);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                    /* Computing eigen value of matrix of covariance */
                }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                fprintf(ficgp,")");                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
              }                    /* Eigen vectors */
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                    /*v21=sqrt(1.-v11*v11); *//* error */
              i=i+ncovmodel;                    v21=(lc1-v1)/cv12*v11;
            }                    v12=-v21;
          } /* end k */                    v22=v11;
        } /* end k2 */                    tnalp=v21/v11;
      } /* end jk */                    if(first1==1){
    } /* end ng */                      first1=0;
    fclose(ficgp);                      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);
 }  /* end gnuplot */                    }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
 /*************** Moving average **************/                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
   int i, cpt, cptcod;                      first=0;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)                      fprintf(ficgp,"\nset parametric;unset label");
       for (i=1; i<=nlstate;i++)                      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);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           mobaverage[(int)agedeb][i][cptcod]=0.;                      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);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       for (i=1; i<=nlstate;i++){                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           for (cpt=0;cpt<=4;cpt++){                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
           }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         }                    }else{
       }                      first=0;
     }                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
                          fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
 }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
 /************** Forecasting ******************/                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
 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 first */
                    } /* age mod 5 */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                } /* end loop age */
   int *popage;                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                first=1;
   double *popeffectif,*popcount;              } /*l12 */
   double ***p3mat;            } /* k12 */
   char fileresf[FILENAMELENGTH];          } /*l1 */
         }/* k1 */
  agelim=AGESUP;      } /* loop covariates */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      free_vector(xp,1,npar);
      fclose(ficresprob);
   strcpy(fileresf,"f");    fclose(ficresprobcov);
   strcat(fileresf,fileres);    fclose(ficresprobcor);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fclose(ficgp);
     printf("Problem with forecast resultfile: %s\n", fileresf);    fclose(fichtm);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);  }
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);  /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                    int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   if (mobilav==1) {                    int popforecast, int estepm ,\
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    double jprev1, double mprev1,double anprev1, \
     movingaverage(agedeb, fage, ageminpar, mobaverage);                    double jprev2, double mprev2,double anprev2){
   }    int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   if (stepm<=12) stepsize=1;      printf("Problem with %s \n",optionfilehtm), exit(0);
        fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   agelim=AGESUP;    }
    
   hstepm=1;     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   hstepm=hstepm/stepm;   - 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
   yp1=modf(dateintmean,&yp);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   anprojmean=yp;   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   yp2=modf((yp1*12),&yp);   - Life expectancies by age and initial health status (estepm=%2d months): 
   mprojmean=yp;     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   yp1=modf((yp2*30.5),&yp);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   if(mprojmean==0) jprojmean=1;  
     m=cptcoveff;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
   for(cptcov=1;cptcov<=i2;cptcov++){   jj1=0;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   for(k1=1; k1<=m;k1++){
       k=k+1;     for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficresf,"\n#******");       jj1++;
       for(j=1;j<=cptcoveff;j++) {       if (cptcovn > 0) {
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       }         for (cpt=1; cpt<=cptcoveff;cpt++) 
       fprintf(ficresf,"******\n");           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       fprintf(ficresf,"# StartingAge FinalAge");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);       }
             /* 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 (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
         fprintf(ficresf,"\n");       /* Quasi-incidences */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);         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); 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){         /* Stable prevalence in each health state */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);         for(cpt=1; cpt<nlstate;cpt++){
           nhstepm = nhstepm/hstepm;           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);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         }
           oldm=oldms;savm=savms;       for(cpt=1; cpt<=nlstate;cpt++) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
          <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           for (h=0; h<=nhstepm; h++){       }
             if (h==(int) (calagedate+YEARM*cpt)) {       fprintf(fichtm,"\n<br>- Total life expectancy by age and
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  health expectancies in states (1) and (2): e%s%d.png<br>
             }  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
             for(j=1; j<=nlstate+ndeath;j++) {     } /* end i1 */
               kk1=0.;kk2=0;   }/* End k1 */
               for(i=1; i<=nlstate;i++) {                 fprintf(fichtm,"</ul>");
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
                 }   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
                   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
               }   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
               if (h==(int)(calagedate+12*cpt)){   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
                 fprintf(ficresf," %.3f", kk1);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
                           - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
               }  
             }  /*  if(popforecast==1) fprintf(fichtm,"\n */
           }  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
         }  /*      <br>",fileres,fileres,fileres,fileres); */
       }  /*  else  */
     }  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   }  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   fclose(ficresf);  
 }   jj1=0;
 /************** Forecasting ******************/   for(k1=1; k1<=m;k1++){
 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(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       if (cptcovn > 0) {
   int *popage;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;         for (cpt=1; cpt<=cptcoveff;cpt++) 
   double *popeffectif,*popcount;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   double ***p3mat,***tabpop,***tabpopprev;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   char filerespop[FILENAMELENGTH];       }
        for(cpt=1; cpt<=nlstate;cpt++) {
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  interval) in state (%d): v%s%d%d.png <br>
   agelim=AGESUP;  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;       }
       } /* end i1 */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   }/* End k1 */
     fprintf(fichtm,"</ul>");
    fclose(fichtm);
   strcpy(filerespop,"pop");  }
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  /******************* Gnuplot file **************/
     printf("Problem with forecast resultfile: %s\n", filerespop);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);  
   }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   printf("Computing forecasting: result on file '%s' \n", filerespop);    int ng;
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*#ifdef windows */
     movingaverage(agedeb, fage, ageminpar, mobaverage);      fprintf(ficgp,"cd \"%s\" \n",pathc);
   }      /*#endif */
   m=pow(2,cptcoveff);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    
   if (stepm<=12) stepsize=1;   /* 1eme*/
      for (cpt=1; cpt<= nlstate ; cpt ++) {
   agelim=AGESUP;     for (k1=1; k1<= m ; k1 ++) {
         fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   hstepm=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);
   hstepm=hstepm/stepm;  
         for (i=1; i<= nlstate ; i ++) {
   if (popforecast==1) {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     if((ficpop=fopen(popfile,"r"))==NULL) {         else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf("Problem with population file : %s\n",popfile);exit(0);       }
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
     }       for (i=1; i<= nlstate ; i ++) {
     popage=ivector(0,AGESUP);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     popeffectif=vector(0,AGESUP);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     popcount=vector(0,AGESUP);       } 
           fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
     i=1;         for (i=1; i<= nlstate ; i ++) {
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             else fprintf(ficgp," \%%*lf (\%%*lf)");
     imx=i;       }  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
   }     }
     }
   for(cptcov=1;cptcov<=i2;cptcov++){    /*2 eme*/
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
       k=k+1;    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficrespop,"\n#******");      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       for(j=1;j<=cptcoveff;j++) {      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      
       }      for (i=1; i<= nlstate+1 ; i ++) {
       fprintf(ficrespop,"******\n");        k=2*i;
       fprintf(ficrespop,"# Age");        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);        for (j=1; j<= nlstate+1 ; j ++) {
       if (popforecast==1)  fprintf(ficrespop," [Population]");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                else fprintf(ficgp," \%%*lf (\%%*lf)");
       for (cpt=0; cpt<=0;cpt++) {        }   
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
                else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for (j=1; j<= nlstate+1 ; j ++) {
           nhstepm = nhstepm/hstepm;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                    else fprintf(ficgp," \%%*lf (\%%*lf)");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }   
           oldm=oldms;savm=savms;        fprintf(ficgp,"\" t\"\" w l 0,");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
                for (j=1; j<= nlstate+1 ; j ++) {
           for (h=0; h<=nhstepm; h++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
             if (h==(int) (calagedate+YEARM*cpt)) {          else fprintf(ficgp," \%%*lf (\%%*lf)");
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        }   
             }        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
             for(j=1; j<=nlstate+ndeath;j++) {        else fprintf(ficgp,"\" t\"\" w l 0,");
               kk1=0.;kk2=0;      }
               for(i=1; i<=nlstate;i++) {                  }
                 if (mobilav==1)    
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /*3eme*/
                 else {    
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    for (k1=1; k1<= m ; k1 ++) { 
                 }      for (cpt=1; cpt<= nlstate ; cpt ++) {
               }        k=2+nlstate*(2*cpt-2);
               if (h==(int)(calagedate+12*cpt)){        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
                   /*fprintf(ficrespop," %.3f", kk1);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
               }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
             }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
             for(i=1; i<=nlstate;i++){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
               kk1=0.;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                 for(j=1; j<=nlstate;j++){          
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        */
                 }        for (i=1; i< nlstate ; i ++) {
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
             }          
         } 
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    }
           }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* CV preval stable (period) */
         }    for (k1=1; k1<= m ; k1 ++) { 
       }      for (cpt=1; cpt<=nlstate ; cpt ++) {
          k=3;
   /******/        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          for (i=1; i<= nlstate ; i ++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          fprintf(ficgp,"+$%d",k+i+1);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
           nhstepm = nhstepm/hstepm;        
                  l=3+(nlstate+ndeath)*cpt;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
           oldm=oldms;savm=savms;        for (i=1; i< nlstate ; i ++) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            l=3+(nlstate+ndeath)*cpt;
           for (h=0; h<=nhstepm; h++){          fprintf(ficgp,"+$%d",l+i+1);
             if (h==(int) (calagedate+YEARM*cpt)) {        }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
             }      } 
             for(j=1; j<=nlstate+ndeath;j++) {    }  
               kk1=0.;kk2=0;    
               for(i=1; i<=nlstate;i++) {                  /* proba elementaires */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        for(i=1,jk=1; i <=nlstate; i++){
               }      for(k=1; k <=(nlstate+ndeath); k++){
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        if (k != i) {
             }          for(j=1; j <=ncovmodel; j++){
           }            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            jk++; 
         }            fprintf(ficgp,"\n");
       }          }
    }        }
   }      }
       }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   if (popforecast==1) {       for(jk=1; jk <=m; jk++) {
     free_ivector(popage,0,AGESUP);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
     free_vector(popeffectif,0,AGESUP);         if (ng==2)
     free_vector(popcount,0,AGESUP);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   }         else
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);           fprintf(ficgp,"\nset title \"Probability\"\n");
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   fclose(ficrespop);         i=1;
 }         for(k2=1; k2<=nlstate; k2++) {
            k3=i;
 /***********************************************/           for(k=1; k<=(nlstate+ndeath); k++) {
 /**************** Main Program *****************/             if (k != k2){
 /***********************************************/               if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
 int main(int argc, char *argv[])               else
 {                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;               for(j=3; j <=ncovmodel; j++) {
   double agedeb, agefin,hf;                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
   double fret;                 }
   double **xi,tmp,delta;                 else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   double dum; /* Dummy variable */               }
   double ***p3mat;               fprintf(ficgp,")/(1");
   int *indx;               
   char line[MAXLINE], linepar[MAXLINE];               for(k1=1; k1 <=nlstate; k1++){   
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   int firstobs=1, lastobs=10;                 ij=1;
   int sdeb, sfin; /* Status at beginning and end */                 for(j=3; j <=ncovmodel; j++){
   int c,  h , cpt,l;                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   int ju,jl, mi;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                     ij++;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                   }
   int mobilav=0,popforecast=0;                   else
   int hstepm, nhstepm;                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;                 }
                  fprintf(ficgp,")");
   double bage, fage, age, agelim, agebase;               }
   double ftolpl=FTOL;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   double **prlim;               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   double *severity;               i=i+ncovmodel;
   double ***param; /* Matrix of parameters */             }
   double  *p;           } /* end k */
   double **matcov; /* Matrix of covariance */         } /* end k2 */
   double ***delti3; /* Scale */       } /* end jk */
   double *delti; /* Scale */     } /* end ng */
   double ***eij, ***vareij;     fclose(ficgp); 
   double **varpl; /* Variances of prevalence limits by age */  }  /* end gnuplot */
   double *epj, vepp;  
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  /*************** Moving average **************/
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
   char *alph[]={"a","a","b","c","d","e"}, str[4];    int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
   char z[1]="c", occ;    double age;
 #include <sys/time.h>  
 #include <time.h>    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                             a covariate has 2 modalities */
      if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   /* long total_usecs;  
   struct timeval start_time, end_time;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
        if(mobilav==1) mobilavrange=5; /* default */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      else mobilavrange=mobilav;
   getcwd(pathcd, size);      for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
   printf("\n%s",version);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   if(argc <=1){            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     printf("\nEnter the parameter file name: ");      /* We keep the original values on the extreme ages bage, fage and for 
     scanf("%s",pathtot);         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. 
   else{      */ 
     strcpy(pathtot,argv[1]);      for (mob=3;mob <=mobilavrange;mob=mob+2){
   }        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          for (i=1; i<=nlstate;i++){
   /*cygwin_split_path(pathtot,path,optionfile);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   /* cutv(path,optionfile,pathtot,'\\');*/                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                }
   chdir(path);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   replace(pathc,path);            }
           }
 /*-------- arguments in the command line --------*/        }/* end age */
       }/* end mob */
   /* Log file */    }else return -1;
   strcat(filelog, optionfilefiname);    return 0;
   strcat(filelog,".log");    /* */  }/* End movingaverage */
   if((ficlog=fopen(filelog,"w"))==NULL)    {  
     printf("Problem with logfile %s\n",filelog);  
     goto end;  /************** Forecasting ******************/
   }  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
   fprintf(ficlog,"Log filename:%s\n",filelog);    /* proj1, year, month, day of starting projection 
   fprintf(ficlog,"\n%s",version);       agemin, agemax range of age
   fprintf(ficlog,"\nEnter the parameter file name: ");       dateprev1 dateprev2 range of dates during which prevalence is computed
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);       anproj2 year of en of projection (same day and month as proj1).
   fflush(ficlog);    */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   /* */    int *popage;
   strcpy(fileres,"r");    double agec; /* generic age */
   strcat(fileres, optionfilefiname);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   strcat(fileres,".txt");    /* Other files have txt extension */    double *popeffectif,*popcount;
     double ***p3mat;
   /*---------arguments file --------*/    double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);    agelim=AGESUP;
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     goto end;   
   }    strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
   strcpy(filereso,"o");    if((ficresf=fopen(fileresf,"w"))==NULL) {
   strcat(filereso,fileres);      printf("Problem with forecast resultfile: %s\n", fileresf);
   if((ficparo=fopen(filereso,"w"))==NULL) {      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     printf("Problem with Output resultfile: %s\n", filereso);    }
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);    printf("Computing forecasting: result on file '%s' \n", fileresf);
     goto end;    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   }  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    if (mobilav!=0) {
     ungetc(c,ficpar);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fgets(line, MAXLINE, ficpar);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     puts(line);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     fputs(line,ficparo);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   }      }
   ungetc(c,ficpar);    }
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    stepsize=(int) (stepm+YEARM-1)/YEARM;
   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);    if (stepm<=12) stepsize=1;
   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);    if(estepm < stepm){
 while((c=getc(ficpar))=='#' && c!= EOF){      printf ("Problem %d lower than %d\n",estepm, stepm);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    else  hstepm=estepm;   
     puts(line);  
     fputs(line,ficparo);    hstepm=hstepm/stepm; 
   }    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   ungetc(c,ficpar);                                 fractional in yp1 */
      anprojmean=yp;
        yp2=modf((yp1*12),&yp);
   covar=matrix(0,NCOVMAX,1,n);    mprojmean=yp;
   cptcovn=0;    yp1=modf((yp2*30.5),&yp);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
   ncovmodel=2+cptcovn;    if(mprojmean==0) jprojmean=1;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
      i1=cptcoveff;
   /* Read guess parameters */    if (cptcovn < 1){i1=1;}
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    fprintf(ficresf,"#****** Routine prevforecast **\n");
     puts(line);  
     fputs(line,ficparo);  /*            if (h==(int)(YEARM*yearp)){ */
   }    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   ungetc(c,ficpar);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
          k=k+1;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        fprintf(ficresf,"\n#******");
     for(i=1; i <=nlstate; i++)        for(j=1;j<=cptcoveff;j++) {
     for(j=1; j <=nlstate+ndeath-1; j++){          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fscanf(ficpar,"%1d%1d",&i1,&j1);        }
       fprintf(ficparo,"%1d%1d",i1,j1);        fprintf(ficresf,"******\n");
       if(mle==1)        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         printf("%1d%1d",i,j);        for(j=1; j<=nlstate+ndeath;j++){ 
       fprintf(ficlog,"%1d%1d",i,j);          for(i=1; i<=nlstate;i++)              
       for(k=1; k<=ncovmodel;k++){            fprintf(ficresf," p%d%d",i,j);
         fscanf(ficpar," %lf",&param[i][j][k]);          fprintf(ficresf," p.%d",j);
         if(mle==1){        }
           printf(" %lf",param[i][j][k]);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficlog," %lf",param[i][j][k]);          fprintf(ficresf,"\n");
         }          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
         else  
           fprintf(ficlog," %lf",param[i][j][k]);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
         fprintf(ficparo," %lf",param[i][j][k]);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
       }            nhstepm = nhstepm/hstepm; 
       fscanf(ficpar,"\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if(mle==1)            oldm=oldms;savm=savms;
         printf("\n");            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
       fprintf(ficlog,"\n");          
       fprintf(ficparo,"\n");            for (h=0; h<=nhstepm; h++){
     }              if (h*hstepm/YEARM*stepm ==yearp) {
                  fprintf(ficresf,"\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   p=param[1][1];                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
                } 
   /* Reads comments: lines beginning with '#' */              for(j=1; j<=nlstate+ndeath;j++) {
   while((c=getc(ficpar))=='#' && c!= EOF){                ppij=0.;
     ungetc(c,ficpar);                for(i=1; i<=nlstate;i++) {
     fgets(line, MAXLINE, ficpar);                  if (mobilav==1) 
     puts(line);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
     fputs(line,ficparo);                  else {
   }                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   ungetc(c,ficpar);                  }
                   if (h*hstepm/YEARM*stepm== yearp) {
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                  }
   for(i=1; i <=nlstate; i++){                } /* end i */
     for(j=1; j <=nlstate+ndeath-1; j++){                if (h*hstepm/YEARM*stepm==yearp) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);                  fprintf(ficresf," %.3f", ppij);
       printf("%1d%1d",i,j);                }
       fprintf(ficparo,"%1d%1d",i1,j1);              }/* end j */
       for(k=1; k<=ncovmodel;k++){            } /* end h */
         fscanf(ficpar,"%le",&delti3[i][j][k]);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         printf(" %le",delti3[i][j][k]);          } /* end agec */
         fprintf(ficparo," %le",delti3[i][j][k]);        } /* end yearp */
       }      } /* end cptcod */
       fscanf(ficpar,"\n");    } /* end  cptcov */
       printf("\n");         
       fprintf(ficparo,"\n");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  
   }    fclose(ficresf);
   delti=delti3[1][1];  }
    
   /* Reads comments: lines beginning with '#' */  /************** Forecasting *****not tested NB*************/
   while((c=getc(ficpar))=='#' && c!= EOF){  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){
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     puts(line);    int *popage;
     fputs(line,ficparo);    double calagedatem, agelim, kk1, kk2;
   }    double *popeffectif,*popcount;
   ungetc(c,ficpar);    double ***p3mat,***tabpop,***tabpopprev;
      double ***mobaverage;
   matcov=matrix(1,npar,1,npar);    char filerespop[FILENAMELENGTH];
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if(mle==1)    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       printf("%s",str);    agelim=AGESUP;
     fprintf(ficlog,"%s",str);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     fprintf(ficparo,"%s",str);    
     for(j=1; j <=i; j++){    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       fscanf(ficpar," %le",&matcov[i][j]);    
       if(mle==1){    
         printf(" %.5le",matcov[i][j]);    strcpy(filerespop,"pop"); 
         fprintf(ficlog," %.5le",matcov[i][j]);    strcat(filerespop,fileres);
       }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
       else      printf("Problem with forecast resultfile: %s\n", filerespop);
         fprintf(ficlog," %.5le",matcov[i][j]);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficparo," %.5le",matcov[i][j]);    }
     }    printf("Computing forecasting: result on file '%s' \n", filerespop);
     fscanf(ficpar,"\n");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
     if(mle==1)  
       printf("\n");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     fprintf(ficlog,"\n");  
     fprintf(ficparo,"\n");    if (mobilav!=0) {
   }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   for(i=1; i <=npar; i++)      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     for(j=i+1;j<=npar;j++)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       matcov[i][j]=matcov[j][i];        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }
   if(mle==1)    }
     printf("\n");  
   fprintf(ficlog,"\n");    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     /*-------- Rewriting paramater file ----------*/    agelim=AGESUP;
      strcpy(rfileres,"r");    /* "Rparameterfile */    
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    hstepm=1;
      strcat(rfileres,".");    /* */    hstepm=hstepm/stepm; 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    
     if((ficres =fopen(rfileres,"w"))==NULL) {    if (popforecast==1) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      if((ficpop=fopen(popfile,"r"))==NULL) {
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;        printf("Problem with population file : %s\n",popfile);exit(0);
     }        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
     fprintf(ficres,"#%s\n",version);      } 
          popage=ivector(0,AGESUP);
     /*-------- data file ----------*/      popeffectif=vector(0,AGESUP);
     if((fic=fopen(datafile,"r"))==NULL)    {      popcount=vector(0,AGESUP);
       printf("Problem with datafile: %s\n", datafile);goto end;      
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;      i=1;   
     }      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
     n= lastobs;      imx=i;
     severity = vector(1,maxwav);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     outcome=imatrix(1,maxwav+1,1,n);    }
     num=ivector(1,n);  
     moisnais=vector(1,n);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
     annais=vector(1,n);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     moisdc=vector(1,n);        k=k+1;
     andc=vector(1,n);        fprintf(ficrespop,"\n#******");
     agedc=vector(1,n);        for(j=1;j<=cptcoveff;j++) {
     cod=ivector(1,n);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     weight=vector(1,n);        }
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        fprintf(ficrespop,"******\n");
     mint=matrix(1,maxwav,1,n);        fprintf(ficrespop,"# Age");
     anint=matrix(1,maxwav,1,n);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     s=imatrix(1,maxwav+1,1,n);        if (popforecast==1)  fprintf(ficrespop," [Population]");
     adl=imatrix(1,maxwav+1,1,n);            
     tab=ivector(1,NCOVMAX);        for (cpt=0; cpt<=0;cpt++) { 
     ncodemax=ivector(1,8);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
     i=1;          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     while (fgets(line, MAXLINE, fic) != NULL)    {            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       if ((i >= firstobs) && (i <=lastobs)) {            nhstepm = nhstepm/hstepm; 
                    
         for (j=maxwav;j>=1;j--){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            oldm=oldms;savm=savms;
           strcpy(line,stra);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           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);            for (h=0; h<=nhstepm; h++){
         }              if (h==(int) (calagedatem+YEARM*cpt)) {
                        fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              } 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                for(i=1; i<=nlstate;i++) {              
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                  if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                  else {
         for (j=ncovcol;j>=1;j--){                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                  }
         }                }
         num[i]=atol(stra);                if (h==(int)(calagedatem+12*cpt)){
                          tabpop[(int)(agedeb)][j][cptcod]=kk1;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                    /*fprintf(ficrespop," %.3f", kk1);
           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;}*/                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
         i=i+1;              }
       }              for(i=1; i<=nlstate;i++){
     }                kk1=0.;
     /* printf("ii=%d", ij);                  for(j=1; j<=nlstate;j++){
        scanf("%d",i);*/                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   imx=i-1; /* Number of individuals */                  }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
   /* for (i=1; i<=imx; i++){              }
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
     }*/            }
    /*  for (i=1; i<=imx; i++){            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      if (s[4][i]==9)  s[4][i]=-1;          }
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/        }
     
      /******/
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
   Tprod=ivector(1,15);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   Tvaraff=ivector(1,15);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   Tvard=imatrix(1,15,1,2);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   Tage=ivector(1,15);                  nhstepm = nhstepm/hstepm; 
                
   if (strlen(model) >1){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     j=0, j1=0, k1=1, k2=1;            oldm=oldms;savm=savms;
     j=nbocc(model,'+');            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     j1=nbocc(model,'*');            for (h=0; h<=nhstepm; h++){
     cptcovn=j+1;              if (h==(int) (calagedatem+YEARM*cpt)) {
     cptcovprod=j1;                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                  } 
     strcpy(modelsav,model);              for(j=1; j<=nlstate+ndeath;j++) {
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                kk1=0.;kk2=0;
       printf("Error. Non available option model=%s ",model);                for(i=1; i<=nlstate;i++) {              
       fprintf(ficlog,"Error. Non available option model=%s ",model);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
       goto end;                }
     }                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
                  }
     for(i=(j+1); i>=1;i--){            }
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */          }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        }
       /*scanf("%d",i);*/     } 
       if (strchr(strb,'*')) {  /* Model includes a product */    }
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/   
         if (strcmp(strc,"age")==0) { /* Vn*age */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           cptcovprod--;  
           cutv(strb,stre,strd,'V');    if (popforecast==1) {
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/      free_ivector(popage,0,AGESUP);
           cptcovage++;      free_vector(popeffectif,0,AGESUP);
             Tage[cptcovage]=i;      free_vector(popcount,0,AGESUP);
             /*printf("stre=%s ", stre);*/    }
         }    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         else if (strcmp(strd,"age")==0) { /* or age*Vn */    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           cptcovprod--;    fclose(ficrespop);
           cutv(strb,stre,strc,'V');  }
           Tvar[i]=atoi(stre);  
           cptcovage++;  /***********************************************/
           Tage[cptcovage]=i;  /**************** Main Program *****************/
         }  /***********************************************/
         else {  /* Age is not in the model */  
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/  int main(int argc, char *argv[])
           Tvar[i]=ncovcol+k1;  {
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
           Tprod[k1]=i;    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
           Tvard[k1][1]=atoi(strc); /* m*/    double agedeb, agefin,hf;
           Tvard[k1][2]=atoi(stre); /* n */    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    double fret;
           for (k=1; k<=lastobs;k++)    double **xi,tmp,delta;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;    double dum; /* Dummy variable */
           k2=k2+2;    double ***p3mat;
         }    double ***mobaverage;
       }    int *indx;
       else { /* no more sum */    char line[MAXLINE], linepar[MAXLINE];
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
        /*  scanf("%d",i);*/    int firstobs=1, lastobs=10;
       cutv(strd,strc,strb,'V');    int sdeb, sfin; /* Status at beginning and end */
       Tvar[i]=atoi(strc);    int c,  h , cpt,l;
       }    int ju,jl, mi;
       strcpy(modelsav,stra);      int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
         scanf("%d",i);*/    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     } /* end of loop + */    int mobilav=0,popforecast=0;
   } /* end model */    int hstepm, nhstepm;
      double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   printf("cptcovprod=%d ", cptcovprod);  
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    double bage, fage, age, agelim, agebase;
   scanf("%d ",i);*/    double ftolpl=FTOL;
     fclose(fic);    double **prlim;
     double *severity;
     /*  if(mle==1){*/    double ***param; /* Matrix of parameters */
     if (weightopt != 1) { /* Maximisation without weights*/    double  *p;
       for(i=1;i<=n;i++) weight[i]=1.0;    double **matcov; /* Matrix of covariance */
     }    double ***delti3; /* Scale */
     /*-calculation of age at interview from date of interview and age at death -*/    double *delti; /* Scale */
     agev=matrix(1,maxwav,1,imx);    double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     for (i=1; i<=imx; i++) {    double *epj, vepp;
       for(m=2; (m<= maxwav); m++) {    double kk1, kk2;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
          anint[m][i]=9999;  
          s[m][i]=-1;    char *alph[]={"a","a","b","c","d","e"}, str[4];
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  
       }    char z[1]="c", occ;
     }  #include <sys/time.h>
   #include <time.h>
     for (i=1; i<=imx; i++)  {    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);   
       for(m=1; (m<= maxwav); m++){    /* long total_usecs;
         if(s[m][i] >0){       struct timeval start_time, end_time;
           if (s[m][i] >= nlstate+1) {    
             if(agedc[i]>0)       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
               if(moisdc[i]!=99 && andc[i]!=9999)    getcwd(pathcd, size);
                 agev[m][i]=agedc[i];  
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    printf("\n%s",version);
            else {    if(argc <=1){
               if (andc[i]!=9999){      printf("\nEnter the parameter file name: ");
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      scanf("%s",pathtot);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);    }
               agev[m][i]=-1;    else{
               }      strcpy(pathtot,argv[1]);
             }    }
           }    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
           else if(s[m][i] !=9){ /* Should no more exist */    /*cygwin_split_path(pathtot,path,optionfile);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
             if(mint[m][i]==99 || anint[m][i]==9999)    /* cutv(path,optionfile,pathtot,'\\');*/
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
               agemin=agev[m][i];    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    chdir(path);
             }    replace(pathc,path);
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];    /*-------- arguments in the command line --------*/
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }    /* Log file */
             /*agev[m][i]=anint[m][i]-annais[i];*/    strcat(filelog, optionfilefiname);
             /*   agev[m][i] = age[i]+2*m;*/    strcat(filelog,".log");    /* */
           }    if((ficlog=fopen(filelog,"w"))==NULL)    {
           else { /* =9 */      printf("Problem with logfile %s\n",filelog);
             agev[m][i]=1;      goto end;
             s[m][i]=-1;    }
           }    fprintf(ficlog,"Log filename:%s\n",filelog);
         }    fprintf(ficlog,"\n%s",version);
         else /*= 0 Unknown */    fprintf(ficlog,"\nEnter the parameter file name: ");
           agev[m][i]=1;    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
       }    fflush(ficlog);
      
     }    /* */
     for (i=1; i<=imx; i++)  {    strcpy(fileres,"r");
       for(m=1; (m<= maxwav); m++){    strcat(fileres, optionfilefiname);
         if (s[m][i] > (nlstate+ndeath)) {    strcat(fileres,".txt");    /* Other files have txt extension */
           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);      /*---------arguments file --------*/
           goto end;  
         }    if((ficpar=fopen(optionfile,"r"))==NULL)    {
       }      printf("Problem with optionfile %s\n",optionfile);
     }      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    }
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
     strcpy(filereso,"o");
     free_vector(severity,1,maxwav);    strcat(filereso,fileres);
     free_imatrix(outcome,1,maxwav+1,1,n);    if((ficparo=fopen(filereso,"w"))==NULL) {
     free_vector(moisnais,1,n);      printf("Problem with Output resultfile: %s\n", filereso);
     free_vector(annais,1,n);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
     /* free_matrix(mint,1,maxwav,1,n);      goto end;
        free_matrix(anint,1,maxwav,1,n);*/    }
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);    /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
          ungetc(c,ficpar);
     wav=ivector(1,imx);      fgets(line, MAXLINE, ficpar);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      puts(line);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      fputs(line,ficparo);
        }
     /* Concatenates waves */    ungetc(c,ficpar);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     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);
       Tcode=ivector(1,100);    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);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    while((c=getc(ficpar))=='#' && c!= EOF){
       ncodemax[1]=1;      ungetc(c,ficpar);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      fgets(line, MAXLINE, ficpar);
            puts(line);
    codtab=imatrix(1,100,1,10);      fputs(line,ficparo);
    h=0;    }
    m=pow(2,cptcoveff);    ungetc(c,ficpar);
      
    for(k=1;k<=cptcoveff; k++){     
      for(i=1; i <=(m/pow(2,k));i++){    covar=matrix(0,NCOVMAX,1,n); 
        for(j=1; j <= ncodemax[k]; j++){    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
            h++;  
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
          }    
        }    /* Read guess parameters */
      }    /* Reads comments: lines beginning with '#' */
    }    while((c=getc(ficpar))=='#' && c!= EOF){
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      ungetc(c,ficpar);
       codtab[1][2]=1;codtab[2][2]=2; */      fgets(line, MAXLINE, ficpar);
    /* for(i=1; i <=m ;i++){      puts(line);
       for(k=1; k <=cptcovn; k++){      fputs(line,ficparo);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    }
       }    ungetc(c,ficpar);
       printf("\n");    
       }    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       scanf("%d",i);*/    for(i=1; i <=nlstate; i++)
          for(j=1; j <=nlstate+ndeath-1; j++){
    /* Calculates basic frequencies. Computes observed prevalence at single age        fscanf(ficpar,"%1d%1d",&i1,&j1);
        and prints on file fileres'p'. */        fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
              printf("%1d%1d",i,j);
            fprintf(ficlog,"%1d%1d",i,j);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(k=1; k<=ncovmodel;k++){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fscanf(ficpar," %lf",&param[i][j][k]);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if(mle==1){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            printf(" %lf",param[i][j][k]);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            fprintf(ficlog," %lf",param[i][j][k]);
                }
     /* For Powell, parameters are in a vector p[] starting at p[1]          else
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */            fprintf(ficlog," %lf",param[i][j][k]);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          fprintf(ficparo," %lf",param[i][j][k]);
         }
     if(mle==1){        fscanf(ficpar,"\n");
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        if(mle==1)
     }          printf("\n");
            fprintf(ficlog,"\n");
     /*--------- results files --------------*/        fprintf(ficparo,"\n");
     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);      }
      
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
    jk=1;  
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    p=param[1][1];
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    /* Reads comments: lines beginning with '#' */
    for(i=1,jk=1; i <=nlstate; i++){    while((c=getc(ficpar))=='#' && c!= EOF){
      for(k=1; k <=(nlstate+ndeath); k++){      ungetc(c,ficpar);
        if (k != i)      fgets(line, MAXLINE, ficpar);
          {      puts(line);
            printf("%d%d ",i,k);      fputs(line,ficparo);
            fprintf(ficlog,"%d%d ",i,k);    }
            fprintf(ficres,"%1d%1d ",i,k);    ungetc(c,ficpar);
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
              fprintf(ficlog,"%f ",p[jk]);    /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
              fprintf(ficres,"%f ",p[jk]);    for(i=1; i <=nlstate; i++){
              jk++;      for(j=1; j <=nlstate+ndeath-1; j++){
            }        fscanf(ficpar,"%1d%1d",&i1,&j1);
            printf("\n");        printf("%1d%1d",i,j);
            fprintf(ficlog,"\n");        fprintf(ficparo,"%1d%1d",i1,j1);
            fprintf(ficres,"\n");        for(k=1; k<=ncovmodel;k++){
          }          fscanf(ficpar,"%le",&delti3[i][j][k]);
      }          printf(" %le",delti3[i][j][k]);
    }          fprintf(ficparo," %le",delti3[i][j][k]);
    if(mle==1){        }
      /* Computing hessian and covariance matrix */        fscanf(ficpar,"\n");
      ftolhess=ftol; /* Usually correct */        printf("\n");
      hesscov(matcov, p, npar, delti, ftolhess, func);        fprintf(ficparo,"\n");
    }      }
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    }
    printf("# Scales (for hessian or gradient estimation)\n");    delti=delti3[1][1];
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");  
    for(i=1,jk=1; i <=nlstate; i++){  
      for(j=1; j <=nlstate+ndeath; j++){    /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
        if (j!=i) {    
          fprintf(ficres,"%1d%1d",i,j);    /* Reads comments: lines beginning with '#' */
          printf("%1d%1d",i,j);    while((c=getc(ficpar))=='#' && c!= EOF){
          fprintf(ficlog,"%1d%1d",i,j);      ungetc(c,ficpar);
          for(k=1; k<=ncovmodel;k++){      fgets(line, MAXLINE, ficpar);
            printf(" %.5e",delti[jk]);      puts(line);
            fprintf(ficlog," %.5e",delti[jk]);      fputs(line,ficparo);
            fprintf(ficres," %.5e",delti[jk]);    }
            jk++;    ungetc(c,ficpar);
          }    
          printf("\n");    matcov=matrix(1,npar,1,npar);
          fprintf(ficlog,"\n");    for(i=1; i <=npar; i++){
          fprintf(ficres,"\n");      fscanf(ficpar,"%s",&str);
        }      if(mle==1)
      }        printf("%s",str);
    }      fprintf(ficlog,"%s",str);
          fprintf(ficparo,"%s",str);
    k=1;      for(j=1; j <=i; j++){
    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");        fscanf(ficpar," %le",&matcov[i][j]);
    if(mle==1)        if(mle==1){
      printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");          printf(" %.5le",matcov[i][j]);
    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");          fprintf(ficlog," %.5le",matcov[i][j]);
    for(i=1;i<=npar;i++){        }
      /*  if (k>nlstate) k=1;        else
          i1=(i-1)/(ncovmodel*nlstate)+1;          fprintf(ficlog," %.5le",matcov[i][j]);
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        fprintf(ficparo," %.5le",matcov[i][j]);
          printf("%s%d%d",alph[k],i1,tab[i]);*/      }
      fprintf(ficres,"%3d",i);      fscanf(ficpar,"\n");
      if(mle==1)      if(mle==1)
        printf("%3d",i);        printf("\n");
      fprintf(ficlog,"%3d",i);      fprintf(ficlog,"\n");
      for(j=1; j<=i;j++){      fprintf(ficparo,"\n");
        fprintf(ficres," %.5e",matcov[i][j]);    }
        if(mle==1)    for(i=1; i <=npar; i++)
          printf(" %.5e",matcov[i][j]);      for(j=i+1;j<=npar;j++)
        fprintf(ficlog," %.5e",matcov[i][j]);        matcov[i][j]=matcov[j][i];
      }     
      fprintf(ficres,"\n");    if(mle==1)
      if(mle==1)      printf("\n");
        printf("\n");    fprintf(ficlog,"\n");
      fprintf(ficlog,"\n");  
      k++;  
    }    /*-------- Rewriting paramater file ----------*/
        strcpy(rfileres,"r");    /* "Rparameterfile */
    while((c=getc(ficpar))=='#' && c!= EOF){    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
      ungetc(c,ficpar);    strcat(rfileres,".");    /* */
      fgets(line, MAXLINE, ficpar);    strcat(rfileres,optionfilext);    /* Other files have txt extension */
      puts(line);    if((ficres =fopen(rfileres,"w"))==NULL) {
      fputs(line,ficparo);      printf("Problem writing new parameter file: %s\n", fileres);goto end;
    }      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
    ungetc(c,ficpar);    }
    estepm=0;    fprintf(ficres,"#%s\n",version);
    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;    /*-------- data file ----------*/
    if (fage <= 2) {    if((fic=fopen(datafile,"r"))==NULL)    {
      bage = ageminpar;      printf("Problem with datafile: %s\n", datafile);goto end;
      fage = agemaxpar;      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
    }    }
      
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    n= lastobs;
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    severity = vector(1,maxwav);
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    outcome=imatrix(1,maxwav+1,1,n);
        num=ivector(1,n);
    while((c=getc(ficpar))=='#' && c!= EOF){    moisnais=vector(1,n);
      ungetc(c,ficpar);    annais=vector(1,n);
      fgets(line, MAXLINE, ficpar);    moisdc=vector(1,n);
      puts(line);    andc=vector(1,n);
      fputs(line,ficparo);    agedc=vector(1,n);
    }    cod=ivector(1,n);
    ungetc(c,ficpar);    weight=vector(1,n);
      for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    mint=matrix(1,maxwav,1,n);
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    anint=matrix(1,maxwav,1,n);
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    s=imatrix(1,maxwav+1,1,n);
        tab=ivector(1,NCOVMAX);
    while((c=getc(ficpar))=='#' && c!= EOF){    ncodemax=ivector(1,8);
      ungetc(c,ficpar);  
      fgets(line, MAXLINE, ficpar);    i=1;
      puts(line);    while (fgets(line, MAXLINE, fic) != NULL)    {
      fputs(line,ficparo);      if ((i >= firstobs) && (i <=lastobs)) {
    }          
    ungetc(c,ficpar);        for (j=maxwav;j>=1;j--){
            cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
   fscanf(ficpar,"pop_based=%d\n",&popbased);          
   fprintf(ficparo,"pop_based=%d\n",popbased);          cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
   fprintf(ficres,"pop_based=%d\n",popbased);          cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
    
   while((c=getc(ficpar))=='#' && c!= EOF){        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
     ungetc(c,ficpar);        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
     fgets(line, MAXLINE, ficpar);  
     puts(line);        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
     fputs(line,ficparo);        for (j=ncovcol;j>=1;j--){
   }          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
   ungetc(c,ficpar);        } 
         num[i]=atol(stra);
   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);        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
 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);          printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
 while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    /* printf("ii=%d", ij);
     puts(line);       scanf("%d",i);*/
     fputs(line,ficparo);    imx=i-1; /* Number of individuals */
   }  
   ungetc(c,ficpar);    /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      }*/
      /*  for (i=1; i<=imx; i++){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
 /*------------ gnuplot -------------*/    
   strcpy(optionfilegnuplot,optionfilefiname);   for (i=1; i<=imx; i++)
   strcat(optionfilegnuplot,".gp");   
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {     /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
     printf("Problem with file %s",optionfilegnuplot);       else weight[i]=1;*/
   }  
   fclose(ficgp);    /* Calculation of the number of parameter from char model*/
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
 /*--------- index.htm --------*/    Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
   strcpy(optionfilehtm,optionfile);    Tvard=imatrix(1,15,1,2);
   strcat(optionfilehtm,".htm");    Tage=ivector(1,15);      
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {     
     printf("Problem with %s \n",optionfilehtm), exit(0);    if (strlen(model) >1){ /* If there is at least 1 covariate */
   }      j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n      j1=nbocc(model,'*'); /* j1=Number of '*' */
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      cptcovn=j+1; 
 \n      cptcovprod=j1; /*Number of products */
 Total number of observations=%d <br>\n      
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      strcpy(modelsav,model); 
 <hr  size=\"2\" color=\"#EC5E5E\">      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
  <ul><li><h4>Parameter files</h4>\n        printf("Error. Non available option model=%s ",model);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        fprintf(ficlog,"Error. Non available option model=%s ",model);
  - Log file of the run: <a href=\"%s\">%s</a><br>\n        goto end;
  - 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);      }
   fclose(fichtm);      
       /* This loop fills the array Tvar from the string 'model'.*/
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
        for(i=(j+1); i>=1;i--){
 /*------------ free_vector  -------------*/        cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
  chdir(path);        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
          /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
  free_ivector(wav,1,imx);        /*scanf("%d",i);*/
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        if (strchr(strb,'*')) {  /* Model includes a product */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
  free_ivector(num,1,n);          if (strcmp(strc,"age")==0) { /* Vn*age */
  free_vector(agedc,1,n);            cptcovprod--;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            cutv(strb,stre,strd,'V');
  fclose(ficparo);            Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
  fclose(ficres);            cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
   /*--------------- Prevalence limit --------------*/          }
            else if (strcmp(strd,"age")==0) { /* or age*Vn */
   strcpy(filerespl,"pl");            cptcovprod--;
   strcat(filerespl,fileres);            cutv(strb,stre,strc,'V');
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            Tvar[i]=atoi(stre);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            cptcovage++;
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;            Tage[cptcovage]=i;
   }          }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          else {  /* Age is not in the model */
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);            cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
   fprintf(ficrespl,"#Prevalence limit\n");            Tvar[i]=ncovcol+k1;
   fprintf(ficrespl,"#Age ");            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            Tprod[k1]=i;
   fprintf(ficrespl,"\n");            Tvard[k1][1]=atoi(strc); /* m*/
              Tvard[k1][2]=atoi(stre); /* n */
   prlim=matrix(1,nlstate,1,nlstate);            Tvar[cptcovn+k2]=Tvard[k1][1];
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for (k=1; k<=lastobs;k++) 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            k1++;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            k2=k2+2;
   k=0;          }
   agebase=ageminpar;        }
   agelim=agemaxpar;        else { /* no more sum */
   ftolpl=1.e-10;          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
   i1=cptcoveff;         /*  scanf("%d",i);*/
   if (cptcovn < 1){i1=1;}        cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        strcpy(modelsav,stra);  
         k=k+1;        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          scanf("%d",i);*/
         fprintf(ficrespl,"\n#******");      } /* end of loop + */
         printf("\n#******");    } /* end model */
         fprintf(ficlog,"\n#******");    
         for(j=1;j<=cptcoveff;j++) {    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
           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]]);    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
         }    printf("cptcovprod=%d ", cptcovprod);
         fprintf(ficrespl,"******\n");    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
         printf("******\n");  
         fprintf(ficlog,"******\n");    scanf("%d ",i);
            fclose(fic);*/
         for (age=agebase; age<=agelim; age++){  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      /*  if(mle==1){*/
           fprintf(ficrespl,"%.0f",age );    if (weightopt != 1) { /* Maximisation without weights*/
           for(i=1; i<=nlstate;i++)      for(i=1;i<=n;i++) weight[i]=1.0;
           fprintf(ficrespl," %.5f", prlim[i][i]);    }
           fprintf(ficrespl,"\n");      /*-calculation of age at interview from date of interview and age at death -*/
         }    agev=matrix(1,maxwav,1,imx);
       }  
     }    for (i=1; i<=imx; i++) {
   fclose(ficrespl);      for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
   /*------------- h Pij x at various ages ------------*/          anint[m][i]=9999;
            s[m][i]=-1;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          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,"Problem with Pij resultfile: %s\n", filerespij);goto end;          fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
   }          s[m][i]=-1;
   printf("Computing pij: result on file '%s' \n", filerespij);        }
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);        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]); 
   stepsize=(int) (stepm+YEARM-1)/YEARM;          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]); 
   /*if (stepm<=24) stepsize=2;*/          s[m][i]=-1;
         }
   agelim=AGESUP;      }
   hstepm=stepsize*YEARM; /* Every year of age */    }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
     for (i=1; i<=imx; i++)  {
   /* hstepm=1;   aff par mois*/      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
   k=0;        if(s[m][i] >0){
   for(cptcov=1;cptcov<=i1;cptcov++){          if (s[m][i] >= nlstate+1) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            if(agedc[i]>0)
       k=k+1;              if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
         fprintf(ficrespij,"\n#****** ");                agev[m][i]=agedc[i];
         for(j=1;j<=cptcoveff;j++)            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              else {
         fprintf(ficrespij,"******\n");                if ((int)andc[i]!=9999){
                          printf("Warning negative age at death: %d line:%d\n",num[i],i);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                  fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                  agev[m][i]=-1;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                }
               }
           /*      nhstepm=nhstepm*YEARM; aff par mois*/          }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                   years but with the precision of a
           oldm=oldms;savm=savms;                                   month */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
           fprintf(ficrespij,"# Age");            if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
           for(i=1; i<=nlstate;i++)              agev[m][i]=1;
             for(j=1; j<=nlstate+ndeath;j++)            else if(agev[m][i] <agemin){ 
               fprintf(ficrespij," %1d-%1d",i,j);              agemin=agev[m][i];
           fprintf(ficrespij,"\n");              /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
            for (h=0; h<=nhstepm; h++){            }
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            else if(agev[m][i] >agemax){
             for(i=1; i<=nlstate;i++)              agemax=agev[m][i];
               for(j=1; j<=nlstate+ndeath;j++)              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            }
             fprintf(ficrespij,"\n");            /*agev[m][i]=anint[m][i]-annais[i];*/
              }            /*     agev[m][i] = age[i]+2*m;*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
           fprintf(ficrespij,"\n");          else { /* =9 */
         }            agev[m][i]=1;
     }            s[m][i]=-1;
   }          }
         }
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);        else /*= 0 Unknown */
           agev[m][i]=1;
   fclose(ficrespij);      }
       
     }
   /*---------- Forecasting ------------------*/    for (i=1; i<=imx; i++)  {
   if((stepm == 1) && (strcmp(model,".")==0)){      for(m=firstpass; (m<=lastpass); m++){
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);        if (s[m][i] > (nlstate+ndeath)) {
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);          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);     
   else{          goto end;
     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);    }
   }  
      /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
   /*---------- Health expectancies and variances ------------*/       printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   strcpy(filerest,"t");  
   strcat(filerest,fileres);  }*/
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;    fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    free_vector(severity,1,maxwav);
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);    free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
   strcpy(filerese,"e");    /* free_matrix(mint,1,maxwav,1,n);
   strcat(filerese,fileres);       free_matrix(anint,1,maxwav,1,n);*/
   if((ficreseij=fopen(filerese,"w"))==NULL) {    free_vector(moisdc,1,n);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    free_vector(andc,1,n);
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }     
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    wav=ivector(1,imx);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);    dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
   strcpy(fileresv,"v");    mw=imatrix(1,lastpass-firstpass+1,1,imx);
   strcat(fileresv,fileres);     
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    /* Concatenates waves */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    Tcode=ivector(1,100);
   calagedate=-1;    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
   k=0;        
   for(cptcov=1;cptcov<=i1;cptcov++){    codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                                   the estimations*/
       k=k+1;    h=0;
       fprintf(ficrest,"\n#****** ");    m=pow(2,cptcoveff);
       for(j=1;j<=cptcoveff;j++)   
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(k=1;k<=cptcoveff; k++){
       fprintf(ficrest,"******\n");      for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
       fprintf(ficreseij,"\n#****** ");          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
       for(j=1;j<=cptcoveff;j++)            h++;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
       fprintf(ficreseij,"******\n");            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
       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");    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    /* for(i=1; i <=m ;i++){ 
       oldm=oldms;savm=savms;       for(k=1; k <=cptcovn; k++){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);         printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
         }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       printf("\n");
       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);       scanf("%d",i);*/
       if(popbased==1){      
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);    /* Calculates basic frequencies. Computes observed prevalence at single age
        }       and prints on file fileres'p'. */
   
        pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       fprintf(ficrest,"\n");      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       epj=vector(1,nlstate+1);      
       for(age=bage; age <=fage ;age++){     
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /* For Powell, parameters are in a vector p[] starting at p[1]
         if (popbased==1) {       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
           for(i=1; i<=nlstate;i++)    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
             prlim[i][i]=probs[(int)age][i][k];  
         }    if(mle>=1){ /* Could be 1 or 2 */
              mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
         fprintf(ficrest," %4.0f",age);    }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    /*--------- results files --------------*/
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    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);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    
           }  
           epj[nlstate+1] +=epj[j];    jk=1;
         }    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
           for(j=1;j <=nlstate;j++)    for(i=1,jk=1; i <=nlstate; i++){
             vepp += vareij[i][j][(int)age];      for(k=1; k <=(nlstate+ndeath); k++){
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));        if (k != i) 
         for(j=1;j <=nlstate;j++){          {
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));            printf("%d%d ",i,k);
         }            fprintf(ficlog,"%d%d ",i,k);
         fprintf(ficrest,"\n");            fprintf(ficres,"%1d%1d ",i,k);
       }            for(j=1; j <=ncovmodel; j++){
     }              printf("%f ",p[jk]);
   }              fprintf(ficlog,"%f ",p[jk]);
 free_matrix(mint,1,maxwav,1,n);              fprintf(ficres,"%f ",p[jk]);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);              jk++; 
     free_vector(weight,1,n);            }
   fclose(ficreseij);            printf("\n");
   fclose(ficresvij);            fprintf(ficlog,"\n");
   fclose(ficrest);            fprintf(ficres,"\n");
   fclose(ficpar);          }
   free_vector(epj,1,nlstate+1);      }
      }
   /*------- Variance limit prevalence------*/      if(mle==1){
       /* Computing hessian and covariance matrix */
   strcpy(fileresvpl,"vpl");      ftolhess=ftol; /* Usually correct */
   strcat(fileresvpl,fileres);      hesscov(matcov, p, npar, delti, ftolhess, func);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     exit(0);    printf("# Scales (for hessian or gradient estimation)\n");
   }    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
   k=0;        if (j!=i) {
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficres,"%1d%1d",i,j);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          printf("%1d%1d",i,j);
       k=k+1;          fprintf(ficlog,"%1d%1d",i,j);
       fprintf(ficresvpl,"\n#****** ");          for(k=1; k<=ncovmodel;k++){
       for(j=1;j<=cptcoveff;j++)            printf(" %.5e",delti[jk]);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficlog," %.5e",delti[jk]);
       fprintf(ficresvpl,"******\n");            fprintf(ficres," %.5e",delti[jk]);
                  jk++;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          }
       oldm=oldms;savm=savms;          printf("\n");
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          fprintf(ficlog,"\n");
     }          fprintf(ficres,"\n");
  }        }
       }
   fclose(ficresvpl);    }
      
   /*---------- End : free ----------------*/    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");
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    if(mle==1)
        printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    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");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    for(i=1,k=1;i<=npar;i++){
        /*  if (k>nlstate) k=1;
            i1=(i-1)/(ncovmodel*nlstate)+1; 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          printf("%s%d%d",alph[k],i1,tab[i]);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficres,"%3d",i);
        if(mle==1)
   free_matrix(matcov,1,npar,1,npar);        printf("%3d",i);
   free_vector(delti,1,npar);      fprintf(ficlog,"%3d",i);
   free_matrix(agev,1,maxwav,1,imx);      for(j=1; j<=i;j++){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
   fprintf(fichtm,"\n</body>");          printf(" %.5e",matcov[i][j]);
   fclose(fichtm);        fprintf(ficlog," %.5e",matcov[i][j]);
   fclose(ficgp);      }
        fprintf(ficres,"\n");
       if(mle==1)
   if(erreur >0){        printf("\n");
     printf("End of Imach with error or warning %d\n",erreur);      fprintf(ficlog,"\n");
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);      k++;
   }else{    }
    printf("End of Imach\n");     
    fprintf(ficlog,"End of Imach\n");    while((c=getc(ficpar))=='#' && c!= EOF){
   }      ungetc(c,ficpar);
   printf("See log file on %s\n",filelog);      fgets(line, MAXLINE, ficpar);
   fclose(ficlog);      puts(line);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      fputs(line,ficparo);
      }
   /* 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);*/    ungetc(c,ficpar);
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/    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;
  end:    if (fage <= 2) {
 #ifdef windows      bage = ageminpar;
   /* chdir(pathcd);*/      fage = agemaxpar;
 #endif    }
  /*system("wgnuplot graph.plt");*/     
  /*system("../gp37mgw/wgnuplot graph.plt");*/    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
  /*system("cd ../gp37mgw");*/    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
  strcpy(plotcmd,GNUPLOTPROGRAM);     
  strcat(plotcmd," ");    while((c=getc(ficpar))=='#' && c!= EOF){
  strcat(plotcmd,optionfilegnuplot);      ungetc(c,ficpar);
  system(plotcmd);      fgets(line, MAXLINE, ficpar);
       puts(line);
 #ifdef windows      fputs(line,ficparo);
   while (z[0] != 'q') {    }
     /* chdir(path); */    ungetc(c,ficpar);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    
     scanf("%s",z);    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);
     if (z[0] == 'c') system("./imach");    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);
     else if (z[0] == 'e') system(optionfilehtm);    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);
     else if (z[0] == 'g') system(plotcmd);    printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     else if (z[0] == 'q') exit(0);    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);
   }     
 #endif    while((c=getc(ficpar))=='#' && c!= EOF){
 }      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

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changed lines
  Added in v.1.80


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