Diff for /imach/src/imach.c between versions 1.19 and 1.78

version 1.19, 2002/02/20 17:19:10 version 1.78, 2003/05/27 17:26:53
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************             Interpolated Markov Chain
   This program computes Healthy Life Expectancies from cross-longitudinal  
   data. Cross-longitudinal consist in a first survey ("cross") where    Short summary of the programme:
   individuals from different ages are interviewed on their health status    
   or degree of  disability. At least a second wave of interviews    This program computes Healthy Life Expectancies from
   ("longitudinal") should  measure each new individual health status.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   Health expectancies are computed from the transistions observed between    first survey ("cross") where individuals from different ages are
   waves and are computed for each degree of severity of disability (number    interviewed on their health status or degree of disability (in the
   of life states). More degrees you consider, more time is necessary to    case of a health survey which is our main interest) -2- at least a
   reach the Maximum Likelihood of the parameters involved in the model.    second wave of interviews ("longitudinal") which measure each change
   The simplest model is the multinomial logistic model where pij is    (if any) in individual health status.  Health expectancies are
   the probabibility to be observed in state j at the second wave conditional    computed from the time spent in each health state according to a
   to be observed in state i at the first wave. Therefore the model is:    model. More health states you consider, more time is necessary to reach the
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Maximum Likelihood of the parameters involved in the model.  The
   is a covariate. If you want to have a more complex model than "constant and    simplest model is the multinomial logistic model where pij is the
   age", you should modify the program where the markup    probability to be observed in state j at the second wave
     *Covariates have to be included here again* invites you to do it.    conditional to be observed in state i at the first wave. Therefore
   More covariates you add, less is the speed of the convergence.    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
   The advantage that this computer programme claims, comes from that if the    complex model than "constant and age", you should modify the program
   delay between waves is not identical for each individual, or if some    where the markup *Covariates have to be included here again* invites
   individual missed an interview, the information is not rounded or lost, but    you to do it.  More covariates you add, slower the
   taken into account using an interpolation or extrapolation.    convergence.
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    The advantage of this computer programme, compared to a simple
   x. The delay 'h' can be split into an exact number (nh*stepm) of    multinomial logistic model, is clear when the delay between waves is not
   unobserved intermediate  states. This elementary transition (by month or    identical for each individual. Also, if a individual missed an
   quarter trimester, semester or year) is model as a multinomial logistic.    intermediate interview, the information is lost, but taken into
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    account using an interpolation or extrapolation.  
   and the contribution of each individual to the likelihood is simply hPijx.  
     hPijx is the probability to be observed in state i at age x+h
   Also this programme outputs the covariance matrix of the parameters but also    conditional to the observed state i at age x. The delay 'h' can be
   of the life expectancies. It also computes the prevalence limits.    split into an exact number (nh*stepm) of unobserved intermediate
      states. This elementary transition (by month, quarter,
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    semester or year) is modelled as a multinomial logistic.  The hPx
            Institut national d'études démographiques, Paris.    matrix is simply the matrix product of nh*stepm elementary matrices
   This software have been partly granted by Euro-REVES, a concerted action    and the contribution of each individual to the likelihood is simply
   from the European Union.    hPijx.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Also this programme outputs the covariance matrix of the parameters but also
   can be accessed at http://euroreves.ined.fr/imach .    of the life expectancies. It also computes the stable prevalence. 
   **********************************************************************/    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #include <math.h>             Institut national d'études démographiques, Paris.
 #include <stdio.h>    This software have been partly granted by Euro-REVES, a concerted action
 #include <stdlib.h>    from the European Union.
 #include <unistd.h>    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define MAXLINE 256    can be accessed at http://euroreves.ined.fr/imach .
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define windows    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    **********************************************************************/
   /*
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    main
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    read parameterfile
     read datafile
 #define NINTERVMAX 8    concatwav
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    if (mle >= 1)
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */      mlikeli
 #define NCOVMAX 8 /* Maximum number of covariates */    print results files
 #define MAXN 20000    if mle==1 
 #define YEARM 12. /* Number of months per year */       computes hessian
 #define AGESUP 130    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define AGEBASE 40        begin-prev-date,...
     open gnuplot file
     open html file
 int nvar;    stable prevalence
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;     for age prevalim()
 int npar=NPARMAX;    h Pij x
 int nlstate=2; /* Number of live states */    variance of p varprob
 int ndeath=1; /* Number of dead states */    forecasting if prevfcast==1 prevforecast call prevalence()
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    health expectancies
 int popbased=0;    Variance-covariance of DFLE
     prevalence()
 int *wav; /* Number of waves for this individuual 0 is possible */     movingaverage()
 int maxwav; /* Maxim number of waves */    varevsij() 
 int jmin, jmax; /* min, max spacing between 2 waves */    if popbased==1 varevsij(,popbased)
 int mle, weightopt;    total life expectancies
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Variance of stable prevalence
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */   end
 double jmean; /* Mean space between 2 waves */  */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;   
 FILE *ficreseij;  #include <math.h>
   char filerese[FILENAMELENGTH];  #include <stdio.h>
  FILE  *ficresvij;  #include <stdlib.h>
   char fileresv[FILENAMELENGTH];  #include <unistd.h>
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 #define NR_END 1  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FREE_ARG char*  #define FILENAMELENGTH 80
 #define FTOL 1.0e-10  /*#define DEBUG*/
   #define windows
 #define NRANSI  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define ITMAX 200  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define TOL 2.0e-4  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10  #define NINTERVMAX 8
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define GOLD 1.618034  #define NCOVMAX 8 /* Maximum number of covariates */
 #define GLIMIT 100.0  #define MAXN 20000
 #define TINY 1.0e-20  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 static double maxarg1,maxarg2;  #define AGEBASE 40
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #ifdef windows
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define DIRSEPARATOR '\\'
    #define ODIRSEPARATOR '/'
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #else
 #define rint(a) floor(a+0.5)  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 static double sqrarg;  #endif
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  char version[80]="Imach version 0.95a, May 2003, INED-EUROREVES ";
   int erreur; /* Error number */
 int imx;  int nvar;
 int stepm;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 /* Stepm, step in month: minimum step interpolation*/  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 int m,nb;  int ndeath=1; /* Number of dead states */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  int popbased=0;
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 double *weight;  int jmin, jmax; /* min, max spacing between 2 waves */
 int **s; /* Status */  int mle, weightopt;
 double *agedc, **covar, idx;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 double ftolhess; /* Tolerance for computing hessian */  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 /**************** split *************************/  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 static  int split( char *path, char *dirc, char *name )  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 {  FILE *ficlog, *ficrespow;
    char *s;                             /* pointer */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    int  l1, l2;                         /* length counters */  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
    l1 = strlen( path );                 /* length of path */  FILE *ficreseij;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  char filerese[FILENAMELENGTH];
    s = strrchr( path, '\\' );           /* find last / */  FILE  *ficresvij;
    if ( s == NULL ) {                   /* no directory, so use current */  char fileresv[FILENAMELENGTH];
 #if     defined(__bsd__)                /* get current working directory */  FILE  *ficresvpl;
       extern char       *getwd( );  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
       if ( getwd( dirc ) == NULL ) {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #else  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
       extern char       *getcwd( );  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  char filelog[FILENAMELENGTH]; /* Log file */
 #endif  char filerest[FILENAMELENGTH];
          return( GLOCK_ERROR_GETCWD );  char fileregp[FILENAMELENGTH];
       }  char popfile[FILENAMELENGTH];
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  #define NR_END 1
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FREE_ARG char*
       strcpy( name, s );                /* save file name */  #define FTOL 1.0e-10
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  #define NRANSI 
    }  #define ITMAX 200 
    l1 = strlen( dirc );                 /* length of directory */  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define TOL 2.0e-4 
    return( 0 );                         /* we're done */  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 /******************************************/  
   #define GOLD 1.618034 
 void replace(char *s, char*t)  #define GLIMIT 100.0 
 {  #define TINY 1.0e-20 
   int i;  
   int lg=20;  static double maxarg1,maxarg2;
   i=0;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   lg=strlen(t);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   for(i=0; i<= lg; i++) {    
     (s[i] = t[i]);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     if (t[i]== '\\') s[i]='/';  #define rint(a) floor(a+0.5)
   }  
 }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 int nbocc(char *s, char occ)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 {  
   int i,j=0;  int imx; 
   int lg=20;  int stepm;
   i=0;  /* Stepm, step in month: minimum step interpolation*/
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  int estepm;
   if  (s[i] == occ ) j++;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   }  
   return j;  int m,nb;
 }  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 void cutv(char *u,char *v, char*t, char occ)  double **pmmij, ***probs;
 {  double dateintmean=0;
   int i,lg,j,p=0;  
   i=0;  double *weight;
   for(j=0; j<=strlen(t)-1; j++) {  int **s; /* Status */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  double *agedc, **covar, idx;
   }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
   lg=strlen(t);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   for(j=0; j<p; j++) {  double ftolhess; /* Tolerance for computing hessian */
     (u[j] = t[j]);  
   }  /**************** split *************************/
      u[p]='\0';  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
    for(j=0; j<= lg; j++) {    char  *ss;                            /* pointer */
     if (j>=(p+1))(v[j-p-1] = t[j]);    int   l1, l2;                         /* length counters */
   }  
 }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 /********************** nrerror ********************/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
 void nrerror(char error_text[])      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   fprintf(stderr,"ERREUR ...\n");      /* get current working directory */
   fprintf(stderr,"%s\n",error_text);      /*    extern  char* getcwd ( char *buf , int len);*/
   exit(1);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 }        return( GLOCK_ERROR_GETCWD );
 /*********************** vector *******************/      }
 double *vector(int nl, int nh)      strcpy( name, path );               /* we've got it */
 {    } else {                              /* strip direcotry from path */
   double *v;      ss++;                               /* after this, the filename */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));      l2 = strlen( ss );                  /* length of filename */
   if (!v) nrerror("allocation failure in vector");      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   return v-nl+NR_END;      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 /************************ free vector ******************/    }
 void free_vector(double*v, int nl, int nh)    l1 = strlen( dirc );                  /* length of directory */
 {  #ifdef windows
   free((FREE_ARG)(v+nl-NR_END));    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 }  #else
     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 /************************ivector *******************************/  #endif
 int *ivector(long nl,long nh)    ss = strrchr( name, '.' );            /* find last / */
 {    ss++;
   int *v;    strcpy(ext,ss);                       /* save extension */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    l1= strlen( name);
   if (!v) nrerror("allocation failure in ivector");    l2= strlen(ss)+1;
   return v-nl+NR_END;    strncpy( finame, name, l1-l2);
 }    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
 /******************free ivector **************************/  }
 void free_ivector(int *v, long nl, long nh)  
 {  
   free((FREE_ARG)(v+nl-NR_END));  /******************************************/
 }  
   void replace(char *s, char*t)
 /******************* imatrix *******************************/  {
 int **imatrix(long nrl, long nrh, long ncl, long nch)    int i;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    int lg=20;
 {    i=0;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    lg=strlen(t);
   int **m;    for(i=0; i<= lg; i++) {
        (s[i] = t[i]);
   /* allocate pointers to rows */      if (t[i]== '\\') s[i]='/';
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   m += NR_END;  
   m -= nrl;  int nbocc(char *s, char occ)
    {
      int i,j=0;
   /* allocate rows and set pointers to them */    int lg=20;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    i=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    lg=strlen(s);
   m[nrl] += NR_END;    for(i=0; i<= lg; i++) {
   m[nrl] -= ncl;    if  (s[i] == occ ) j++;
      }
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    return j;
    }
   /* return pointer to array of pointers to rows */  
   return m;  void cutv(char *u,char *v, char*t, char occ)
 }  {
     /* cuts string t into u and v where u is ended by char occ excluding it
 /****************** free_imatrix *************************/       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 void free_imatrix(m,nrl,nrh,ncl,nch)       gives u="abcedf" and v="ghi2j" */
       int **m;    int i,lg,j,p=0;
       long nch,ncl,nrh,nrl;    i=0;
      /* free an int matrix allocated by imatrix() */    for(j=0; j<=strlen(t)-1; j++) {
 {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    }
   free((FREE_ARG) (m+nrl-NR_END));  
 }    lg=strlen(t);
     for(j=0; j<p; j++) {
 /******************* matrix *******************************/      (u[j] = t[j]);
 double **matrix(long nrl, long nrh, long ncl, long nch)    }
 {       u[p]='\0';
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;     for(j=0; j<= lg; j++) {
       if (j>=(p+1))(v[j-p-1] = t[j]);
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   m += NR_END;  
   m -= nrl;  /********************** nrerror ********************/
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  void nrerror(char error_text[])
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  {
   m[nrl] += NR_END;    fprintf(stderr,"ERREUR ...\n");
   m[nrl] -= ncl;    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  /*********************** vector *******************/
 }  double *vector(int nl, int nh)
   {
 /*************************free matrix ************************/    double *v;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 {    if (!v) nrerror("allocation failure in vector");
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    return v-nl+NR_END;
   free((FREE_ARG)(m+nrl-NR_END));  }
 }  
   /************************ free vector ******************/
 /******************* ma3x *******************************/  void free_vector(double*v, int nl, int nh)
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  {
 {    free((FREE_ARG)(v+nl-NR_END));
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  }
   double ***m;  
   /************************ivector *******************************/
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char *cvector(long nl,long nh)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    char *v;
   m -= nrl;    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
     if (!v) nrerror("allocation failure in cvector");
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    return v-nl+NR_END;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  }
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /******************free ivector **************************/
   void free_cvector(char *v, long nl, long nh)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  {
     free((FREE_ARG)(v+nl-NR_END));
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  }
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  /************************ivector *******************************/
   m[nrl][ncl] -= nll;  int *ivector(long nl,long nh)
   for (j=ncl+1; j<=nch; j++)  {
     m[nrl][j]=m[nrl][j-1]+nlay;    int *v;
      v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   for (i=nrl+1; i<=nrh; i++) {    if (!v) nrerror("allocation failure in ivector");
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    return v-nl+NR_END;
     for (j=ncl+1; j<=nch; j++)  }
       m[i][j]=m[i][j-1]+nlay;  
   }  /******************free ivector **************************/
   return m;  void free_ivector(int *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /*************************free ma3x ************************/  }
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  /******************* imatrix *******************************/
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   free((FREE_ARG)(m+nrl-NR_END));  { 
 }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
 /***************** f1dim *************************/    
 extern int ncom;    /* allocate pointers to rows */ 
 extern double *pcom,*xicom;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 extern double (*nrfunc)(double []);    if (!m) nrerror("allocation failure 1 in matrix()"); 
      m += NR_END; 
 double f1dim(double x)    m -= nrl; 
 {    
   int j;    
   double f;    /* allocate rows and set pointers to them */ 
   double *xt;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   xt=vector(1,ncom);    m[nrl] += NR_END; 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    m[nrl] -= ncl; 
   f=(*nrfunc)(xt);    
   free_vector(xt,1,ncom);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   return f;    
 }    /* return pointer to array of pointers to rows */ 
     return m; 
 /*****************brent *************************/  } 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  /****************** free_imatrix *************************/
   int iter;  void free_imatrix(m,nrl,nrh,ncl,nch)
   double a,b,d,etemp;        int **m;
   double fu,fv,fw,fx;        long nch,ncl,nrh,nrl; 
   double ftemp;       /* free an int matrix allocated by imatrix() */ 
   double p,q,r,tol1,tol2,u,v,w,x,xm;  { 
   double e=0.0;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      free((FREE_ARG) (m+nrl-NR_END)); 
   a=(ax < cx ? ax : cx);  } 
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  /******************* matrix *******************************/
   fw=fv=fx=(*f)(x);  double **matrix(long nrl, long nrh, long ncl, long nch)
   for (iter=1;iter<=ITMAX;iter++) {  {
     xm=0.5*(a+b);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    double **m;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 #ifdef DEBUG    if (!m) nrerror("allocation failure 1 in matrix()");
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    m += 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;
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       *xmin=x;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       return fx;    m[nrl] += NR_END;
     }    m[nrl] -= ncl;
     ftemp=fu;  
     if (fabs(e) > tol1) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       r=(x-w)*(fx-fv);    return m;
       q=(x-v)*(fx-fw);    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
       p=(x-v)*q-(x-w)*r;     */
       q=2.0*(q-r);  }
       if (q > 0.0) p = -p;  
       q=fabs(q);  /*************************free matrix ************************/
       etemp=e;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       e=d;  {
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    free((FREE_ARG)(m+nrl-NR_END));
       else {  }
         d=p/q;  
         u=x+d;  /******************* ma3x *******************************/
         if (u-a < tol2 || b-u < tol2)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
           d=SIGN(tol1,xm-x);  {
       }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     } else {    double ***m;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    if (!m) nrerror("allocation failure 1 in matrix()");
     fu=(*f)(u);    m += NR_END;
     if (fu <= fx) {    m -= nrl;
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         SHFT(fv,fw,fx,fu)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         } else {    m[nrl] += NR_END;
           if (u < x) a=u; else b=u;    m[nrl] -= ncl;
           if (fu <= fw || w == x) {  
             v=w;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
             w=u;  
             fv=fw;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
             fw=fu;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
           } else if (fu <= fv || v == x || v == w) {    m[nrl][ncl] += NR_END;
             v=u;    m[nrl][ncl] -= nll;
             fv=fu;    for (j=ncl+1; j<=nch; j++) 
           }      m[nrl][j]=m[nrl][j-1]+nlay;
         }    
   }    for (i=nrl+1; i<=nrh; i++) {
   nrerror("Too many iterations in brent");      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   *xmin=x;      for (j=ncl+1; j<=nch; j++) 
   return fx;        m[i][j]=m[i][j-1]+nlay;
 }    }
     return m; 
 /****************** mnbrak ***********************/    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
              &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    */
             double (*func)(double))  }
 {  
   double ulim,u,r,q, dum;  /*************************free ma3x ************************/
   double fu;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
    {
   *fa=(*func)(*ax);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   *fb=(*func)(*bx);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   if (*fb > *fa) {    free((FREE_ARG)(m+nrl-NR_END));
     SHFT(dum,*ax,*bx,dum)  }
       SHFT(dum,*fb,*fa,dum)  
       }  /***************** f1dim *************************/
   *cx=(*bx)+GOLD*(*bx-*ax);  extern int ncom; 
   *fc=(*func)(*cx);  extern double *pcom,*xicom;
   while (*fb > *fc) {  extern double (*nrfunc)(double []); 
     r=(*bx-*ax)*(*fb-*fc);   
     q=(*bx-*cx)*(*fb-*fa);  double f1dim(double x) 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  { 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    int j; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    double f;
     if ((*bx-u)*(u-*cx) > 0.0) {    double *xt; 
       fu=(*func)(u);   
     } else if ((*cx-u)*(u-ulim) > 0.0) {    xt=vector(1,ncom); 
       fu=(*func)(u);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       if (fu < *fc) {    f=(*nrfunc)(xt); 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    free_vector(xt,1,ncom); 
           SHFT(*fb,*fc,fu,(*func)(u))    return f; 
           }  } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  /*****************brent *************************/
       fu=(*func)(u);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     } else {  { 
       u=(*cx)+GOLD*(*cx-*bx);    int iter; 
       fu=(*func)(u);    double a,b,d,etemp;
     }    double fu,fv,fw,fx;
     SHFT(*ax,*bx,*cx,u)    double ftemp;
       SHFT(*fa,*fb,*fc,fu)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       }    double e=0.0; 
 }   
     a=(ax < cx ? ax : cx); 
 /*************** linmin ************************/    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
 int ncom;    fw=fv=fx=(*f)(x); 
 double *pcom,*xicom;    for (iter=1;iter<=ITMAX;iter++) { 
 double (*nrfunc)(double []);      xm=0.5*(a+b); 
        tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 {      printf(".");fflush(stdout);
   double brent(double ax, double bx, double cx,      fprintf(ficlog,".");fflush(ficlog);
                double (*f)(double), double tol, double *xmin);  #ifdef DEBUG
   double f1dim(double x);      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);
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      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);
               double *fc, double (*func)(double));      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   int j;  #endif
   double xx,xmin,bx,ax;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double fx,fb,fa;        *xmin=x; 
          return fx; 
   ncom=n;      } 
   pcom=vector(1,n);      ftemp=fu;
   xicom=vector(1,n);      if (fabs(e) > tol1) { 
   nrfunc=func;        r=(x-w)*(fx-fv); 
   for (j=1;j<=n;j++) {        q=(x-v)*(fx-fw); 
     pcom[j]=p[j];        p=(x-v)*q-(x-w)*r; 
     xicom[j]=xi[j];        q=2.0*(q-r); 
   }        if (q > 0.0) p = -p; 
   ax=0.0;        q=fabs(q); 
   xx=1.0;        etemp=e; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);        e=d; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 #ifdef DEBUG          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);        else { 
 #endif          d=p/q; 
   for (j=1;j<=n;j++) {          u=x+d; 
     xi[j] *= xmin;          if (u-a < tol2 || b-u < tol2) 
     p[j] += xi[j];            d=SIGN(tol1,xm-x); 
   }        } 
   free_vector(xicom,1,n);      } else { 
   free_vector(pcom,1,n);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 }      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 /*************** powell ************************/      fu=(*f)(u); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      if (fu <= fx) { 
             double (*func)(double []))        if (u >= x) a=x; else b=x; 
 {        SHFT(v,w,x,u) 
   void linmin(double p[], double xi[], int n, double *fret,          SHFT(fv,fw,fx,fu) 
               double (*func)(double []));          } else { 
   int i,ibig,j;            if (u < x) a=u; else b=u; 
   double del,t,*pt,*ptt,*xit;            if (fu <= fw || w == x) { 
   double fp,fptt;              v=w; 
   double *xits;              w=u; 
   pt=vector(1,n);              fv=fw; 
   ptt=vector(1,n);              fw=fu; 
   xit=vector(1,n);            } else if (fu <= fv || v == x || v == w) { 
   xits=vector(1,n);              v=u; 
   *fret=(*func)(p);              fv=fu; 
   for (j=1;j<=n;j++) pt[j]=p[j];            } 
   for (*iter=1;;++(*iter)) {          } 
     fp=(*fret);    } 
     ibig=0;    nrerror("Too many iterations in brent"); 
     del=0.0;    *xmin=x; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    return fx; 
     for (i=1;i<=n;i++)  } 
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  /****************** mnbrak ***********************/
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       fptt=(*fret);              double (*func)(double)) 
 #ifdef DEBUG  { 
       printf("fret=%lf \n",*fret);    double ulim,u,r,q, dum;
 #endif    double fu; 
       printf("%d",i);fflush(stdout);   
       linmin(p,xit,n,fret,func);    *fa=(*func)(*ax); 
       if (fabs(fptt-(*fret)) > del) {    *fb=(*func)(*bx); 
         del=fabs(fptt-(*fret));    if (*fb > *fa) { 
         ibig=i;      SHFT(dum,*ax,*bx,dum) 
       }        SHFT(dum,*fb,*fa,dum) 
 #ifdef DEBUG        } 
       printf("%d %.12e",i,(*fret));    *cx=(*bx)+GOLD*(*bx-*ax); 
       for (j=1;j<=n;j++) {    *fc=(*func)(*cx); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    while (*fb > *fc) { 
         printf(" x(%d)=%.12e",j,xit[j]);      r=(*bx-*ax)*(*fb-*fc); 
       }      q=(*bx-*cx)*(*fb-*fa); 
       for(j=1;j<=n;j++)      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         printf(" p=%.12e",p[j]);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       printf("\n");      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 #endif      if ((*bx-u)*(u-*cx) > 0.0) { 
     }        fu=(*func)(u); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 #ifdef DEBUG        fu=(*func)(u); 
       int k[2],l;        if (fu < *fc) { 
       k[0]=1;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       k[1]=-1;            SHFT(*fb,*fc,fu,(*func)(u)) 
       printf("Max: %.12e",(*func)(p));            } 
       for (j=1;j<=n;j++)      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         printf(" %.12e",p[j]);        u=ulim; 
       printf("\n");        fu=(*func)(u); 
       for(l=0;l<=1;l++) {      } else { 
         for (j=1;j<=n;j++) {        u=(*cx)+GOLD*(*cx-*bx); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        fu=(*func)(u); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      } 
         }      SHFT(*ax,*bx,*cx,u) 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        SHFT(*fa,*fb,*fc,fu) 
       }        } 
 #endif  } 
   
   /*************** linmin ************************/
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  int ncom; 
       free_vector(ptt,1,n);  double *pcom,*xicom;
       free_vector(pt,1,n);  double (*nrfunc)(double []); 
       return;   
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  { 
     for (j=1;j<=n;j++) {    double brent(double ax, double bx, double cx, 
       ptt[j]=2.0*p[j]-pt[j];                 double (*f)(double), double tol, double *xmin); 
       xit[j]=p[j]-pt[j];    double f1dim(double x); 
       pt[j]=p[j];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     }                double *fc, double (*func)(double)); 
     fptt=(*func)(ptt);    int j; 
     if (fptt < fp) {    double xx,xmin,bx,ax; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    double fx,fb,fa;
       if (t < 0.0) {   
         linmin(p,xit,n,fret,func);    ncom=n; 
         for (j=1;j<=n;j++) {    pcom=vector(1,n); 
           xi[j][ibig]=xi[j][n];    xicom=vector(1,n); 
           xi[j][n]=xit[j];    nrfunc=func; 
         }    for (j=1;j<=n;j++) { 
 #ifdef DEBUG      pcom[j]=p[j]; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      xicom[j]=xi[j]; 
         for(j=1;j<=n;j++)    } 
           printf(" %.12e",xit[j]);    ax=0.0; 
         printf("\n");    xx=1.0; 
 #endif    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
   }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
 /**** Prevalence limit ****************/    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      p[j] += xi[j]; 
 {    } 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    free_vector(xicom,1,n); 
      matrix by transitions matrix until convergence is reached */    free_vector(pcom,1,n); 
   } 
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  /*************** powell ************************/
   double **matprod2();  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   double **out, cov[NCOVMAX], **pmij();              double (*func)(double [])) 
   double **newm;  { 
   double agefin, delaymax=50 ; /* Max number of years to converge */    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   for (ii=1;ii<=nlstate+ndeath;ii++)    int i,ibig,j; 
     for (j=1;j<=nlstate+ndeath;j++){    double del,t,*pt,*ptt,*xit;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    double fp,fptt;
     }    double *xits;
     pt=vector(1,n); 
    cov[1]=1.;    ptt=vector(1,n); 
      xit=vector(1,n); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    xits=vector(1,n); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    *fret=(*func)(p); 
     newm=savm;    for (j=1;j<=n;j++) pt[j]=p[j]; 
     /* Covariates have to be included here again */    for (*iter=1;;++(*iter)) { 
      cov[2]=agefin;      fp=(*fret); 
        ibig=0; 
       for (k=1; k<=cptcovn;k++) {      del=0.0; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       }      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       for (k=1; k<=cptcovage;k++)      for (i=1;i<=n;i++) {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        printf(" %d %.12f",i, p[i]);
       for (k=1; k<=cptcovprod;k++)        fprintf(ficlog," %d %.12lf",i, p[i]);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        fprintf(ficrespow," %.12lf", p[i]);
       }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      printf("\n");
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     savm=oldm;        fptt=(*fret); 
     oldm=newm;  #ifdef DEBUG
     maxmax=0.;        printf("fret=%lf \n",*fret);
     for(j=1;j<=nlstate;j++){        fprintf(ficlog,"fret=%lf \n",*fret);
       min=1.;  #endif
       max=0.;        printf("%d",i);fflush(stdout);
       for(i=1; i<=nlstate; i++) {        fprintf(ficlog,"%d",i);fflush(ficlog);
         sumnew=0;        linmin(p,xit,n,fret,func); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        if (fabs(fptt-(*fret)) > del) { 
         prlim[i][j]= newm[i][j]/(1-sumnew);          del=fabs(fptt-(*fret)); 
         max=FMAX(max,prlim[i][j]);          ibig=i; 
         min=FMIN(min,prlim[i][j]);        } 
       }  #ifdef DEBUG
       maxmin=max-min;        printf("%d %.12e",i,(*fret));
       maxmax=FMAX(maxmax,maxmin);        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     if(maxmax < ftolpl){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       return prlim;          printf(" x(%d)=%.12e",j,xit[j]);
     }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   }        }
 }        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
 /*************** transition probabilities ***************/          fprintf(ficlog," p=%.12e",p[j]);
         }
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        printf("\n");
 {        fprintf(ficlog,"\n");
   double s1, s2;  #endif
   /*double t34;*/      } 
   int i,j,j1, nc, ii, jj;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
     for(i=1; i<= nlstate; i++){        int k[2],l;
     for(j=1; j<i;j++){        k[0]=1;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        k[1]=-1;
         /*s2 += param[i][j][nc]*cov[nc];*/        printf("Max: %.12e",(*func)(p));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        fprintf(ficlog,"Max: %.12e",(*func)(p));
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        for (j=1;j<=n;j++) {
       }          printf(" %.12e",p[j]);
       ps[i][j]=s2;          fprintf(ficlog," %.12e",p[j]);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        }
     }        printf("\n");
     for(j=i+1; j<=nlstate+ndeath;j++){        fprintf(ficlog,"\n");
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        for(l=0;l<=1;l++) {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          for (j=1;j<=n;j++) {
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       ps[i][j]=(s2);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }          }
   }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     /*ps[3][2]=1;*/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   for(i=1; i<= nlstate; i++){  #endif
      s1=0;  
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);        free_vector(xit,1,n); 
     for(j=i+1; j<=nlstate+ndeath; j++)        free_vector(xits,1,n); 
       s1+=exp(ps[i][j]);        free_vector(ptt,1,n); 
     ps[i][i]=1./(s1+1.);        free_vector(pt,1,n); 
     for(j=1; j<i; j++)        return; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      } 
     for(j=i+1; j<=nlstate+ndeath; j++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      for (j=1;j<=n;j++) { 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        ptt[j]=2.0*p[j]-pt[j]; 
   } /* end i */        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      } 
     for(jj=1; jj<= nlstate+ndeath; jj++){      fptt=(*func)(ptt); 
       ps[ii][jj]=0;      if (fptt < fp) { 
       ps[ii][ii]=1;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     }        if (t < 0.0) { 
   }          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){            xi[j][n]=xit[j]; 
     for(jj=1; jj<= nlstate+ndeath; jj++){          }
      printf("%lf ",ps[ii][jj]);  #ifdef DEBUG
    }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     printf("\n ");          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     }          for(j=1;j<=n;j++){
     printf("\n ");printf("%lf ",cov[2]);*/            printf(" %.12e",xit[j]);
 /*            fprintf(ficlog," %.12e",xit[j]);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          }
   goto end;*/          printf("\n");
     return ps;          fprintf(ficlog,"\n");
 }  #endif
         }
 /**************** Product of 2 matrices ******************/      } 
     } 
 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  /**** Prevalence limit (stable prevalence)  ****************/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
      before: only the contents of out is modified. The function returns  {
      a pointer to pointers identical to out */    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   long i, j, k;       matrix by transitions matrix until convergence is reached */
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)    int i, ii,j,k;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    double min, max, maxmin, maxmax,sumnew=0.;
         out[i][k] +=in[i][j]*b[j][k];    double **matprod2();
     double **out, cov[NCOVMAX], **pmij();
   return out;    double **newm;
 }    double agefin, delaymax=50 ; /* Max number of years to converge */
   
     for (ii=1;ii<=nlstate+ndeath;ii++)
 /************* Higher Matrix Product ***************/      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      }
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month     cov[1]=1.;
      duration (i.e. until   
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
      (typically every 2 years instead of every month which is too big).      newm=savm;
      Model is determined by parameters x and covariates have to be      /* Covariates have to be included here again */
      included manually here.       cov[2]=agefin;
     
      */        for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int i, j, d, h, 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]]);*/
   double **out, cov[NCOVMAX];        }
   double **newm;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   /* Hstepm could be zero and should return the unit matrix */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for (i=1;i<=nlstate+ndeath;i++)  
     for (j=1;j<=nlstate+ndeath;j++){        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       oldm[i][j]=(i==j ? 1.0 : 0.0);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       po[i][j][0]=(i==j ? 1.0 : 0.0);        /*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);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){      savm=oldm;
     for(d=1; d <=hstepm; d++){      oldm=newm;
       newm=savm;      maxmax=0.;
       /* Covariates have to be included here again */      for(j=1;j<=nlstate;j++){
       cov[1]=1.;        min=1.;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        max=0.;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        for(i=1; i<=nlstate; i++) {
       for (k=1; k<=cptcovage;k++)          sumnew=0;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       for (k=1; k<=cptcovprod;k++)          prlim[i][j]= newm[i][j]/(1-sumnew);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
         }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        maxmin=max-min;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        maxmax=FMAX(maxmax,maxmin);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      if(maxmax < ftolpl){
       savm=oldm;        return prlim;
       oldm=newm;      }
     }    }
     for(i=1; i<=nlstate+ndeath; i++)  }
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  /*************** transition probabilities ***************/ 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       }  {
   } /* end h */    double s1, s2;
   return po;    /*double t34;*/
 }    int i,j,j1, nc, ii, jj;
   
       for(i=1; i<= nlstate; i++){
 /*************** log-likelihood *************/      for(j=1; j<i;j++){
 double func( double *x)        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 {          /*s2 += param[i][j][nc]*cov[nc];*/
   int i, ii, j, k, mi, d, kk;          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double l, ll[NLSTATEMAX], cov[NCOVMAX];          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   double **out;        }
   double sw; /* Sum of weights */        ps[i][j]=s2;
   double lli; /* Individual log likelihood */        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   long ipmx;      }
   /*extern weight */      for(j=i+1; j<=nlstate+ndeath;j++){
   /* We are differentiating ll according to initial status */        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   /*for(i=1;i<imx;i++)          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     printf(" %d\n",s[4][i]);        }
   */        ps[i][j]=s2;
   cov[1]=1.;      }
     }
   for(k=1; k<=nlstate; k++) ll[k]=0.;      /*ps[3][2]=1;*/
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    for(i=1; i<= nlstate; i++){
     for(mi=1; mi<= wav[i]-1; mi++){       s1=0;
       for (ii=1;ii<=nlstate+ndeath;ii++)      for(j=1; j<i; j++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        s1+=exp(ps[i][j]);
       for(d=0; d<dh[mi][i]; d++){      for(j=i+1; j<=nlstate+ndeath; j++)
         newm=savm;        s1+=exp(ps[i][j]);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      ps[i][i]=1./(s1+1.);
         for (kk=1; kk<=cptcovage;kk++) {      for(j=1; j<i; j++)
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        ps[i][j]= exp(ps[i][j])*ps[i][i];
         }      for(j=i+1; j<=nlstate+ndeath; j++)
                ps[i][j]= exp(ps[i][j])*ps[i][i];
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    } /* end i */
         savm=oldm;  
         oldm=newm;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
              for(jj=1; jj<= nlstate+ndeath; jj++){
                ps[ii][jj]=0;
       } /* end mult */        ps[ii][ii]=1;
            }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;  
       sw += weight[i];    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      for(jj=1; jj<= nlstate+ndeath; jj++){
     } /* end of wave */       printf("%lf ",ps[ii][jj]);
   } /* end of individual */     }
       printf("\n ");
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      printf("\n ");printf("%lf ",cov[2]);*/
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  /*
   return -l;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
 }    goto end;*/
       return ps;
   }
 /*********** Maximum Likelihood Estimation ***************/  
   /**************** Product of 2 matrices ******************/
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   int i,j, iter;  {
   double **xi,*delti;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double fret;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   xi=matrix(1,npar,1,npar);    /* in, b, out are matrice of pointers which should have been initialized 
   for (i=1;i<=npar;i++)       before: only the contents of out is modified. The function returns
     for (j=1;j<=npar;j++)       a pointer to pointers identical to out */
       xi[i][j]=(i==j ? 1.0 : 0.0);    long i, j, k;
   printf("Powell\n");    for(i=nrl; i<= nrh; i++)
   powell(p,xi,npar,ftol,&iter,&fret,func);      for(k=ncolol; k<=ncoloh; k++)
         for(j=ncl,out[i][k]=0.; j<=nch; j++)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          out[i][k] +=in[i][j]*b[j][k];
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  
     return out;
 }  }
   
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /************* Higher Matrix Product ***************/
 {  
   double  **a,**y,*x,pd;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   double **hess;  {
   int i, j,jk;    /* Computes the transition matrix starting at age 'age' over 
   int *indx;       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   double hessii(double p[], double delta, int theta, double delti[]);       nhstepm*hstepm matrices. 
   double hessij(double p[], double delti[], int i, int j);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   void lubksb(double **a, int npar, int *indx, double b[]) ;       (typically every 2 years instead of every month which is too big 
   void ludcmp(double **a, int npar, int *indx, double *d) ;       for the memory).
        Model is determined by parameters x and covariates have to be 
   hess=matrix(1,npar,1,npar);       included manually here. 
   
   printf("\nCalculation of the hessian matrix. Wait...\n");       */
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);    int i, j, d, h, k;
     hess[i][i]=hessii(p,ftolhess,i,delti);    double **out, cov[NCOVMAX];
     /*printf(" %f ",p[i]);*/    double **newm;
     /*printf(" %lf ",hess[i][i]);*/  
   }    /* Hstepm could be zero and should return the unit matrix */
      for (i=1;i<=nlstate+ndeath;i++)
   for (i=1;i<=npar;i++) {      for (j=1;j<=nlstate+ndeath;j++){
     for (j=1;j<=npar;j++)  {        oldm[i][j]=(i==j ? 1.0 : 0.0);
       if (j>i) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
         printf(".%d%d",i,j);fflush(stdout);      }
         hess[i][j]=hessij(p,delti,i,j);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         hess[j][i]=hess[i][j];        for(h=1; h <=nhstepm; h++){
         /*printf(" %lf ",hess[i][j]);*/      for(d=1; d <=hstepm; d++){
       }        newm=savm;
     }        /* Covariates have to be included here again */
   }        cov[1]=1.;
   printf("\n");        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        for (k=1; k<=cptcovage;k++)
            cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   a=matrix(1,npar,1,npar);        for (k=1; k<=cptcovprod;k++)
   y=matrix(1,npar,1,npar);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   x=vector(1,npar);  
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   ludcmp(a,npar,indx,&pd);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (j=1;j<=npar;j++) {        savm=oldm;
     for (i=1;i<=npar;i++) x[i]=0;        oldm=newm;
     x[j]=1;      }
     lubksb(a,npar,indx,x);      for(i=1; i<=nlstate+ndeath; i++)
     for (i=1;i<=npar;i++){        for(j=1;j<=nlstate+ndeath;j++) {
       matcov[i][j]=x[i];          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]);
   }           */
         }
   printf("\n#Hessian matrix#\n");    } /* end h */
   for (i=1;i<=npar;i++) {    return po;
     for (j=1;j<=npar;j++) {  }
       printf("%.3e ",hess[i][j]);  
     }  
     printf("\n");  /*************** log-likelihood *************/
   }  double func( double *x)
   {
   /* Recompute Inverse */    int i, ii, j, k, mi, d, kk;
   for (i=1;i<=npar;i++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    double **out;
   ludcmp(a,npar,indx,&pd);    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
   /*  printf("\n#Hessian matrix recomputed#\n");    int s1, s2;
     double bbh, survp;
   for (j=1;j<=npar;j++) {    long ipmx;
     for (i=1;i<=npar;i++) x[i]=0;    /*extern weight */
     x[j]=1;    /* We are differentiating ll according to initial status */
     lubksb(a,npar,indx,x);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for (i=1;i<=npar;i++){    /*for(i=1;i<imx;i++) 
       y[i][j]=x[i];      printf(" %d\n",s[4][i]);
       printf("%.3e ",y[i][j]);    */
     }    cov[1]=1.;
     printf("\n");  
   }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   */  
     if(mle==1){
   free_matrix(a,1,npar,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_matrix(y,1,npar,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_vector(x,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   free_ivector(indx,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_matrix(hess,1,npar,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<dh[mi][i]; d++){
 /*************** hessian matrix ****************/            newm=savm;
 double hessii( double x[], double delta, int theta, double delti[])            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
   int i;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int l=1, lmax=20;            }
   double k1,k2;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double p2[NPARMAX+1];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double res;            savm=oldm;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            oldm=newm;
   double fx;          } /* end mult */
   int k=0,kmax=10;        
   double l1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias and large stepm.
   fx=func(x);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   for (i=1;i<=npar;i++) p2[i]=x[i];           * (in months) between two waves is not a multiple of stepm, we rounded to 
   for(l=0 ; l <=lmax; l++){           * the nearest (and in case of equal distance, to the lowest) interval but now
     l1=pow(10,l);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     delts=delt;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     for(k=1 ; k <kmax; k=k+1){           * probability in order to take into account the bias as a fraction of the way
       delt = delta*(l1*k);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       p2[theta]=x[theta] +delt;           * -stepm/2 to stepm/2 .
       k1=func(p2)-fx;           * For stepm=1 the results are the same as for previous versions of Imach.
       p2[theta]=x[theta]-delt;           * For stepm > 1 the results are less biased than in previous versions. 
       k2=func(p2)-fx;           */
       /*res= (k1-2.0*fx+k2)/delt/delt; */          s1=s[mw[mi][i]][i];
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          s2=s[mw[mi+1][i]][i];
                bbh=(double)bh[mi][i]/(double)stepm; 
 #ifdef DEBUG          /* bias is positive if real duration
       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);           * is higher than the multiple of stepm and negative otherwise.
 #endif           */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          if( s2 > nlstate){ 
         k=kmax;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       }               to the likelihood is the probability to die between last step unit time and current 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */               step unit time, which is also the differences between probability to die before dh 
         k=kmax; l=lmax*10.;               and probability to die before dh-stepm . 
       }               In version up to 0.92 likelihood was computed
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          as if date of death was unknown. Death was treated as any other
         delts=delt;          health state: the date of the interview describes the actual state
       }          and not the date of a change in health state. The former idea was
     }          to consider that at each interview the state was recorded
   }          (healthy, disable or death) and IMaCh was corrected; but when we
   delti[theta]=delts;          introduced the exact date of death then we should have modified
   return res;          the contribution of an exact death to the likelihood. This new
            contribution is smaller and very dependent of the step unit
 }          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
 double hessij( double x[], double delti[], int thetai,int thetaj)          interview up to one month before death multiplied by the
 {          probability to die within a month. Thanks to Chris
   int i;          Jackson for correcting this bug.  Former versions increased
   int l=1, l1, lmax=20;          mortality artificially. The bad side is that we add another loop
   double k1,k2,k3,k4,res,fx;          which slows down the processing. The difference can be up to 10%
   double p2[NPARMAX+1];          lower mortality.
   int k;            */
             lli=log(out[s1][s2] - savm[s1][s2]);
   fx=func(x);          }else{
   for (k=1; k<=2; k++) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for (i=1;i<=npar;i++) p2[i]=x[i];            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     p2[thetai]=x[thetai]+delti[thetai]/k;          } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     k1=func(p2)-fx;          /*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); */
     p2[thetai]=x[thetai]+delti[thetai]/k;          ipmx +=1;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          sw += weight[i];
     k2=func(p2)-fx;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
     p2[thetai]=x[thetai]-delti[thetai]/k;      } /* end of individual */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    }  else if(mle==2){
     k3=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetai]=x[thetai]-delti[thetai]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
     k4=func(p2)-fx;            for (j=1;j<=nlstate+ndeath;j++){
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef DEBUG              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     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);            }
 #endif          for(d=0; d<=dh[mi][i]; d++){
   }            newm=savm;
   return res;            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];
 /************** Inverse of matrix **************/            }
 void ludcmp(double **a, int n, int *indx, double *d)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i,imax,j,k;            savm=oldm;
   double big,dum,sum,temp;            oldm=newm;
   double *vv;          } /* end mult */
          
   vv=vector(1,n);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   *d=1.0;          /* But now since version 0.9 we anticipate for bias and large stepm.
   for (i=1;i<=n;i++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     big=0.0;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     for (j=1;j<=n;j++)           * the nearest (and in case of equal distance, to the lowest) interval but now
       if ((temp=fabs(a[i][j])) > big) big=temp;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     vv[i]=1.0/big;           * probability in order to take into account the bias as a fraction of the way
   }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for (j=1;j<=n;j++) {           * -stepm/2 to stepm/2 .
     for (i=1;i<j;i++) {           * For stepm=1 the results are the same as for previous versions of Imach.
       sum=a[i][j];           * For stepm > 1 the results are less biased than in previous versions. 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];           */
       a[i][j]=sum;          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
     big=0.0;          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=j;i<=n;i++) {          /* bias is positive if real duration
       sum=a[i][j];           * is higher than the multiple of stepm and negative otherwise.
       for (k=1;k<j;k++)           */
         sum -= a[i][k]*a[k][j];          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 */
       a[i][j]=sum;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       if ( (dum=vv[i]*fabs(sum)) >= big) {          /*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 */
         big=dum;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         imax=i;          /*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;
     if (j != imax) {          sw += weight[i];
       for (k=1;k<=n;k++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         dum=a[imax][k];        } /* end of wave */
         a[imax][k]=a[j][k];      } /* end of individual */
         a[j][k]=dum;    }  else if(mle==3){  /* exponential inter-extrapolation */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       *d = -(*d);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       vv[imax]=vv[j];        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
     indx[j]=imax;            for (j=1;j<=nlstate+ndeath;j++){
     if (a[j][j] == 0.0) a[j][j]=TINY;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (j != n) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       dum=1.0/(a[j][j]);            }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_vector(vv,1,n);  /* Doesn't work */            for (kk=1; kk<=cptcovage;kk++) {
 ;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 }            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 void lubksb(double **a, int n, int *indx, double b[])                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {            savm=oldm;
   int i,ii=0,ip,j;            oldm=newm;
   double sum;          } /* end mult */
          
   for (i=1;i<=n;i++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     ip=indx[i];          /* But now since version 0.9 we anticipate for bias and large stepm.
     sum=b[ip];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     b[ip]=b[i];           * (in months) between two waves is not a multiple of stepm, we rounded to 
     if (ii)           * the nearest (and in case of equal distance, to the lowest) interval but now
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     else if (sum) ii=i;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     b[i]=sum;           * probability in order to take into account the bias as a fraction of the way
   }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for (i=n;i>=1;i--) {           * -stepm/2 to stepm/2 .
     sum=b[i];           * For stepm=1 the results are the same as for previous versions of Imach.
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];           * For stepm > 1 the results are less biased than in previous versions. 
     b[i]=sum/a[i][i];           */
   }          s1=s[mw[mi][i]][i];
 }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
 /************ Frequencies ********************/          /* bias is positive if real duration
 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)           * is higher than the multiple of stepm and negative otherwise.
 {  /* Some frequencies */           */
            /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          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 ***freq; /* Frequencies */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double *pp;          /*if(lli ==000.0)*/
   double pos, k2, dateintsum=0,k2cpt=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); */
   FILE *ficresp;          ipmx +=1;
   char fileresp[FILENAMELENGTH];          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   pp=vector(1,nlstate);        } /* end of wave */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      } /* end of individual */
   strcpy(fileresp,"p");    }else{  /* ml=4 no inter-extrapolation */
   strcat(fileresp,fileres);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if((ficresp=fopen(fileresp,"w"))==NULL) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for(mi=1; mi<= wav[i]-1; mi++){
     exit(0);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   j1=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   j=cptcoveff;          for(d=0; d<dh[mi][i]; d++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(k1=1; k1<=j;k1++){            for (kk=1; kk<=cptcovage;kk++) {
    for(i1=1; i1<=ncodemax[k1];i1++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        j1++;            }
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          
          scanf("%d", i);*/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for (i=-1; i<=nlstate+ndeath; i++)                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          for (jk=-1; jk<=nlstate+ndeath; jk++)              savm=oldm;
            for(m=agemin; m <= agemax+3; m++)            oldm=newm;
              freq[i][jk][m]=0;          } /* end mult */
         
         dateintsum=0;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         k2cpt=0;          ipmx +=1;
        for (i=1; i<=imx; i++) {          sw += weight[i];
          bool=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          if  (cptcovn>0) {        } /* end of wave */
            for (z1=1; z1<=cptcoveff; z1++)      } /* end of individual */
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    } /* End of if */
                bool=0;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
          }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          if (bool==1) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
            for(m=firstpass; m<=lastpass; m++){    return -l;
              k2=anint[m][i]+(mint[m][i]/12.);  }
              if ((k2>=dateprev1) && (k2<=dateprev2)) {  
                if(agev[m][i]==0) agev[m][i]=agemax+1;  
                if(agev[m][i]==1) agev[m][i]=agemax+2;  /*********** Maximum Likelihood Estimation ***************/
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  {
                  dateintsum=dateintsum+k2;    int i,j, iter;
                  k2cpt++;    double **xi;
                }    double fret;
     char filerespow[FILENAMELENGTH];
              }    xi=matrix(1,npar,1,npar);
            }    for (i=1;i<=npar;i++)
          }      for (j=1;j<=npar;j++)
        }        xi[i][j]=(i==j ? 1.0 : 0.0);
         if  (cptcovn>0) {    printf("Powell\n");  fprintf(ficlog,"Powell\n");
          fprintf(ficresp, "\n#********** Variable ");    strcpy(filerespow,"pow"); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    strcat(filerespow,fileres);
        fprintf(ficresp, "**********\n#");    if((ficrespow=fopen(filerespow,"w"))==NULL) {
         }      printf("Problem with resultfile: %s\n", filerespow);
        for(i=1; i<=nlstate;i++)      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    }
        fprintf(ficresp, "\n");    fprintf(ficrespow,"# Powell\n# iter -2*LL");
            for (i=1;i<=nlstate;i++)
   for(i=(int)agemin; i <= (int)agemax+3; i++){      for(j=1;j<=nlstate+ndeath;j++)
     if(i==(int)agemax+3)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       printf("Total");    fprintf(ficrespow,"\n");
     else    powell(p,xi,npar,ftol,&iter,&fret,func);
       printf("Age %d", i);  
     for(jk=1; jk <=nlstate ; jk++){    fclose(ficrespow);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         pp[jk] += freq[jk][m][i];    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)  }
         pos += freq[jk][m][i];  
       if(pp[jk]>=1.e-10)  /**** Computes Hessian and covariance matrix ***/
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       else  {
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    double  **a,**y,*x,pd;
     }    double **hess;
     int i, j,jk;
      for(jk=1; jk <=nlstate ; jk++){    int *indx;
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
         pp[jk] += freq[jk][m][i];    double hessii(double p[], double delta, int theta, double delti[]);
      }    double hessij(double p[], double delti[], int i, int j);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
     for(jk=1,pos=0; jk <=nlstate ; jk++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
       pos += pp[jk];  
     for(jk=1; jk <=nlstate ; jk++){    hess=matrix(1,npar,1,npar);
       if(pos>=1.e-5)  
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    printf("\nCalculation of the hessian matrix. Wait...\n");
       else    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for (i=1;i<=npar;i++){
       if( i <= (int) agemax){      printf("%d",i);fflush(stdout);
         if(pos>=1.e-5){      fprintf(ficlog,"%d",i);fflush(ficlog);
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      hess[i][i]=hessii(p,ftolhess,i,delti);
           probs[i][jk][j1]= pp[jk]/pos;      /*printf(" %f ",p[i]);*/
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      /*printf(" %lf ",hess[i][i]);*/
         }    }
       else    
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    for (i=1;i<=npar;i++) {
       }      for (j=1;j<=npar;j++)  {
     }        if (j>i) { 
     for(jk=-1; jk <=nlstate+ndeath; jk++)          printf(".%d%d",i,j);fflush(stdout);
       for(m=-1; m <=nlstate+ndeath; m++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          hess[i][j]=hessij(p,delti,i,j);
     if(i <= (int) agemax)          hess[j][i]=hess[i][j];    
       fprintf(ficresp,"\n");          /*printf(" %lf ",hess[i][j]);*/
     printf("\n");        }
     }      }
     }    }
  }    printf("\n");
   dateintmean=dateintsum/k2cpt;    fprintf(ficlog,"\n");
    
   fclose(ficresp);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   free_vector(pp,1,nlstate);    
     a=matrix(1,npar,1,npar);
   /* End of Freq */    y=matrix(1,npar,1,npar);
 }    x=vector(1,npar);
     indx=ivector(1,npar);
 /************ Prevalence ********************/    for (i=1;i<=npar;i++)
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 {  /* Some frequencies */    ludcmp(a,npar,indx,&pd);
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    for (j=1;j<=npar;j++) {
   double ***freq; /* Frequencies */      for (i=1;i<=npar;i++) x[i]=0;
   double *pp;      x[j]=1;
   double pos, k2;      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   pp=vector(1,nlstate);        matcov[i][j]=x[i];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      }
      }
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;    printf("\n#Hessian matrix#\n");
      fprintf(ficlog,"\n#Hessian matrix#\n");
   j=cptcoveff;    for (i=1;i<=npar;i++) { 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for (j=1;j<=npar;j++) { 
          printf("%.3e ",hess[i][j]);
  for(k1=1; k1<=j;k1++){        fprintf(ficlog,"%.3e ",hess[i][j]);
     for(i1=1; i1<=ncodemax[k1];i1++){      }
       j1++;      printf("\n");
        fprintf(ficlog,"\n");
       for (i=-1; i<=nlstate+ndeath; i++)      }
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)    /* Recompute Inverse */
             freq[i][jk][m]=0;    for (i=1;i<=npar;i++)
            for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       for (i=1; i<=imx; i++) {    ludcmp(a,npar,indx,&pd);
         bool=1;  
         if  (cptcovn>0) {    /*  printf("\n#Hessian matrix recomputed#\n");
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    for (j=1;j<=npar;j++) {
               bool=0;      for (i=1;i<=npar;i++) x[i]=0;
         }      x[j]=1;
         if (bool==1) {      lubksb(a,npar,indx,x);
           for(m=firstpass; m<=lastpass; m++){      for (i=1;i<=npar;i++){ 
             k2=anint[m][i]+(mint[m][i]/12.);        y[i][j]=x[i];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        printf("%.3e ",y[i][j]);
               if(agev[m][i]==0) agev[m][i]=agemax+1;        fprintf(ficlog,"%.3e ",y[i][j]);
               if(agev[m][i]==1) agev[m][i]=agemax+2;      }
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-1/12.)] += weight[i];      printf("\n");
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];        fprintf(ficlog,"\n");
             }    }
           }    */
         }  
       }    free_matrix(a,1,npar,1,npar);
          free_matrix(y,1,npar,1,npar);
         for(i=(int)agemin; i <= (int)agemax+3; i++){    free_vector(x,1,npar);
           for(jk=1; jk <=nlstate ; jk++){    free_ivector(indx,1,npar);
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    free_matrix(hess,1,npar,1,npar);
               pp[jk] += freq[jk][m][i];  
           }  
           for(jk=1; jk <=nlstate ; jk++){  }
             for(m=-1, pos=0; m <=0 ; m++)  
             pos += freq[jk][m][i];  /*************** hessian matrix ****************/
         }  double hessii( double x[], double delta, int theta, double delti[])
          {
          for(jk=1; jk <=nlstate ; jk++){    int i;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    int l=1, lmax=20;
              pp[jk] += freq[jk][m][i];    double k1,k2;
          }    double p2[NPARMAX+1];
              double res;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
          for(jk=1; jk <=nlstate ; jk++){              int k=0,kmax=10;
            if( i <= (int) agemax){    double l1;
              if(pos>=1.e-5){  
                probs[i][jk][j1]= pp[jk]/pos;    fx=func(x);
              }    for (i=1;i<=npar;i++) p2[i]=x[i];
            }    for(l=0 ; l <=lmax; l++){
          }      l1=pow(10,l);
                delts=delt;
         }      for(k=1 ; k <kmax; k=k+1){
     }        delt = delta*(l1*k);
   }        p2[theta]=x[theta] +delt;
          k1=func(p2)-fx;
          p2[theta]=x[theta]-delt;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        k2=func(p2)-fx;
   free_vector(pp,1,nlstate);        /*res= (k1-2.0*fx+k2)/delt/delt; */
          res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 }  /* End of Freq */        
   #ifdef DEBUG
 /************* Waves Concatenation ***************/        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);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  #endif
 {        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
      Death is a valid wave (if date is known).          k=kmax;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        }
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
      and mw[mi+1][i]. dh depends on stepm.          k=kmax; l=lmax*10.;
      */        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   int i, mi, m;          delts=delt;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        }
      double sum=0., jmean=0.;*/      }
     }
   int j, k=0,jk, ju, jl;    delti[theta]=delts;
   double sum=0.;    return res; 
   jmin=1e+5;    
   jmax=-1;  }
   jmean=0.;  
   for(i=1; i<=imx; i++){  double hessij( double x[], double delti[], int thetai,int thetaj)
     mi=0;  {
     m=firstpass;    int i;
     while(s[m][i] <= nlstate){    int l=1, l1, lmax=20;
       if(s[m][i]>=1)    double k1,k2,k3,k4,res,fx;
         mw[++mi][i]=m;    double p2[NPARMAX+1];
       if(m >=lastpass)    int k;
         break;  
       else    fx=func(x);
         m++;    for (k=1; k<=2; k++) {
     }/* end while */      for (i=1;i<=npar;i++) p2[i]=x[i];
     if (s[m][i] > nlstate){      p2[thetai]=x[thetai]+delti[thetai]/k;
       mi++;     /* Death is another wave */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       /* if(mi==0)  never been interviewed correctly before death */      k1=func(p2)-fx;
          /* Only death is a correct wave */    
       mw[mi][i]=m;      p2[thetai]=x[thetai]+delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
     wav[i]=mi;    
     if(mi==0)      p2[thetai]=x[thetai]-delti[thetai]/k;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   }      k3=func(p2)-fx;
     
   for(i=1; i<=imx; i++){      p2[thetai]=x[thetai]-delti[thetai]/k;
     for(mi=1; mi<wav[i];mi++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       if (stepm <=0)      k4=func(p2)-fx;
         dh[mi][i]=1;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       else{  #ifdef DEBUG
         if (s[mw[mi+1][i]][i] > nlstate) {      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);
           if (agedc[i] < 2*AGESUP) {      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);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  #endif
           if(j==0) j=1;  /* Survives at least one month after exam */    }
           k=k+1;    return res;
           if (j >= jmax) jmax=j;  }
           if (j <= jmin) jmin=j;  
           sum=sum+j;  /************** Inverse of matrix **************/
           /* if (j<10) printf("j=%d num=%d ",j,i); */  void ludcmp(double **a, int n, int *indx, double *d) 
           }  { 
         }    int i,imax,j,k; 
         else{    double big,dum,sum,temp; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    double *vv; 
           k=k+1;   
           if (j >= jmax) jmax=j;    vv=vector(1,n); 
           else if (j <= jmin)jmin=j;    *d=1.0; 
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    for (i=1;i<=n;i++) { 
           sum=sum+j;      big=0.0; 
         }      for (j=1;j<=n;j++) 
         jk= j/stepm;        if ((temp=fabs(a[i][j])) > big) big=temp; 
         jl= j -jk*stepm;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         ju= j -(jk+1)*stepm;      vv[i]=1.0/big; 
         if(jl <= -ju)    } 
           dh[mi][i]=jk;    for (j=1;j<=n;j++) { 
         else      for (i=1;i<j;i++) { 
           dh[mi][i]=jk+1;        sum=a[i][j]; 
         if(dh[mi][i]==0)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           dh[mi][i]=1; /* At least one step */        a[i][j]=sum; 
       }      } 
     }      big=0.0; 
   }      for (i=j;i<=n;i++) { 
   jmean=sum/k;        sum=a[i][j]; 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        for (k=1;k<j;k++) 
  }          sum -= a[i][k]*a[k][j]; 
 /*********** Tricode ****************************/        a[i][j]=sum; 
 void tricode(int *Tvar, int **nbcode, int imx)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
 {          big=dum; 
   int Ndum[20],ij=1, k, j, i;          imax=i; 
   int cptcode=0;        } 
   cptcoveff=0;      } 
        if (j != imax) { 
   for (k=0; k<19; k++) Ndum[k]=0;        for (k=1;k<=n;k++) { 
   for (k=1; k<=7; k++) ncodemax[k]=0;          dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          a[j][k]=dum; 
     for (i=1; i<=imx; i++) {        } 
       ij=(int)(covar[Tvar[j]][i]);        *d = -(*d); 
       Ndum[ij]++;        vv[imax]=vv[j]; 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      } 
       if (ij > cptcode) cptcode=ij;      indx[j]=imax; 
     }      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
     for (i=0; i<=cptcode; i++) {        dum=1.0/(a[j][j]); 
       if(Ndum[i]!=0) ncodemax[j]++;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     }      } 
     ij=1;    } 
     free_vector(vv,1,n);  /* Doesn't work */
   ;
     for (i=1; i<=ncodemax[j]; i++) {  } 
       for (k=0; k<=19; k++) {  
         if (Ndum[k] != 0) {  void lubksb(double **a, int n, int *indx, double b[]) 
           nbcode[Tvar[j]][ij]=k;  { 
           ij++;    int i,ii=0,ip,j; 
         }    double sum; 
         if (ij > ncodemax[j]) break;   
       }      for (i=1;i<=n;i++) { 
     }      ip=indx[i]; 
   }        sum=b[ip]; 
       b[ip]=b[i]; 
  for (k=0; k<19; k++) Ndum[k]=0;      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
  for (i=1; i<=ncovmodel-2; i++) {      else if (sum) ii=i; 
       ij=Tvar[i];      b[i]=sum; 
       Ndum[ij]++;    } 
     }    for (i=n;i>=1;i--) { 
       sum=b[i]; 
  ij=1;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
  for (i=1; i<=10; i++) {      b[i]=sum/a[i][i]; 
    if((Ndum[i]!=0) && (i<=ncov)){    } 
      Tvaraff[ij]=i;  } 
      ij++;  
    }  /************ Frequencies ********************/
  }  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)
    {  /* Some frequencies */
     cptcoveff=ij-1;    
 }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     int first;
 /*********** Health Expectancies ****************/    double ***freq; /* Frequencies */
     double *pp, **prop;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    double pos,posprop, k2, dateintsum=0,k2cpt=0;
 {    FILE *ficresp;
   /* Health expectancies */    char fileresp[FILENAMELENGTH];
   int i, j, nhstepm, hstepm, h;    
   double age, agelim,hf;    pp=vector(1,nlstate);
   double ***p3mat;    prop=matrix(1,nlstate,iagemin,iagemax+3);
      strcpy(fileresp,"p");
   fprintf(ficreseij,"# Health expectancies\n");    strcat(fileresp,fileres);
   fprintf(ficreseij,"# Age");    if((ficresp=fopen(fileresp,"w"))==NULL) {
   for(i=1; i<=nlstate;i++)      printf("Problem with prevalence resultfile: %s\n", fileresp);
     for(j=1; j<=nlstate;j++)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficreseij," %1d-%1d",i,j);      exit(0);
   fprintf(ficreseij,"\n");    }
     freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   hstepm=1*YEARM; /*  Every j years of age (in month) */    j1=0;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    
     j=cptcoveff;
   agelim=AGESUP;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     /* nhstepm age range expressed in number of stepm */    first=1;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years = 20*12/6=40 stepm */    for(k1=1; k1<=j;k1++){
     if (stepm >= YEARM) hstepm=1;      for(i1=1; i1<=ncodemax[k1];i1++){
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        j1++;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          scanf("%d", i);*/
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        for (i=-1; i<=nlstate+ndeath; i++)  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            for (jk=-1; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++)      for (i=1; i<=nlstate; i++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        for(m=iagemin; m <= iagemax+3; m++)
           eij[i][j][(int)age] +=p3mat[i][j][h];          prop[i][m]=0;
         }        
            dateintsum=0;
     hf=1;        k2cpt=0;
     if (stepm >= YEARM) hf=stepm/YEARM;        for (i=1; i<=imx; i++) {
     fprintf(ficreseij,"%.0f",age );          bool=1;
     for(i=1; i<=nlstate;i++)          if  (cptcovn>0) {
       for(j=1; j<=nlstate;j++){            for (z1=1; z1<=cptcoveff; z1++) 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       }                bool=0;
     fprintf(ficreseij,"\n");          }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if (bool==1){
   }            for(m=firstpass; m<=lastpass; m++){
 }              k2=anint[m][i]+(mint[m][i]/12.);
               if ((k2>=dateprev1) && (k2<=dateprev2)) {
 /************ Variance ******************/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 {                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   /* Variance of health expectancies */                if (m<lastpass) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   double **newm;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   double **dnewm,**doldm;                }
   int i, j, nhstepm, hstepm, h;                
   int k, cptcode;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   double *xp;                  dateintsum=dateintsum+k2;
   double **gp, **gm;                  k2cpt++;
   double ***gradg, ***trgradg;                }
   double ***p3mat;              }
   double age,agelim;            }
   int theta;          }
         }
    fprintf(ficresvij,"# Covariances of life expectancies\n");         
   fprintf(ficresvij,"# Age");        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)        if  (cptcovn>0) {
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          fprintf(ficresp, "\n#********** Variable "); 
   fprintf(ficresvij,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
   xp=vector(1,npar);        }
   dnewm=matrix(1,nlstate,1,npar);        for(i=1; i<=nlstate;i++) 
   doldm=matrix(1,nlstate,1,nlstate);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
          fprintf(ficresp, "\n");
   hstepm=1*YEARM; /* Every year of age */        
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for(i=iagemin; i <= iagemax+3; i++){
   agelim = AGESUP;          if(i==iagemax+3){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            fprintf(ficlog,"Total");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          }else{
     if (stepm >= YEARM) hstepm=1;            if(first==1){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              first=0;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              printf("See log file for details...\n");
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            }
     gp=matrix(0,nhstepm,1,nlstate);            fprintf(ficlog,"Age %d", i);
     gm=matrix(0,nhstepm,1,nlstate);          }
           for(jk=1; jk <=nlstate ; jk++){
     for(theta=1; theta <=npar; theta++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       for(i=1; i<=npar; i++){ /* Computes gradient */              pp[jk] += freq[jk][m][i]; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
       }          for(jk=1; jk <=nlstate ; jk++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              for(m=-1, pos=0; m <=0 ; m++)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
       if (popbased==1) {              if(first==1){
         for(i=1; i<=nlstate;i++)              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           prlim[i][i]=probs[(int)age][i][ij];              }
       }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                  }else{
       for(j=1; j<= nlstate; j++){              if(first==1)
         for(h=0; h<=nhstepm; h++){                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            }
         }          }
       }  
              for(jk=1; jk <=nlstate ; jk++){
       for(i=1; i<=npar; i++) /* Computes gradient */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              pp[jk] += freq[jk][m][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            }       
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
       if (popbased==1) {            posprop += prop[jk][i];
         for(i=1; i<=nlstate;i++)          }
           prlim[i][i]=probs[(int)age][i][ij];          for(jk=1; jk <=nlstate ; jk++){
       }            if(pos>=1.e-5){
               if(first==1)
       for(j=1; j<= nlstate; j++){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         for(h=0; h<=nhstepm; h++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            }else{
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              if(first==1)
         }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
       for(j=1; j<= nlstate; j++)            if( i <= iagemax){
         for(h=0; h<=nhstepm; h++){              if(pos>=1.e-5){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
         }                probs[i][jk][j1]= pp[jk]/pos;
     } /* End theta */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     for(h=0; h<=nhstepm; h++)            }
       for(j=1; j<=nlstate;j++)          }
         for(theta=1; theta <=npar; theta++)          
           trgradg[h][j][theta]=gradg[h][theta][j];          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
     for(i=1;i<=nlstate;i++)              if(freq[jk][m][i] !=0 ) {
       for(j=1;j<=nlstate;j++)              if(first==1)
         vareij[i][j][(int)age] =0.;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(h=0;h<=nhstepm;h++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       for(k=0;k<=nhstepm;k++){              }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          if(i <= iagemax)
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            fprintf(ficresp,"\n");
         for(i=1;i<=nlstate;i++)          if(first==1)
           for(j=1;j<=nlstate;j++)            printf("Others in log...\n");
             vareij[i][j][(int)age] += doldm[i][j];          fprintf(ficlog,"\n");
       }        }
     }      }
     h=1;    }
     if (stepm >= YEARM) h=stepm/YEARM;    dateintmean=dateintsum/k2cpt; 
     fprintf(ficresvij,"%.0f ",age );   
     for(i=1; i<=nlstate;i++)    fclose(ficresp);
       for(j=1; j<=nlstate;j++){    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    free_vector(pp,1,nlstate);
       }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     fprintf(ficresvij,"\n");    /* End of Freq */
     free_matrix(gp,0,nhstepm,1,nlstate);  }
     free_matrix(gm,0,nhstepm,1,nlstate);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  /************ Prevalence ********************/
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  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)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {  
   } /* End age */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         in each health status at the date of interview (if between dateprev1 and dateprev2).
   free_vector(xp,1,npar);       We still use firstpass and lastpass as another selection.
   free_matrix(doldm,1,nlstate,1,npar);    */
   free_matrix(dnewm,1,nlstate,1,nlstate);   
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
 }    double ***freq; /* Frequencies */
     double *pp, **prop;
 /************ Variance of prevlim ******************/    double pos,posprop; 
 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)    double  y2; /* in fractional years */
 {    int iagemin, iagemax;
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    iagemin= (int) agemin;
   double **newm;    iagemax= (int) agemax;
   double **dnewm,**doldm;    /*pp=vector(1,nlstate);*/
   int i, j, nhstepm, hstepm;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   int k, cptcode;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   double *xp;    j1=0;
   double *gp, *gm;    
   double **gradg, **trgradg;    j=cptcoveff;
   double age,agelim;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   int theta;    
        for(k1=1; k1<=j;k1++){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficresvpl,"# Age");        j1++;
   for(i=1; i<=nlstate;i++)        
       fprintf(ficresvpl," %1d-%1d",i,i);        for (i=1; i<=nlstate; i++)  
   fprintf(ficresvpl,"\n");          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
   xp=vector(1,npar);       
   dnewm=matrix(1,nlstate,1,npar);        for (i=1; i<=imx; i++) { /* Each individual */
   doldm=matrix(1,nlstate,1,nlstate);          bool=1;
            if  (cptcovn>0) {
   hstepm=1*YEARM; /* Every year of age */            for (z1=1; z1<=cptcoveff; z1++) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   agelim = AGESUP;                bool=0;
   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 (bool==1) { 
     if (stepm >= YEARM) hstepm=1;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     gradg=matrix(1,npar,1,nlstate);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     gp=vector(1,nlstate);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     gm=vector(1,nlstate);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 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(theta=1; theta <=npar; theta++){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */                  /*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]]);*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       }                  prop[s[m][i]][iagemax+3] += weight[i]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                } 
       for(i=1;i<=nlstate;i++)              }
         gp[i] = prlim[i][i];            } /* end selection of waves */
              }
       for(i=1; i<=npar; i++) /* Computes gradient */        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for(i=iagemin; i <= iagemax+3; i++){  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          
       for(i=1;i<=nlstate;i++)          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         gm[i] = prlim[i][i];            posprop += prop[jk][i]; 
           } 
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          for(jk=1; jk <=nlstate ; jk++){     
     } /* End theta */            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
     trgradg =matrix(1,nlstate,1,npar);                probs[i][jk][j1]= prop[jk][i]/posprop;
               } 
     for(j=1; j<=nlstate;j++)            } 
       for(theta=1; theta <=npar; theta++)          }/* end jk */ 
         trgradg[j][theta]=gradg[theta][j];        }/* end i */ 
       } /* end i1 */
     for(i=1;i<=nlstate;i++)    } /* end k1 */
       varpl[i][(int)age] =0.;    
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    /*free_vector(pp,1,nlstate);*/
     for(i=1;i<=nlstate;i++)    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  }  /* End of prevalence */
   
     fprintf(ficresvpl,"%.0f ",age );  /************* Waves Concatenation ***************/
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  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)
     fprintf(ficresvpl,"\n");  {
     free_vector(gp,1,nlstate);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     free_vector(gm,1,nlstate);       Death is a valid wave (if date is known).
     free_matrix(gradg,1,npar,1,nlstate);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     free_matrix(trgradg,1,nlstate,1,npar);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   } /* End age */       and mw[mi+1][i]. dh depends on stepm.
        */
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    int i, mi, m;
   free_matrix(dnewm,1,nlstate,1,nlstate);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
 }    int first;
     int j, k=0,jk, ju, jl;
 /************ Variance of one-step probabilities  ******************/    double sum=0.;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    first=0;
 {    jmin=1e+5;
   int i, j;    jmax=-1;
   int k=0, cptcode;    jmean=0.;
   double **dnewm,**doldm;    for(i=1; i<=imx; i++){
   double *xp;      mi=0;
   double *gp, *gm;      m=firstpass;
   double **gradg, **trgradg;      while(s[m][i] <= nlstate){
   double age,agelim, cov[NCOVMAX];        if(s[m][i]>=1)
   int theta;          mw[++mi][i]=m;
   char fileresprob[FILENAMELENGTH];        if(m >=lastpass)
           break;
   strcpy(fileresprob,"prob");        else
   strcat(fileresprob,fileres);          m++;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      }/* end while */
     printf("Problem with resultfile: %s\n", fileresprob);      if (s[m][i] > nlstate){
   }        mi++;     /* Death is another wave */
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        /* if(mi==0)  never been interviewed correctly before death */
             /* Only death is a correct wave */
         mw[mi][i]=m;
   xp=vector(1,npar);      }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      wav[i]=mi;
        if(mi==0){
   cov[1]=1;        if(first==0){
   for (age=bage; age<=fage; age ++){          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
     cov[2]=age;          first=1;
     gradg=matrix(1,npar,1,9);        }
     trgradg=matrix(1,9,1,npar);        if(first==1){
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        }
          } /* end mi==0 */
     for(theta=1; theta <=npar; theta++){    } /* End individuals */
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for(i=1; i<=imx; i++){
            for(mi=1; mi<wav[i];mi++){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        if (stepm <=0)
              dh[mi][i]=1;
       k=0;        else{
       for(i=1; i<= (nlstate+ndeath); i++){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         for(j=1; j<=(nlstate+ndeath);j++){            if (agedc[i] < 2*AGESUP) {
            k=k+1;            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           gp[k]=pmmij[i][j];            if(j==0) j=1;  /* Survives at least one month after exam */
         }            k=k+1;
       }            if (j >= jmax) jmax=j;
             if (j <= jmin) jmin=j;
       for(i=1; i<=npar; i++)            sum=sum+j;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             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]);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            }
       k=0;          }
       for(i=1; i<=(nlstate+ndeath); i++){          else{
         for(j=1; j<=(nlstate+ndeath);j++){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           k=k+1;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           gm[k]=pmmij[i][j];            k=k+1;
         }            if (j >= jmax) jmax=j;
       }            else if (j <= jmin)jmin=j;
                  /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     }            sum=sum+j;
           }
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          jk= j/stepm;
       for(theta=1; theta <=npar; theta++)          jl= j -jk*stepm;
       trgradg[j][theta]=gradg[theta][j];          ju= j -(jk+1)*stepm;
            if(mle <=1){ 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            if(jl==0){
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);              dh[mi][i]=jk;
               bh[mi][i]=0;
      pmij(pmmij,cov,ncovmodel,x,nlstate);            }else{ /* We want a negative bias in order to only have interpolation ie
                     * at the price of an extra matrix product in likelihood */
      k=0;              dh[mi][i]=jk+1;
      for(i=1; i<=(nlstate+ndeath); i++){              bh[mi][i]=ju;
        for(j=1; j<=(nlstate+ndeath);j++){            }
          k=k+1;          }else{
          gm[k]=pmmij[i][j];            if(jl <= -ju){
         }              dh[mi][i]=jk;
      }              bh[mi][i]=jl;       /* bias is positive if real duration
                                         * is higher than the multiple of stepm and negative otherwise.
      /*printf("\n%d ",(int)age);                                   */
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            }
                    else{
               dh[mi][i]=jk+1;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              bh[mi][i]=ju;
      }*/            }
             if(dh[mi][i]==0){
   fprintf(ficresprob,"\n%d ",(int)age);              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          }
   }        } /* end if mle */
       } /* end wave */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    jmean=sum/k;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 }   }
  free_vector(xp,1,npar);  
 fclose(ficresprob);  /*********** Tricode ****************************/
  exit(0);  void tricode(int *Tvar, int **nbcode, int imx)
 }  {
     
 /***********************************************/    int Ndum[20],ij=1, k, j, i, maxncov=19;
 /**************** Main Program *****************/    int cptcode=0;
 /***********************************************/    cptcoveff=0; 
    
 /*int main(int argc, char *argv[])*/    for (k=0; k<maxncov; k++) Ndum[k]=0;
 int main()    for (k=1; k<=7; k++) ncodemax[k]=0;
 {  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   double agedeb, agefin,hf;                                 modality*/ 
   double agemin=1.e20, agemax=-1.e20;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
   double fret;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   double **xi,tmp,delta;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                          Tvar[j]. If V=sex and male is 0 and 
   double dum; /* Dummy variable */                                         female is 1, then  cptcode=1.*/
   double ***p3mat;      }
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];      for (i=0; i<=cptcode; i++) {
   char title[MAXLINE];        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 */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];      }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];  
   char filerest[FILENAMELENGTH];      ij=1; 
   char fileregp[FILENAMELENGTH];      for (i=1; i<=ncodemax[j]; i++) {
   char popfile[FILENAMELENGTH];        for (k=0; k<= maxncov; k++) {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          if (Ndum[k] != 0) {
   int firstobs=1, lastobs=10;            nbcode[Tvar[j]][ij]=k; 
   int sdeb, sfin; /* Status at beginning and end */            /* 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; */
   int c,  h , cpt,l;            
   int ju,jl, mi;            ij++;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          if (ij > ncodemax[j]) break; 
   int mobilav=0,popforecast=0;        }  
   int hstepm, nhstepm;      } 
   int *popage;/*boolprev=0 if date and zero if wave*/    }  
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;  
    for (k=0; k< maxncov; k++) Ndum[k]=0;
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;   for (i=1; i<=ncovmodel-2; i++) { 
   double **prlim;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   double *severity;     ij=Tvar[i];
   double ***param; /* Matrix of parameters */     Ndum[ij]++;
   double  *p;   }
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */   ij=1;
   double *delti; /* Scale */   for (i=1; i<= maxncov; i++) {
   double ***eij, ***vareij;     if((Ndum[i]!=0) && (i<=ncovcol)){
   double **varpl; /* Variances of prevalence limits by age */       Tvaraff[ij]=i; /*For printing */
   double *epj, vepp;       ij++;
   double kk1, kk2;     }
   double *popeffectif,*popcount;   }
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;   
   double yp,yp1,yp2;   cptcoveff=ij-1; /*Number of simple covariates*/
   }
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];  /*********** Health Expectancies ****************/
   
   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 )
   char z[1]="c", occ;  
 #include <sys/time.h>  {
 #include <time.h>    /* Health expectancies */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
      double age, agelim, hf;
   /* long total_usecs;    double ***p3mat,***varhe;
   struct timeval start_time, end_time;    double **dnewm,**doldm;
      double *xp;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   printf("\nIMACH, Version 0.7");  
   printf("\nEnter the parameter file name: ");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
 #ifdef windows    dnewm=matrix(1,nlstate*nlstate,1,npar);
   scanf("%s",pathtot);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   getcwd(pathcd, size);    
   /*cygwin_split_path(pathtot,path,optionfile);    fprintf(ficreseij,"# Health expectancies\n");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    fprintf(ficreseij,"# Age");
   /* cutv(path,optionfile,pathtot,'\\');*/    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
 split(pathtot, path,optionfile);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   chdir(path);    fprintf(ficreseij,"\n");
   replace(pathc,path);  
 #endif    if(estepm < stepm){
 #ifdef unix      printf ("Problem %d lower than %d\n",estepm, stepm);
   scanf("%s",optionfile);    }
 #endif    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
 /*-------- arguments in the command line --------*/     * 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
   strcpy(fileres,"r");     * we are calculating an estimate of the Life Expectancy assuming a linear 
   strcat(fileres, optionfile);     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
   /*---------arguments file --------*/     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {     * hypothesis. A more precise result, taking into account a more precise
     printf("Problem with optionfile %s\n",optionfile);     * curvature will be obtained if estepm is as small as stepm. */
     goto end;  
   }    /* 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. 
   strcpy(filereso,"o");       nhstepm is the number of hstepm from age to agelim 
   strcat(filereso,fileres);       nstepm is the number of stepm from age to agelin. 
   if((ficparo=fopen(filereso,"w"))==NULL) {       Look at hpijx to understand the reason of that which relies in memory size
     printf("Problem with Output resultfile: %s\n", filereso);goto end;       and note for a fixed period like estepm months */
   }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
   /* Reads comments: lines beginning with '#' */       means that if the survival funtion is printed only each two years of age and if
   while((c=getc(ficpar))=='#' && c!= EOF){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     ungetc(c,ficpar);       results. So we changed our mind and took the option of the best precision.
     fgets(line, MAXLINE, ficpar);    */
     puts(line);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     fputs(line,ficparo);  
   }    agelim=AGESUP;
   ungetc(c,ficpar);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* nhstepm age range expressed in number of stepm */
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);      /* if (stepm >= YEARM) hstepm=1;*/
 while((c=getc(ficpar))=='#' && c!= EOF){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     ungetc(c,ficpar);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fgets(line, MAXLINE, ficpar);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     puts(line);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     fputs(line,ficparo);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   }  
   ungetc(c,ficpar);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
          hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   covar=matrix(0,NCOVMAX,1,n);   
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
   ncovmodel=2+cptcovn;      /* Computing Variances of health expectancies */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
         for(theta=1; theta <=npar; theta++){
   /* Read guess parameters */        for(i=1; i<=npar; i++){ 
   /* Reads comments: lines beginning with '#' */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fgets(line, MAXLINE, ficpar);    
     puts(line);        cptj=0;
     fputs(line,ficparo);        for(j=1; j<= nlstate; j++){
   }          for(i=1; i<=nlstate; i++){
   ungetc(c,ficpar);            cptj=cptj+1;
              for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     for(i=1; i <=nlstate; i++)            }
     for(j=1; j <=nlstate+ndeath-1; j++){          }
       fscanf(ficpar,"%1d%1d",&i1,&j1);        }
       fprintf(ficparo,"%1d%1d",i1,j1);       
       printf("%1d%1d",i,j);       
       for(k=1; k<=ncovmodel;k++){        for(i=1; i<=npar; i++) 
         fscanf(ficpar," %lf",&param[i][j][k]);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         printf(" %lf",param[i][j][k]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficparo," %lf",param[i][j][k]);        
       }        cptj=0;
       fscanf(ficpar,"\n");        for(j=1; j<= nlstate; j++){
       printf("\n");          for(i=1;i<=nlstate;i++){
       fprintf(ficparo,"\n");            cptj=cptj+1;
     }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
   p=param[1][1];          }
          }
   /* Reads comments: lines beginning with '#' */        for(j=1; j<= nlstate*nlstate; j++)
   while((c=getc(ficpar))=='#' && c!= EOF){          for(h=0; h<=nhstepm-1; h++){
     ungetc(c,ficpar);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     fgets(line, MAXLINE, ficpar);          }
     puts(line);       } 
     fputs(line,ficparo);     
   }  /* End theta */
   ungetc(c,ficpar);  
        trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */       for(h=0; h<=nhstepm-1; h++)
   for(i=1; i <=nlstate; i++){        for(j=1; j<=nlstate*nlstate;j++)
     for(j=1; j <=nlstate+ndeath-1; j++){          for(theta=1; theta <=npar; theta++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);            trgradg[h][j][theta]=gradg[h][theta][j];
       printf("%1d%1d",i,j);       
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){       for(i=1;i<=nlstate*nlstate;i++)
         fscanf(ficpar,"%le",&delti3[i][j][k]);        for(j=1;j<=nlstate*nlstate;j++)
         printf(" %le",delti3[i][j][k]);          varhe[i][j][(int)age] =0.;
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }       printf("%d|",(int)age);fflush(stdout);
       fscanf(ficpar,"\n");       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       printf("\n");       for(h=0;h<=nhstepm-1;h++){
       fprintf(ficparo,"\n");        for(k=0;k<=nhstepm-1;k++){
     }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   delti=delti3[1][1];          for(i=1;i<=nlstate*nlstate;i++)
              for(j=1;j<=nlstate*nlstate;j++)
   /* Reads comments: lines beginning with '#' */              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);      /* Computing expectancies */
     puts(line);      for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);        for(j=1; j<=nlstate;j++)
   }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   ungetc(c,ficpar);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
              
   matcov=matrix(1,npar,1,npar);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);          }
     printf("%s",str);  
     fprintf(ficparo,"%s",str);      fprintf(ficreseij,"%3.0f",age );
     for(j=1; j <=i; j++){      cptj=0;
       fscanf(ficpar," %le",&matcov[i][j]);      for(i=1; i<=nlstate;i++)
       printf(" %.5le",matcov[i][j]);        for(j=1; j<=nlstate;j++){
       fprintf(ficparo," %.5le",matcov[i][j]);          cptj++;
     }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     fscanf(ficpar,"\n");        }
     printf("\n");      fprintf(ficreseij,"\n");
     fprintf(ficparo,"\n");     
   }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   for(i=1; i <=npar; i++)      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     for(j=i+1;j<=npar;j++)      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       matcov[i][j]=matcov[j][i];      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("\n");    }
     printf("\n");
     fprintf(ficlog,"\n");
     /*-------- data file ----------*/  
     if((ficres =fopen(fileres,"w"))==NULL) {    free_vector(xp,1,npar);
       printf("Problem with resultfile: %s\n", fileres);goto end;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     fprintf(ficres,"#%s\n",version);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
      }
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;  /************ Variance ******************/
     }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
   {
     n= lastobs;    /* Variance of health expectancies */
     severity = vector(1,maxwav);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     outcome=imatrix(1,maxwav+1,1,n);    /* double **newm;*/
     num=ivector(1,n);    double **dnewm,**doldm;
     moisnais=vector(1,n);    double **dnewmp,**doldmp;
     annais=vector(1,n);    int i, j, nhstepm, hstepm, h, nstepm ;
     moisdc=vector(1,n);    int k, cptcode;
     andc=vector(1,n);    double *xp;
     agedc=vector(1,n);    double **gp, **gm;  /* for var eij */
     cod=ivector(1,n);    double ***gradg, ***trgradg; /*for var eij */
     weight=vector(1,n);    double **gradgp, **trgradgp; /* for var p point j */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double *gpp, *gmp; /* for var p point j */
     mint=matrix(1,maxwav,1,n);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     anint=matrix(1,maxwav,1,n);    double ***p3mat;
     s=imatrix(1,maxwav+1,1,n);    double age,agelim, hf;
     adl=imatrix(1,maxwav+1,1,n);        double ***mobaverage;
     tab=ivector(1,NCOVMAX);    int theta;
     ncodemax=ivector(1,8);    char digit[4];
     char digitp[25];
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {    char fileresprobmorprev[FILENAMELENGTH];
       if ((i >= firstobs) && (i <=lastobs)) {  
            if(popbased==1){
         for (j=maxwav;j>=1;j--){      if(mobilav!=0)
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        strcpy(digitp,"-populbased-mobilav-");
           strcpy(line,stra);      else strcpy(digitp,"-populbased-nomobil-");
           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);    else 
         }      strcpy(digitp,"-stablbased-");
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    if (mobilav!=0) {
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    }
         for (j=ncov;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    strcpy(fileresprobmorprev,"prmorprev"); 
         }    sprintf(digit,"%-d",ij);
         num[i]=atol(stra);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
            strcat(fileresprobmorprev,digit); /* Tvar to be done */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           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;}*/    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         i=i+1;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }    }
     /* printf("ii=%d", ij);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
        scanf("%d",i);*/    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   imx=i-1; /* Number of individuals */    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   /* for (i=1; i<=imx; i++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      fprintf(ficresprobmorprev," p.%-d SE",j);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      for(i=1; i<=nlstate;i++)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }    }  
     fprintf(ficresprobmorprev,"\n");
     for (i=1; i<=imx; i++)    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   /* Calculation of the number of parameter from char model*/      exit(0);
   Tvar=ivector(1,15);    }
   Tprod=ivector(1,15);    else{
   Tvaraff=ivector(1,15);      fprintf(ficgp,"\n# Routine varevsij");
   Tvard=imatrix(1,15,1,2);    }
   Tage=ivector(1,15);          if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
          printf("Problem with html file: %s\n", optionfilehtm);
   if (strlen(model) >1){      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     j=0, j1=0, k1=1, k2=1;      exit(0);
     j=nbocc(model,'+');    }
     j1=nbocc(model,'*');    else{
     cptcovn=j+1;      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");
     cptcovprod=j1;      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
        }
        varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
       printf("Error. Non available option model=%s ",model);    fprintf(ficresvij,"# Age");
       goto end;    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
            fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     for(i=(j+1); i>=1;i--){    fprintf(ficresvij,"\n");
       cutv(stra,strb,modelsav,'+');  
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    xp=vector(1,npar);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    dnewm=matrix(1,nlstate,1,npar);
       /*scanf("%d",i);*/    doldm=matrix(1,nlstate,1,nlstate);
       if (strchr(strb,'*')) {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         cutv(strd,strc,strb,'*');    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         if (strcmp(strc,"age")==0) {  
           cptcovprod--;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           cutv(strb,stre,strd,'V');    gpp=vector(nlstate+1,nlstate+ndeath);
           Tvar[i]=atoi(stre);    gmp=vector(nlstate+1,nlstate+ndeath);
           cptcovage++;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             Tage[cptcovage]=i;    
             /*printf("stre=%s ", stre);*/    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
         else if (strcmp(strd,"age")==0) {    }
           cptcovprod--;    else  hstepm=estepm;   
           cutv(strb,stre,strc,'V');    /* For example we decided to compute the life expectancy with the smallest unit */
           Tvar[i]=atoi(stre);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           cptcovage++;       nhstepm is the number of hstepm from age to agelim 
           Tage[cptcovage]=i;       nstepm is the number of stepm from age to agelin. 
         }       Look at hpijx to understand the reason of that which relies in memory size
         else {       and note for a fixed period like k years */
           cutv(strb,stre,strc,'V');    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           Tvar[i]=ncov+k1;       survival function given by stepm (the optimization length). Unfortunately it
           cutv(strb,strc,strd,'V');       means that if the survival funtion is printed every two years of age and if
           Tprod[k1]=i;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           Tvard[k1][1]=atoi(strc);       results. So we changed our mind and took the option of the best precision.
           Tvard[k1][2]=atoi(stre);    */
           Tvar[cptcovn+k2]=Tvard[k1][1];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    agelim = AGESUP;
           for (k=1; k<=lastobs;k++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           k1++;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           k2=k2+2;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       }      gp=matrix(0,nhstepm,1,nlstate);
       else {      gm=matrix(0,nhstepm,1,nlstate);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');      for(theta=1; theta <=npar; theta++){
       Tvar[i]=atoi(strc);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       strcpy(modelsav,stra);          }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         scanf("%d",i);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }  
 }        if (popbased==1) {
            if(mobilav ==0){
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            for(i=1; i<=nlstate;i++)
   printf("cptcovprod=%d ", cptcovprod);              prlim[i][i]=probs[(int)age][i][ij];
   scanf("%d ",i);*/          }else{ /* mobilav */ 
     fclose(fic);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
     /*  if(mle==1){*/          }
     if (weightopt != 1) { /* Maximisation without weights*/        }
       for(i=1;i<=n;i++) weight[i]=1.0;    
     }        for(j=1; j<= nlstate; j++){
     /*-calculation of age at interview from date of interview and age at death -*/          for(h=0; h<=nhstepm; h++){
     agev=matrix(1,maxwav,1,imx);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
    for (i=1; i<=imx; i++)          }
      for(m=2; (m<= maxwav); m++)        }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        /* This for computing probability of death (h=1 means
          anint[m][i]=9999;           computed over hstepm matrices product = hstepm*stepm months) 
          s[m][i]=-1;           as a weighted average of prlim.
        }        */
            for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for (i=1; i<=imx; i++)  {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       for(m=1; (m<= maxwav); m++){        }    
         if(s[m][i] >0){        /* end probability of death */
           if (s[m][i] == nlstate+1) {  
             if(agedc[i]>0)        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
               if(moisdc[i]!=99 && andc[i]!=9999)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
               agev[m][i]=agedc[i];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             else {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               if (andc[i]!=9999){   
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        if (popbased==1) {
               agev[m][i]=-1;          if(mobilav ==0){
               }            for(i=1; i<=nlstate;i++)
             }              prlim[i][i]=probs[(int)age][i][ij];
           }          }else{ /* mobilav */ 
           else if(s[m][i] !=9){ /* Should no more exist */            for(i=1; i<=nlstate;i++)
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);              prlim[i][i]=mobaverage[(int)age][i][ij];
             if(mint[m][i]==99 || anint[m][i]==9999)          }
               agev[m][i]=1;        }
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];        for(j=1; j<= nlstate; j++){
               /*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++){
             }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
             else if(agev[m][i] >agemax){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
               agemax=agev[m][i];          }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        }
             }        /* This for computing probability of death (h=1 means
             /*agev[m][i]=anint[m][i]-annais[i];*/           computed over hstepm matrices product = hstepm*stepm months) 
             /*   agev[m][i] = age[i]+2*m;*/           as a weighted average of prlim.
           }        */
           else { /* =9 */        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             agev[m][i]=1;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
             s[m][i]=-1;           gmp[j] += prlim[i][i]*p3mat[i][j][1];
           }        }    
         }        /* end probability of death */
         else /*= 0 Unknown */  
           agev[m][i]=1;        for(j=1; j<= nlstate; j++) /* vareij */
       }          for(h=0; h<=nhstepm; h++){
                gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     }          }
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         if (s[m][i] > (nlstate+ndeath)) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
           printf("Error: Wrong value in nlstate or ndeath\n");          }
           goto end;  
         }      } /* End theta */
       }  
     }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
     free_vector(severity,1,maxwav);          for(theta=1; theta <=npar; theta++)
     free_imatrix(outcome,1,maxwav+1,1,n);            trgradg[h][j][theta]=gradg[h][theta][j];
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     /* free_matrix(mint,1,maxwav,1,n);        for(theta=1; theta <=npar; theta++)
        free_matrix(anint,1,maxwav,1,n);*/          trgradgp[j][theta]=gradgp[theta][j];
     free_vector(moisdc,1,n);    
     free_vector(andc,1,n);  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
          for(i=1;i<=nlstate;i++)
     wav=ivector(1,imx);        for(j=1;j<=nlstate;j++)
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          vareij[i][j][(int)age] =0.;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
          for(h=0;h<=nhstepm;h++){
     /* Concatenates waves */        for(k=0;k<=nhstepm;k++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
       Tcode=ivector(1,100);            for(j=1;j<=nlstate;j++)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       ncodemax[1]=1;        }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      }
          
    codtab=imatrix(1,100,1,10);      /* pptj */
    h=0;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
    m=pow(2,cptcoveff);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
        for(j=nlstate+1;j<=nlstate+ndeath;j++)
    for(k=1;k<=cptcoveff; k++){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
      for(i=1; i <=(m/pow(2,k));i++){          varppt[j][i]=doldmp[j][i];
        for(j=1; j <= ncodemax[k]; j++){      /* end ppptj */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      /*  x centered again */
            h++;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
            if (h>m) h=1;codtab[h][k]=j;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
          }   
        }      if (popbased==1) {
      }        if(mobilav ==0){
    }          for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
    /* Calculates basic frequencies. Computes observed prevalence at single age        }else{ /* mobilav */ 
        and prints on file fileres'p'. */          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
            }
          }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /* This for computing probability of death (h=1 means
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         as a weighted average of prlim.
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      */
            for(j=nlstate+1;j<=nlstate+ndeath;j++){
     /* For Powell, parameters are in a vector p[] starting at p[1]        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      }    
       /* end probability of death */
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
            fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     /*--------- results files --------------*/        for(i=1; i<=nlstate;i++){
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
          }
       } 
    jk=1;      fprintf(ficresprobmorprev,"\n");
    fprintf(ficres,"# Parameters\n");  
    printf("# Parameters\n");      fprintf(ficresvij,"%.0f ",age );
    for(i=1,jk=1; i <=nlstate; i++){      for(i=1; i<=nlstate;i++)
      for(k=1; k <=(nlstate+ndeath); k++){        for(j=1; j<=nlstate;j++){
        if (k != i)          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
          {        }
            printf("%d%d ",i,k);      fprintf(ficresvij,"\n");
            fprintf(ficres,"%1d%1d ",i,k);      free_matrix(gp,0,nhstepm,1,nlstate);
            for(j=1; j <=ncovmodel; j++){      free_matrix(gm,0,nhstepm,1,nlstate);
              printf("%f ",p[jk]);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
              fprintf(ficres,"%f ",p[jk]);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
              jk++;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            }    } /* End age */
            printf("\n");    free_vector(gpp,nlstate+1,nlstate+ndeath);
            fprintf(ficres,"\n");    free_vector(gmp,nlstate+1,nlstate+ndeath);
          }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
      }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
  if(mle==1){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     /* Computing hessian and covariance matrix */    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     ftolhess=ftol; /* Usually correct */  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     hesscov(matcov, p, npar, delti, ftolhess, func);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
  }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficres,"# Scales\n");    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
     printf("# Scales\n");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
      for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
       for(j=1; j <=nlstate+ndeath; j++){    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
         if (j!=i) {    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
           fprintf(ficres,"%1d%1d",i,j);    /*  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("%1d%1d",i,j);  */
           for(k=1; k<=ncovmodel;k++){    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);    free_vector(xp,1,npar);
             jk++;    free_matrix(doldm,1,nlstate,1,nlstate);
           }    free_matrix(dnewm,1,nlstate,1,npar);
           printf("\n");    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           fprintf(ficres,"\n");    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      }    fclose(ficresprobmorprev);
        fclose(ficgp);
     k=1;    fclose(fichtm);
     fprintf(ficres,"# Covariance\n");  }  
     printf("# Covariance\n");  
     for(i=1;i<=npar;i++){  /************ Variance of prevlim ******************/
       /*  if (k>nlstate) k=1;  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
       i1=(i-1)/(ncovmodel*nlstate)+1;  {
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    /* Variance of prevalence limit */
       printf("%s%d%d",alph[k],i1,tab[i]);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       fprintf(ficres,"%3d",i);    double **newm;
       printf("%3d",i);    double **dnewm,**doldm;
       for(j=1; j<=i;j++){    int i, j, nhstepm, hstepm;
         fprintf(ficres," %.5e",matcov[i][j]);    int k, cptcode;
         printf(" %.5e",matcov[i][j]);    double *xp;
       }    double *gp, *gm;
       fprintf(ficres,"\n");    double **gradg, **trgradg;
       printf("\n");    double age,agelim;
       k++;    int theta;
     }     
        fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresvpl,"# Age");
       ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
       fgets(line, MAXLINE, ficpar);        fprintf(ficresvpl," %1d-%1d",i,i);
       puts(line);    fprintf(ficresvpl,"\n");
       fputs(line,ficparo);  
     }    xp=vector(1,npar);
     ungetc(c,ficpar);    dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    
        hstepm=1*YEARM; /* Every year of age */
     if (fage <= 2) {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       bage = agemin;    agelim = AGESUP;
       fage = agemax;    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;
     fprintf(ficres,"# agemin agemax for life expectancy.\n");      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      gp=vector(1,nlstate);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      gm=vector(1,nlstate);
    
     while((c=getc(ficpar))=='#' && c!= EOF){      for(theta=1; theta <=npar; theta++){
     ungetc(c,ficpar);        for(i=1; i<=npar; i++){ /* Computes gradient */
     fgets(line, MAXLINE, ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     puts(line);        }
     fputs(line,ficparo);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }        for(i=1;i<=nlstate;i++)
   ungetc(c,ficpar);          gp[i] = prlim[i][i];
        
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);        for(i=1; i<=npar; i++) /* Computes gradient */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
              for(i=1;i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){          gm[i] = prlim[i][i];
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);        for(i=1;i<=nlstate;i++)
     puts(line);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     fputs(line,ficparo);      } /* End theta */
   }  
   ungetc(c,ficpar);      trgradg =matrix(1,nlstate,1,npar);
    
       for(j=1; j<=nlstate;j++)
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        for(theta=1; theta <=npar; theta++)
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          trgradg[j][theta]=gradg[theta][j];
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);      for(i=1;i<=nlstate;i++)
    fprintf(ficparo,"pop_based=%d\n",popbased);          varpl[i][(int)age] =0.;
    fprintf(ficres,"pop_based=%d\n",popbased);        matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1;i<=nlstate;i++)
     ungetc(c,ficpar);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     fgets(line, MAXLINE, ficpar);  
     puts(line);      fprintf(ficresvpl,"%.0f ",age );
     fputs(line,ficparo);      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   ungetc(c,ficpar);      fprintf(ficresvpl,"\n");
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);      free_vector(gp,1,nlstate);
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);      free_vector(gm,1,nlstate);
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);    } /* End age */
   
  /*------------ gnuplot -------------*/    free_vector(xp,1,npar);
 chdir(pathcd);    free_matrix(doldm,1,nlstate,1,npar);
   if((ficgp=fopen("graph.plt","w"))==NULL) {    free_matrix(dnewm,1,nlstate,1,nlstate);
     printf("Problem with file graph.gp");goto end;  
   }  }
 #ifdef windows  
   fprintf(ficgp,"cd \"%s\" \n",pathc);  /************ Variance of one-step probabilities  ******************/
 #endif  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=pow(2,cptcoveff);  {
      int i, j=0,  i1, k1, l1, t, tj;
  /* 1eme*/    int k2, l2, j1,  z1;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    int k=0,l, cptcode;
    for (k1=1; k1<= m ; k1 ++) {    int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
 #ifdef windows    double **dnewm,**doldm;
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);    double *xp;
 #endif    double *gp, *gm;
 #ifdef unix    double **gradg, **trgradg;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    double **mu;
 #endif    double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
 for (i=1; i<= nlstate ; i ++) {    int theta;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    char fileresprob[FILENAMELENGTH];
   else fprintf(ficgp," \%%*lf (\%%*lf)");    char fileresprobcov[FILENAMELENGTH];
 }    char fileresprobcor[FILENAMELENGTH];
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  
     for (i=1; i<= nlstate ; i ++) {    double ***varpij;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    strcpy(fileresprob,"prob"); 
 }    strcat(fileresprob,fileres);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      for (i=1; i<= nlstate ; i ++) {      printf("Problem with resultfile: %s\n", fileresprob);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }      strcpy(fileresprobcov,"probcov"); 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    strcat(fileresprobcov,fileres);
 #ifdef unix    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 fprintf(ficgp,"\nset ter gif small size 400,300");      printf("Problem with resultfile: %s\n", fileresprobcov);
 #endif      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
    }    strcpy(fileresprobcor,"probcor"); 
   }    strcat(fileresprobcor,fileres);
   /*2 eme*/    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
   for (k1=1; k1<= m ; k1 ++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    }
        printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     for (i=1; i<= nlstate+1 ; i ++) {    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       k=2*i;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       for (j=1; j<= nlstate+1 ; j ++) {    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    fprintf(ficresprob,"# Age");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficresprobcov,"# Age");
       for (j=1; j<= nlstate+1 ; j ++) {    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficresprobcov,"# Age");
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");    for(i=1; i<=nlstate;i++)
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(j=1; j<=(nlstate+ndeath);j++){
       for (j=1; j<= nlstate+1 ; j ++) {        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficresprobcor," p%1d-%1d ",i,j);
 }        }  
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");   /* fprintf(ficresprob,"\n");
       else fprintf(ficgp,"\" t\"\" w l 0,");    fprintf(ficresprobcov,"\n");
     }    fprintf(ficresprobcor,"\n");
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);   */
   }   xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   /*3eme*/    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   for (k1=1; k1<= m ; k1 ++) {    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    first=1;
       k=2+nlstate*(cpt-1);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       for (i=1; i< nlstate ; i ++) {      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);      exit(0);
       }    }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    else{
     }      fprintf(ficgp,"\n# Routine varprob");
   }    }
      if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   /* CV preval stat */      printf("Problem with html file: %s\n", optionfilehtm);
   for (k1=1; k1<= m ; k1 ++) {      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     for (cpt=1; cpt<nlstate ; cpt ++) {      exit(0);
       k=3;    }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    else{
       for (i=1; i< nlstate ; i ++)      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         fprintf(ficgp,"+$%d",k+i+1);      fprintf(fichtm,"\n");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
            fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       l=3+(nlstate+ndeath)*cpt;      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,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;    }
         fprintf(ficgp,"+$%d",l+i+1);  
       }    cov[1]=1;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      tj=cptcoveff;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     }    j1=0;
   }      for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
   /* proba elementaires */        j1++;
    for(i=1,jk=1; i <=nlstate; i++){        if  (cptcovn>0) {
     for(k=1; k <=(nlstate+ndeath); k++){          fprintf(ficresprob, "\n#********** Variable "); 
       if (k != i) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for(j=1; j <=ncovmodel; j++){          fprintf(ficresprob, "**********\n#\n");
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/          fprintf(ficresprobcov, "\n#********** Variable "); 
           /*fprintf(ficgp,"%s",alph[1]);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          fprintf(ficresprobcov, "**********\n#\n");
           jk++;          
           fprintf(ficgp,"\n");          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, "**********\n#\n");
     }          
     }          
           fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   for(jk=1; jk <=m; jk++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
    i=1;          
    for(k2=1; k2<=nlstate; k2++) {          fprintf(ficresprobcor, "\n#********** Variable ");    
      k3=i;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      for(k=1; k<=(nlstate+ndeath); k++) {          fprintf(ficresprobcor, "**********\n#");    
        if (k != k2){        }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        
 ij=1;        for (age=bage; age<=fage; age ++){ 
         for(j=3; j <=ncovmodel; j++) {          cov[2]=age;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          for (k=1; k<=cptcovn;k++) {
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
             ij++;          }
           }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           else          for (k=1; k<=cptcovprod;k++)
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         }          
           fprintf(ficgp,")/(1");          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                  trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         for(k1=1; k1 <=nlstate; k1++){            gp=vector(1,(nlstate)*(nlstate+ndeath));
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          gm=vector(1,(nlstate)*(nlstate+ndeath));
 ij=1;      
           for(j=3; j <=ncovmodel; j++){          for(theta=1; theta <=npar; theta++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            for(i=1; i<=npar; i++)
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             ij++;            
           }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           else            
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            k=0;
           }            for(i=1; i<= (nlstate); i++){
           fprintf(ficgp,")");              for(j=1; j<=(nlstate+ndeath);j++){
         }                k=k+1;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);                gp[k]=pmmij[i][j];
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              }
         i=i+ncovmodel;            }
        }            
      }            for(i=1; i<=npar; i++)
    }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      
   }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                k=0;
   fclose(ficgp);            for(i=1; i<=(nlstate); i++){
                  for(j=1; j<=(nlstate+ndeath);j++){
 chdir(path);                k=k+1;
                    gm[k]=pmmij[i][j];
     free_ivector(wav,1,imx);              }
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            }
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);         
     free_ivector(num,1,n);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     free_vector(agedc,1,n);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     /*free_matrix(covar,1,NCOVMAX,1,n);*/          }
     fclose(ficparo);  
     fclose(ficres);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     /*  }*/            for(theta=1; theta <=npar; theta++)
                  trgradg[j][theta]=gradg[theta][j];
    /*________fin mle=1_________*/          
              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);
            free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     /* No more information from the sample is required now */          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   /* Reads comments: lines beginning with '#' */          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);          pmij(pmmij,cov,ncovmodel,x,nlstate);
     puts(line);          
     fputs(line,ficparo);          k=0;
   }          for(i=1; i<=(nlstate); i++){
   ungetc(c,ficpar);            for(j=1; j<=(nlstate+ndeath);j++){
                k=k+1;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              mu[k][(int) age]=pmmij[i][j];
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);            }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          }
 /*--------- index.htm --------*/          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   strcpy(optionfilehtm,optionfile);              varpij[i][j][(int)age] = doldm[i][j];
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          /*printf("\n%d ",(int)age);
     printf("Problem with %s \n",optionfilehtm);goto end;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   }            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">            }*/
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  
 Total number of observations=%d <br>          fprintf(ficresprob,"\n%d ",(int)age);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          fprintf(ficresprobcov,"\n%d ",(int)age);
 <hr  size=\"2\" color=\"#EC5E5E\">          fprintf(ficresprobcor,"\n%d ",(int)age);
 <li>Outputs files<br><br>\n  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          }
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          i=0;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>          for (k=1; k<=(nlstate);k++){
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>            for (l=1; l<=(nlstate+ndeath);l++){ 
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>              i=i++;
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
  fprintf(fichtm," <li>Graphs</li><p>");              for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
  m=cptcoveff;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              }
             }
  j1=0;          }/* end of loop for state */
  for(k1=1; k1<=m;k1++){        } /* end of loop for age */
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;        /* Confidence intervalle of pij  */
        if (cptcovn > 0) {        /*
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          fprintf(ficgp,"\nset noparametric;unset label");
          for (cpt=1; cpt<=cptcoveff;cpt++)          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
        }          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
        for(cpt=1; cpt<nlstate;cpt++){        */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
        }        first1=1;
     for(cpt=1; cpt<=nlstate;cpt++) {        for (k2=1; k2<=(nlstate);k2++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
 interval) in state (%d): v%s%d%d.gif <br>            if(l2==k2) continue;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              j=(k2-1)*(nlstate+ndeath)+l2;
      }            for (k1=1; k1<=(nlstate);k1++){
      for(cpt=1; cpt<=nlstate;cpt++) {              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>                if(l1==k1) continue;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                i=(k1-1)*(nlstate+ndeath)+l1;
      }                if(i<=j) continue;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and                for (age=bage; age<=fage; age ++){ 
 health expectancies in states (1) and (2): e%s%d.gif<br>                  if ((int)age %5==0){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
 fprintf(fichtm,"\n</body>");                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
    }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
  }                    mu1=mu[i][(int) age]/stepm*YEARM ;
 fclose(fichtm);                    mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
   /*--------------- Prevalence limit --------------*/                    /* Computing eigen value of matrix of covariance */
                      lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   strcpy(filerespl,"pl");                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   strcat(filerespl,fileres);                    /* Eigen vectors */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                    /*v21=sqrt(1.-v11*v11); *//* error */
   }                    v21=(lc1-v1)/cv12*v11;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                    v12=-v21;
   fprintf(ficrespl,"#Prevalence limit\n");                    v22=v11;
   fprintf(ficrespl,"#Age ");                    tnalp=v21/v11;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                    if(first1==1){
   fprintf(ficrespl,"\n");                      first1=0;
                        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);
   prlim=matrix(1,nlstate,1,nlstate);                    }
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    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);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    /*printf(fignu*/
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                    if(first==1){
   k=0;                      first=0;
   agebase=agemin;                      fprintf(ficgp,"\nset parametric;unset label");
   agelim=agemax;                      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);
   ftolpl=1.e-10;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   i1=cptcoveff;                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
   if (cptcovn < 1){i1=1;}                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   for(cptcov=1;cptcov<=i1;cptcov++){                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         k=k+1;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                      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",\
         fprintf(ficrespl,"\n#******");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         for(j=1;j<=cptcoveff;j++)                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    }else{
         fprintf(ficrespl,"******\n");                      first=0;
                              fprintf(fichtm," %d (%.3f),",(int) age, c12);
         for (age=agebase; age<=agelim; age++){                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           fprintf(ficrespl,"%.0f",age );                      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",\
           for(i=1; i<=nlstate;i++)                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
           fprintf(ficrespl," %.5f", prlim[i][i]);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           fprintf(ficrespl,"\n");                    }/* if first */
         }                  } /* age mod 5 */
       }                } /* end loop age */
     }                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   fclose(ficrespl);                first=1;
               } /*l12 */
   /*------------- h Pij x at various ages ------------*/            } /* k12 */
            } /*l1 */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        }/* k1 */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      } /* loop covariates */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    }
   }    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   printf("Computing pij: result on file '%s' \n", filerespij);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      free_vector(xp,1,npar);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fclose(ficresprob);
   /*if (stepm<=24) stepsize=2;*/    fclose(ficresprobcov);
     fclose(ficresprobcor);
   agelim=AGESUP;    fclose(ficgp);
   hstepm=stepsize*YEARM; /* Every year of age */    fclose(fichtm);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  }
    
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){  /******************* Printing html file ***********/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       k=k+1;                    int lastpass, int stepm, int weightopt, char model[],\
         fprintf(ficrespij,"\n#****** ");                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
         for(j=1;j<=cptcoveff;j++)                    int popforecast, int estepm ,\
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    double jprev1, double mprev1,double anprev1, \
         fprintf(ficrespij,"******\n");                    double jprev2, double mprev2,double anprev2){
            int jj1, k1, i1, cpt;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    /*char optionfilehtm[FILENAMELENGTH];*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      printf("Problem with %s \n",optionfilehtm), exit(0);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
           oldm=oldms;savm=savms;    }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
           for(i=1; i<=nlstate;i++)   - 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
             for(j=1; j<=nlstate+ndeath;j++)   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
               fprintf(ficrespij," %1d-%1d",i,j);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
           fprintf(ficrespij,"\n");   - Life expectancies by age and initial health status (estepm=%2d months): 
           for (h=0; h<=nhstepm; h++){     <a href=\"e%s\">e%s</a> <br>\n</li>", \
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");   m=cptcoveff;
           }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");   jj1=0;
         }   for(k1=1; k1<=m;k1++){
     }     for(i1=1; i1<=ncodemax[k1];i1++){
   }       jj1++;
        if (cptcovn > 0) {
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
   fclose(ficrespij);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   /*---------- Forecasting ------------------*/       }
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;       /* 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>
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   strcpy(fileresf,"f");  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
   strcat(fileresf,fileres);         /* Stable prevalence in each health state */
   if((ficresf=fopen(fileresf,"w"))==NULL) {         for(cpt=1; cpt<nlstate;cpt++){
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;           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);
   printf("Computing forecasting: result on file '%s' \n", fileresf);         }
        for(cpt=1; cpt<=nlstate;cpt++) {
   free_matrix(mint,1,maxwav,1,n);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   free_matrix(anint,1,maxwav,1,n);  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   free_matrix(agev,1,maxwav,1,imx);       }
   /* Mobile average */       fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
      } /* end i1 */
   if (mobilav==1) {   }/* End k1 */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   fprintf(fichtm,"</ul>");
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)  
       for (i=1; i<=nlstate;i++)  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
           mobaverage[(int)agedeb][i][cptcod]=0.;   - 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
     for (agedeb=bage+4; agedeb<=fage; agedeb++){   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
       for (i=1; i<=nlstate;i++){   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
           for (cpt=0;cpt<=4;cpt++){   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];   - 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);
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  /*  if(popforecast==1) fprintf(fichtm,"\n */
         }  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
       }  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     }    /*      <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); */
   stepsize=(int) (stepm+YEARM-1)/YEARM;  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   if (stepm<=12) stepsize=1;  
    m=cptcoveff;
   agelim=AGESUP;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   /*hstepm=stepsize*YEARM; *//* Every year of age */  
   hstepm=1;   jj1=0;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */   for(k1=1; k1<=m;k1++){
   yp1=modf(dateintmean,&yp);     for(i1=1; i1<=ncodemax[k1];i1++){
   anprojmean=yp;       jj1++;
   yp2=modf((yp1*12),&yp);       if (cptcovn > 0) {
   mprojmean=yp;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   yp1=modf((yp2*30.5),&yp);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   jprojmean=yp;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   fprintf(ficresf,"Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   if (popforecast==1) {       for(cpt=1; cpt<=nlstate;cpt++) {
     if((ficpop=fopen(popfile,"r"))==NULL)    {         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
       printf("Problem with population file : %s\n",popfile);goto end;  interval) in state (%d): v%s%d%d.png <br>
     }  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     popage=ivector(0,AGESUP);       }
     popeffectif=vector(0,AGESUP);     } /* end i1 */
     popcount=vector(0,AGESUP);   }/* End k1 */
    fprintf(fichtm,"</ul>");
     i=1;    fclose(fichtm);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)  }
       {  
         i=i+1;  /******************* Gnuplot file **************/
       }  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     imx=i;  
        int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    int ng;
   }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }
       k=k+1;  
       fprintf(ficresf,"\n#******");    /*#ifdef windows */
       for(j=1;j<=cptcoveff;j++) {      fprintf(ficgp,"cd \"%s\" \n",pathc);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /*#endif */
       }  m=pow(2,cptcoveff);
       fprintf(ficresf,"******\n");    
       fprintf(ficresf,"# StartingAge FinalAge");   /* 1eme*/
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    for (cpt=1; cpt<= nlstate ; cpt ++) {
       if (popforecast==1)  fprintf(ficresf," [Population]");     for (k1=1; k1<= m ; k1 ++) {
         fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       for (cpt=0; cpt<=1;cpt++) {       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
         fprintf(ficresf,"\n");  
   fprintf(ficresf,"\nForecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);         for (i=1; i<= nlstate ; i ++) {
       for (agedeb=(fage-(1/12.)); agedeb>=(bage-(1/12.)); agedeb--){ /* If stepm=6 months */         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         nhstepm = nhstepm/hstepm;       }
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/       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 ++) {
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         oldm=oldms;savm=savms;         else fprintf(ficgp," \%%*lf (\%%*lf)");
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         } 
                       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
         for (h=0; h<=nhstepm; h++){       for (i=1; i<= nlstate ; i ++) {
           if (h==(int) (calagedate+12*cpt)) {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             fprintf(ficresf,"h=%d ", h);         else fprintf(ficgp," \%%*lf (\%%*lf)");
             fprintf(ficresf,"\n %f %f ",agedeb,agedeb+h*hstepm/YEARM*stepm);       }  
           }       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
           for(j=1; j<=nlstate+ndeath;j++) {     }
             kk1=0.;kk2=0;    }
             for(i=1; i<=nlstate;i++) {            /*2 eme*/
               if (mobilav==1)    
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];    for (k1=1; k1<= m ; k1 ++) { 
               else {      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
                 /*  fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h],probs[(int)(agedeb)+1][i][cptcod]);*/      
               }      for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
             }        for (j=1; j<= nlstate+1 ; j ++) {
                    if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
             if (h==(int)(calagedate+12*cpt)){          else fprintf(ficgp," \%%*lf (\%%*lf)");
               fprintf(ficresf," %.3f", kk1);        }   
                      if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
             }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
           }        for (j=1; j<= nlstate+1 ; j ++) {
         }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       }        }   
       }        fprintf(ficgp,"\" t\"\" w l 0,");
     }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
   }        for (j=1; j<= nlstate+1 ; j ++) {
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   if (popforecast==1) {          else fprintf(ficgp," \%%*lf (\%%*lf)");
     free_ivector(popage,0,AGESUP);        }   
     free_vector(popeffectif,0,AGESUP);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     free_vector(popcount,0,AGESUP);        else fprintf(ficgp,"\" t\"\" w l 0,");
   }      }
   free_imatrix(s,1,maxwav+1,1,n);    }
   free_vector(weight,1,n);    
   fclose(ficresf);    /*3eme*/
   /*---------- Health expectancies and variances ------------*/    
     for (k1=1; k1<= m ; k1 ++) { 
   strcpy(filerest,"t");      for (cpt=1; cpt<= nlstate ; cpt ++) {
   strcat(filerest,fileres);        k=2+nlstate*(2*cpt-2);
   if((ficrest=fopen(filerest,"w"))==NULL) {        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
   }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   strcpy(filerese,"e");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   strcat(filerese,fileres);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   if((ficreseij=fopen(filerese,"w"))==NULL) {          
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        */
   }        for (i=1; i< nlstate ; i ++) {
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          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);
           
  strcpy(fileresv,"v");        } 
   strcat(fileresv,fileres);      }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    
   }    /* CV preval stable (period) */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
   k=0;        k=3;
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
       k=k+1;        
       fprintf(ficrest,"\n#****** ");        for (i=1; i<= nlstate ; i ++)
       for(j=1;j<=cptcoveff;j++)          fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
       fprintf(ficrest,"******\n");        
         l=3+(nlstate+ndeath)*cpt;
       fprintf(ficreseij,"\n#****** ");        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
       for(j=1;j<=cptcoveff;j++)        for (i=1; i< nlstate ; i ++) {
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          l=3+(nlstate+ndeath)*cpt;
       fprintf(ficreseij,"******\n");          fprintf(ficgp,"+$%d",l+i+1);
         }
       fprintf(ficresvij,"\n#****** ");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       for(j=1;j<=cptcoveff;j++)      } 
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    }  
       fprintf(ficresvij,"******\n");    
     /* proba elementaires */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for(i=1,jk=1; i <=nlstate; i++){
       oldm=oldms;savm=savms;      for(k=1; k <=(nlstate+ndeath); k++){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          if (k != i) {
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for(j=1; j <=ncovmodel; j++){
       oldm=oldms;savm=savms;            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            jk++; 
                  fprintf(ficgp,"\n");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        }
       fprintf(ficrest,"\n");      }
             }
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       epj=vector(1,nlstate+1);       for(jk=1; jk <=m; jk++) {
       for(age=bage; age <=fage ;age++){         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);         if (ng==2)
         if (popbased==1) {           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           for(i=1; i<=nlstate;i++)         else
             prlim[i][i]=probs[(int)age][i][k];           fprintf(ficgp,"\nset title \"Probability\"\n");
         }         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
                 i=1;
         fprintf(ficrest," %.0f",age);         for(k2=1; k2<=nlstate; k2++) {
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){           k3=i;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {           for(k=1; k<=(nlstate+ndeath); k++) {
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];             if (k != k2){
           }               if(ng==2)
           epj[nlstate+1] +=epj[j];                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
         }               else
         for(i=1, vepp=0.;i <=nlstate;i++)                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
           for(j=1;j <=nlstate;j++)               ij=1;
             vepp += vareij[i][j][(int)age];               for(j=3; j <=ncovmodel; j++) {
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
         for(j=1;j <=nlstate;j++){                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));                   ij++;
         }                 }
         fprintf(ficrest,"\n");                 else
       }                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     }               }
   }               fprintf(ficgp,")/(1");
                       
                       for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
  fclose(ficreseij);                 for(j=3; j <=ncovmodel; j++){
  fclose(ficresvij);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   fclose(ficrest);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   fclose(ficpar);                     ij++;
   free_vector(epj,1,nlstate+1);                   }
   /*  scanf("%d ",i); */                   else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   /*------- Variance limit prevalence------*/                   }
                  fprintf(ficgp,")");
 strcpy(fileresvpl,"vpl");               }
   strcat(fileresvpl,fileres);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);               i=i+ncovmodel;
     exit(0);             }
   }           } /* end k */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);         } /* end k2 */
        } /* end jk */
  k=0;     } /* end ng */
  for(cptcov=1;cptcov<=i1;cptcov++){     fclose(ficgp); 
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  }  /* end gnuplot */
      k=k+1;  
      fprintf(ficresvpl,"\n#****** ");  
      for(j=1;j<=cptcoveff;j++)  /*************** Moving average **************/
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
      fprintf(ficresvpl,"******\n");  
          int i, cpt, cptcod;
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    int modcovmax =1;
      oldm=oldms;savm=savms;    int mobilavrange, mob;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    double age;
    }  
  }    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
   fclose(ficresvpl);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   /*---------- End : free ----------------*/    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      if(mobilav==1) mobilavrange=5; /* default */
        else mobilavrange=mobilav;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      for (age=bage; age<=fage; age++)
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        for (i=1; i<=nlstate;i++)
            for (cptcod=1;cptcod<=modcovmax;cptcod++)
              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      /* We keep the original values on the extreme ages bage, fage and for 
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);         we use a 5 terms etc. until the borders are no more concerned. 
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      */ 
        for (mob=3;mob <=mobilavrange;mob=mob+2){
   free_matrix(matcov,1,npar,1,npar);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   free_vector(delti,1,npar);          for (i=1; i<=nlstate;i++){
              for (cptcod=1;cptcod<=modcovmax;cptcod++){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
   printf("End of Imach\n");                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                  }
   /* 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);*/              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   /*printf("Total time was %d uSec.\n", total_usecs);*/            }
   /*------ End -----------*/          }
         }/* end age */
       }/* end mob */
  end:    }else return -1;
 #ifdef windows    return 0;
  chdir(pathcd);  }/* End movingaverage */
 #endif  
    
  system("..\\gp37mgw\\wgnuplot graph.plt");  /************** 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){
 #ifdef windows    /* proj1, year, month, day of starting projection 
   while (z[0] != 'q') {       agemin, agemax range of age
     chdir(pathcd);       dateprev1 dateprev2 range of dates during which prevalence is computed
     printf("\nType e to edit output files, c to start again, and q for exiting: ");       anproj2 year of en of projection (same day and month as proj1).
     scanf("%s",z);    */
     if (z[0] == 'c') system("./imach");    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     else if (z[0] == 'e') {    int *popage;
       chdir(path);    double agec; /* generic age */
       system(optionfilehtm);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     }    double *popeffectif,*popcount;
     else if (z[0] == 'q') exit(0);    double ***p3mat;
   }    double ***mobaverage;
 #endif    char fileresf[FILENAMELENGTH];
 }  
     agelim=AGESUP;
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1;
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     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 */
   }
   
   

Removed from v.1.19  
changed lines
  Added in v.1.78


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