Diff for /imach/src/imach.c between versions 1.39 and 1.63

version 1.39, 2002/04/05 15:45:00 version 1.63, 2002/11/20 17:35:59
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month or quarter trimester,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is model as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/    **********************************************************************/
     
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "wgnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define NCOVMAX 8 /* Maximum number of covariates */
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /* Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
   #ifdef windows
   #define DIRSEPARATOR '\\'
 int erreur; /* Error number */  #define ODIRSEPARATOR '/'
 int nvar;  #else
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define DIRSEPARATOR '/'
 int npar=NPARMAX;  #define ODIRSEPARATOR '\\'
 int nlstate=2; /* Number of live states */  #endif
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  char version[80]="Imach version 0.9, November 2002, INED-EUROREVES ";
 int popbased=0;  int erreur; /* Error number */
   int nvar;
 int *wav; /* Number of waves for this individuual 0 is possible */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int maxwav; /* Maxim number of waves */  int npar=NPARMAX;
 int jmin, jmax; /* min, max spacing between 2 waves */  int nlstate=2; /* Number of live states */
 int mle, weightopt;  int ndeath=1; /* Number of dead states */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int popbased=0;
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int *wav; /* Number of waves for this individuual 0 is possible */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int maxwav; /* Maxim number of waves */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  int jmin, jmax; /* min, max spacing between 2 waves */
 FILE *ficgp,*ficresprob,*ficpop;  int mle, weightopt;
 FILE *ficreseij;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   char filerese[FILENAMELENGTH];  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  FILE  *ficresvij;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   char fileresv[FILENAMELENGTH];             * wave mi and wave mi+1 is not an exact multiple of stepm. */
  FILE  *ficresvpl;  double jmean; /* Mean space between 2 waves */
   char fileresvpl[FILENAMELENGTH];  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define NR_END 1  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define FREE_ARG char*  FILE *ficlog;
 #define FTOL 1.0e-10  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 #define NRANSI  FILE *fichtm; /* Html File */
 #define ITMAX 200  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 #define TOL 2.0e-4  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 #define CGOLD 0.3819660  FILE  *ficresvpl;
 #define ZEPS 1.0e-10  char fileresvpl[FILENAMELENGTH];
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define GOLD 1.618034  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 static double maxarg1,maxarg2;  char filerest[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char fileregp[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char popfile[FILENAMELENGTH];
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  
   #define NR_END 1
 static double sqrarg;  #define FREE_ARG char*
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define FTOL 1.0e-10
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   #define NRANSI 
 int imx;  #define ITMAX 200 
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  #define TOL 2.0e-4 
   
 int estepm;  #define CGOLD 0.3819660 
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define GOLD 1.618034 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define GLIMIT 100.0 
 double **pmmij, ***probs, ***mobaverage;  #define TINY 1.0e-20 
 double dateintmean=0;  
   static double maxarg1,maxarg2;
 double *weight;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 int **s; /* Status */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double *agedc, **covar, idx;    
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /**************** split *************************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  int imx; 
    char *s;                             /* pointer */  int stepm;
    int  l1, l2;                         /* length counters */  /* Stepm, step in month: minimum step interpolation*/
   
    l1 = strlen( path );                 /* length of path */  int estepm;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  int m,nb;
 #else  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    s = strrchr( path, '/' );            /* find last / */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 #endif  double **pmmij, ***probs;
    if ( s == NULL ) {                   /* no directory, so use current */  double dateintmean=0;
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  double *weight;
   int **s; /* Status */
       if ( getwd( dirc ) == NULL ) {  double *agedc, **covar, idx;
 #else  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       extern char       *getcwd( );  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  double ftolhess; /* Tolerance for computing hessian */
 #endif  
          return( GLOCK_ERROR_GETCWD );  /**************** split *************************/
       }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       strcpy( name, path );             /* we've got it */  {
    } else {                             /* strip direcotry from path */    char  *ss;                            /* pointer */
       s++;                              /* after this, the filename */    int   l1, l2;                         /* length counters */
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    l1 = strlen(path );                   /* length of path */
       strcpy( name, s );                /* save file name */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       dirc[l1-l2] = 0;                  /* add zero */    if ( ss == NULL ) {                   /* no directory, so use current */
    }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
    l1 = strlen( dirc );                 /* length of directory */        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #ifdef windows  #if     defined(__bsd__)                /* get current working directory */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }      extern char *getwd( );
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }      if ( getwd( dirc ) == NULL ) {
 #endif  #else
    s = strrchr( name, '.' );            /* find last / */      extern char *getcwd( );
    s++;  
    strcpy(ext,s);                       /* save extension */      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    l1= strlen( name);  #endif
    l2= strlen( s)+1;        return( GLOCK_ERROR_GETCWD );
    strncpy( finame, name, l1-l2);      }
    finame[l1-l2]= 0;      strcpy( name, path );               /* we've got it */
    return( 0 );                         /* we're done */    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /******************************************/      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 void replace(char *s, char*t)      dirc[l1-l2] = 0;                    /* add zero */
 {    }
   int i;    l1 = strlen( dirc );                  /* length of directory */
   int lg=20;  #ifdef windows
   i=0;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   lg=strlen(t);  #else
   for(i=0; i<= lg; i++) {    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
     (s[i] = t[i]);  #endif
     if (t[i]== '\\') s[i]='/';    ss = strrchr( name, '.' );            /* find last / */
   }    ss++;
 }    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
 int nbocc(char *s, char occ)    l2= strlen(ss)+1;
 {    strncpy( finame, name, l1-l2);
   int i,j=0;    finame[l1-l2]= 0;
   int lg=20;    return( 0 );                          /* we're done */
   i=0;  }
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  /******************************************/
   }  
   return j;  void replace(char *s, char*t)
 }  {
     int i;
 void cutv(char *u,char *v, char*t, char occ)    int lg=20;
 {    i=0;
   int i,lg,j,p=0;    lg=strlen(t);
   i=0;    for(i=0; i<= lg; i++) {
   for(j=0; j<=strlen(t)-1; j++) {      (s[i] = t[i]);
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      if (t[i]== '\\') s[i]='/';
   }    }
   }
   lg=strlen(t);  
   for(j=0; j<p; j++) {  int nbocc(char *s, char occ)
     (u[j] = t[j]);  {
   }    int i,j=0;
      u[p]='\0';    int lg=20;
     i=0;
    for(j=0; j<= lg; j++) {    lg=strlen(s);
     if (j>=(p+1))(v[j-p-1] = t[j]);    for(i=0; i<= lg; i++) {
   }    if  (s[i] == occ ) j++;
 }    }
     return j;
 /********************** nrerror ********************/  }
   
 void nrerror(char error_text[])  void cutv(char *u,char *v, char*t, char occ)
 {  {
   fprintf(stderr,"ERREUR ...\n");    /* cuts string t into u and v where u is ended by char occ excluding it
   fprintf(stderr,"%s\n",error_text);       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   exit(1);       gives u="abcedf" and v="ghi2j" */
 }    int i,lg,j,p=0;
 /*********************** vector *******************/    i=0;
 double *vector(int nl, int nh)    for(j=0; j<=strlen(t)-1; j++) {
 {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   double *v;    }
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    lg=strlen(t);
   return v-nl+NR_END;    for(j=0; j<p; j++) {
 }      (u[j] = t[j]);
     }
 /************************ free vector ******************/       u[p]='\0';
 void free_vector(double*v, int nl, int nh)  
 {     for(j=0; j<= lg; j++) {
   free((FREE_ARG)(v+nl-NR_END));      if (j>=(p+1))(v[j-p-1] = t[j]);
 }    }
   }
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  /********************** nrerror ********************/
 {  
   int *v;  void nrerror(char error_text[])
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  {
   if (!v) nrerror("allocation failure in ivector");    fprintf(stderr,"ERREUR ...\n");
   return v-nl+NR_END;    fprintf(stderr,"%s\n",error_text);
 }    exit(EXIT_FAILURE);
   }
 /******************free ivector **************************/  /*********************** vector *******************/
 void free_ivector(int *v, long nl, long nh)  double *vector(int nl, int nh)
 {  {
   free((FREE_ARG)(v+nl-NR_END));    double *v;
 }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 /******************* imatrix *******************************/    return v-nl+NR_END;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  }
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  /************************ free vector ******************/
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  void free_vector(double*v, int nl, int nh)
   int **m;  {
      free((FREE_ARG)(v+nl-NR_END));
   /* allocate pointers to rows */  }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /************************ivector *******************************/
   m += NR_END;  int *ivector(long nl,long nh)
   m -= nrl;  {
      int *v;
      v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   /* allocate rows and set pointers to them */    if (!v) nrerror("allocation failure in ivector");
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    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_ivector(int *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));
   /* return pointer to array of pointers to rows */  }
   return m;  
 }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 /****************** free_imatrix *************************/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 void free_imatrix(m,nrl,nrh,ncl,nch)  { 
       int **m;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       long nch,ncl,nrh,nrl;    int **m; 
      /* free an int matrix allocated by imatrix() */    
 {    /* allocate pointers to rows */ 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   free((FREE_ARG) (m+nrl-NR_END));    if (!m) nrerror("allocation failure 1 in matrix()"); 
 }    m += NR_END; 
     m -= nrl; 
 /******************* matrix *******************************/    
 double **matrix(long nrl, long nrh, long ncl, long nch)    
 {    /* allocate rows and set pointers to them */ 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double **m;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl] -= ncl; 
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m -= nrl;    
     /* return pointer to array of pointers to rows */ 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    return m; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  } 
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;        int **m;
   return m;        long nch,ncl,nrh,nrl; 
 }       /* free an int matrix allocated by imatrix() */ 
   { 
 /*************************free matrix ************************/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    free((FREE_ARG) (m+nrl-NR_END)); 
 {  } 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  /******************* matrix *******************************/
 }  double **matrix(long nrl, long nrh, long ncl, long nch)
   {
 /******************* ma3x *******************************/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    double **m;
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double ***m;    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m -= nrl;
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   m -= nrl;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    m[nrl] -= ncl;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   m[nrl] -= ncl;    return m;
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /*************************free matrix ************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  {
   m[nrl][ncl] += NR_END;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   m[nrl][ncl] -= nll;    free((FREE_ARG)(m+nrl-NR_END));
   for (j=ncl+1; j<=nch; j++)  }
     m[nrl][j]=m[nrl][j-1]+nlay;  
    /******************* ma3x *******************************/
   for (i=nrl+1; i<=nrh; i++) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  {
     for (j=ncl+1; j<=nch; j++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       m[i][j]=m[i][j-1]+nlay;    double ***m;
   }  
   return m;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /*************************free ma3x ************************/    m -= nrl;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl] += NR_END;
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /***************** f1dim *************************/  
 extern int ncom;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 extern double *pcom,*xicom;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 extern double (*nrfunc)(double []);    m[nrl][ncl] += NR_END;
      m[nrl][ncl] -= nll;
 double f1dim(double x)    for (j=ncl+1; j<=nch; j++) 
 {      m[nrl][j]=m[nrl][j-1]+nlay;
   int j;    
   double f;    for (i=nrl+1; i<=nrh; i++) {
   double *xt;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
        for (j=ncl+1; j<=nch; j++) 
   xt=vector(1,ncom);        m[i][j]=m[i][j-1]+nlay;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    }
   f=(*nrfunc)(xt);    return m;
   free_vector(xt,1,ncom);  }
   return f;  
 }  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 /*****************brent *************************/  {
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int iter;    free((FREE_ARG)(m+nrl-NR_END));
   double a,b,d,etemp;  }
   double fu,fv,fw,fx;  
   double ftemp;  /***************** f1dim *************************/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  extern int ncom; 
   double e=0.0;  extern double *pcom,*xicom;
    extern double (*nrfunc)(double []); 
   a=(ax < cx ? ax : cx);   
   b=(ax > cx ? ax : cx);  double f1dim(double x) 
   x=w=v=bx;  { 
   fw=fv=fx=(*f)(x);    int j; 
   for (iter=1;iter<=ITMAX;iter++) {    double f;
     xm=0.5*(a+b);    double *xt; 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);   
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    xt=vector(1,ncom); 
     printf(".");fflush(stdout);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 #ifdef DEBUG    f=(*nrfunc)(xt); 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    free_vector(xt,1,ncom); 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    return f; 
 #endif  } 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /*****************brent *************************/
       return fx;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
     ftemp=fu;    int iter; 
     if (fabs(e) > tol1) {    double a,b,d,etemp;
       r=(x-w)*(fx-fv);    double fu,fv,fw,fx;
       q=(x-v)*(fx-fw);    double ftemp;
       p=(x-v)*q-(x-w)*r;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       q=2.0*(q-r);    double e=0.0; 
       if (q > 0.0) p = -p;   
       q=fabs(q);    a=(ax < cx ? ax : cx); 
       etemp=e;    b=(ax > cx ? ax : cx); 
       e=d;    x=w=v=bx; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    fw=fv=fx=(*f)(x); 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    for (iter=1;iter<=ITMAX;iter++) { 
       else {      xm=0.5*(a+b); 
         d=p/q;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         u=x+d;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         if (u-a < tol2 || b-u < tol2)      printf(".");fflush(stdout);
           d=SIGN(tol1,xm-x);      fprintf(ficlog,".");fflush(ficlog);
       }  #ifdef DEBUG
     } else {      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);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #endif
     fu=(*f)(u);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     if (fu <= fx) {        *xmin=x; 
       if (u >= x) a=x; else b=x;        return fx; 
       SHFT(v,w,x,u)      } 
         SHFT(fv,fw,fx,fu)      ftemp=fu;
         } else {      if (fabs(e) > tol1) { 
           if (u < x) a=u; else b=u;        r=(x-w)*(fx-fv); 
           if (fu <= fw || w == x) {        q=(x-v)*(fx-fw); 
             v=w;        p=(x-v)*q-(x-w)*r; 
             w=u;        q=2.0*(q-r); 
             fv=fw;        if (q > 0.0) p = -p; 
             fw=fu;        q=fabs(q); 
           } else if (fu <= fv || v == x || v == w) {        etemp=e; 
             v=u;        e=d; 
             fv=fu;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         }        else { 
   }          d=p/q; 
   nrerror("Too many iterations in brent");          u=x+d; 
   *xmin=x;          if (u-a < tol2 || b-u < tol2) 
   return fx;            d=SIGN(tol1,xm-x); 
 }        } 
       } else { 
 /****************** mnbrak ***********************/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
             double (*func)(double))      fu=(*f)(u); 
 {      if (fu <= fx) { 
   double ulim,u,r,q, dum;        if (u >= x) a=x; else b=x; 
   double fu;        SHFT(v,w,x,u) 
            SHFT(fv,fw,fx,fu) 
   *fa=(*func)(*ax);          } else { 
   *fb=(*func)(*bx);            if (u < x) a=u; else b=u; 
   if (*fb > *fa) {            if (fu <= fw || w == x) { 
     SHFT(dum,*ax,*bx,dum)              v=w; 
       SHFT(dum,*fb,*fa,dum)              w=u; 
       }              fv=fw; 
   *cx=(*bx)+GOLD*(*bx-*ax);              fw=fu; 
   *fc=(*func)(*cx);            } else if (fu <= fv || v == x || v == w) { 
   while (*fb > *fc) {              v=u; 
     r=(*bx-*ax)*(*fb-*fc);              fv=fu; 
     q=(*bx-*cx)*(*fb-*fa);            } 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/          } 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    } 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    nrerror("Too many iterations in brent"); 
     if ((*bx-u)*(u-*cx) > 0.0) {    *xmin=x; 
       fu=(*func)(u);    return fx; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  } 
       fu=(*func)(u);  
       if (fu < *fc) {  /****************** mnbrak ***********************/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           }              double (*func)(double)) 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  { 
       u=ulim;    double ulim,u,r,q, dum;
       fu=(*func)(u);    double fu; 
     } else {   
       u=(*cx)+GOLD*(*cx-*bx);    *fa=(*func)(*ax); 
       fu=(*func)(u);    *fb=(*func)(*bx); 
     }    if (*fb > *fa) { 
     SHFT(*ax,*bx,*cx,u)      SHFT(dum,*ax,*bx,dum) 
       SHFT(*fa,*fb,*fc,fu)        SHFT(dum,*fb,*fa,dum) 
       }        } 
 }    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
 /*************** linmin ************************/    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
 int ncom;      q=(*bx-*cx)*(*fb-*fa); 
 double *pcom,*xicom;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 double (*nrfunc)(double []);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
        ulim=(*bx)+GLIMIT*(*cx-*bx); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   double brent(double ax, double bx, double cx,      } else if ((*cx-u)*(u-ulim) > 0.0) { 
                double (*f)(double), double tol, double *xmin);        fu=(*func)(u); 
   double f1dim(double x);        if (fu < *fc) { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
               double *fc, double (*func)(double));            SHFT(*fb,*fc,fu,(*func)(u)) 
   int j;            } 
   double xx,xmin,bx,ax;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   double fx,fb,fa;        u=ulim; 
          fu=(*func)(u); 
   ncom=n;      } else { 
   pcom=vector(1,n);        u=(*cx)+GOLD*(*cx-*bx); 
   xicom=vector(1,n);        fu=(*func)(u); 
   nrfunc=func;      } 
   for (j=1;j<=n;j++) {      SHFT(*ax,*bx,*cx,u) 
     pcom[j]=p[j];        SHFT(*fa,*fb,*fc,fu) 
     xicom[j]=xi[j];        } 
   }  } 
   ax=0.0;  
   xx=1.0;  /*************** linmin ************************/
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  int ncom; 
 #ifdef DEBUG  double *pcom,*xicom;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double (*nrfunc)(double []); 
 #endif   
   for (j=1;j<=n;j++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     xi[j] *= xmin;  { 
     p[j] += xi[j];    double brent(double ax, double bx, double cx, 
   }                 double (*f)(double), double tol, double *xmin); 
   free_vector(xicom,1,n);    double f1dim(double x); 
   free_vector(pcom,1,n);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 }                double *fc, double (*func)(double)); 
     int j; 
 /*************** powell ************************/    double xx,xmin,bx,ax; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    double fx,fb,fa;
             double (*func)(double []))   
 {    ncom=n; 
   void linmin(double p[], double xi[], int n, double *fret,    pcom=vector(1,n); 
               double (*func)(double []));    xicom=vector(1,n); 
   int i,ibig,j;    nrfunc=func; 
   double del,t,*pt,*ptt,*xit;    for (j=1;j<=n;j++) { 
   double fp,fptt;      pcom[j]=p[j]; 
   double *xits;      xicom[j]=xi[j]; 
   pt=vector(1,n);    } 
   ptt=vector(1,n);    ax=0.0; 
   xit=vector(1,n);    xx=1.0; 
   xits=vector(1,n);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   *fret=(*func)(p);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for (j=1;j<=n;j++) pt[j]=p[j];  #ifdef DEBUG
   for (*iter=1;;++(*iter)) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fp=(*fret);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     ibig=0;  #endif
     del=0.0;    for (j=1;j<=n;j++) { 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      xi[j] *= xmin; 
     for (i=1;i<=n;i++)      p[j] += xi[j]; 
       printf(" %d %.12f",i, p[i]);    } 
     printf("\n");    free_vector(xicom,1,n); 
     for (i=1;i<=n;i++) {    free_vector(pcom,1,n); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  } 
       fptt=(*fret);  
 #ifdef DEBUG  /*************** powell ************************/
       printf("fret=%lf \n",*fret);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 #endif              double (*func)(double [])) 
       printf("%d",i);fflush(stdout);  { 
       linmin(p,xit,n,fret,func);    void linmin(double p[], double xi[], int n, double *fret, 
       if (fabs(fptt-(*fret)) > del) {                double (*func)(double [])); 
         del=fabs(fptt-(*fret));    int i,ibig,j; 
         ibig=i;    double del,t,*pt,*ptt,*xit;
       }    double fp,fptt;
 #ifdef DEBUG    double *xits;
       printf("%d %.12e",i,(*fret));    pt=vector(1,n); 
       for (j=1;j<=n;j++) {    ptt=vector(1,n); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    xit=vector(1,n); 
         printf(" x(%d)=%.12e",j,xit[j]);    xits=vector(1,n); 
       }    *fret=(*func)(p); 
       for(j=1;j<=n;j++)    for (j=1;j<=n;j++) pt[j]=p[j]; 
         printf(" p=%.12e",p[j]);    for (*iter=1;;++(*iter)) { 
       printf("\n");      fp=(*fret); 
 #endif      ibig=0; 
     }      del=0.0; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 #ifdef DEBUG      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       int k[2],l;      for (i=1;i<=n;i++) 
       k[0]=1;        printf(" %d %.12f",i, p[i]);
       k[1]=-1;      fprintf(ficlog," %d %.12f",i, p[i]);
       printf("Max: %.12e",(*func)(p));      printf("\n");
       for (j=1;j<=n;j++)      fprintf(ficlog,"\n");
         printf(" %.12e",p[j]);      for (i=1;i<=n;i++) { 
       printf("\n");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       for(l=0;l<=1;l++) {        fptt=(*fret); 
         for (j=1;j<=n;j++) {  #ifdef DEBUG
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        printf("fret=%lf \n",*fret);
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        fprintf(ficlog,"fret=%lf \n",*fret);
         }  #endif
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        printf("%d",i);fflush(stdout);
       }        fprintf(ficlog,"%d",i);fflush(ficlog);
 #endif        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
       free_vector(xit,1,n);          ibig=i; 
       free_vector(xits,1,n);        } 
       free_vector(ptt,1,n);  #ifdef DEBUG
       free_vector(pt,1,n);        printf("%d %.12e",i,(*fret));
       return;        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (j=1;j<=n;j++) {          printf(" x(%d)=%.12e",j,xit[j]);
       ptt[j]=2.0*p[j]-pt[j];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       xit[j]=p[j]-pt[j];        }
       pt[j]=p[j];        for(j=1;j<=n;j++) {
     }          printf(" p=%.12e",p[j]);
     fptt=(*func)(ptt);          fprintf(ficlog," p=%.12e",p[j]);
     if (fptt < fp) {        }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        printf("\n");
       if (t < 0.0) {        fprintf(ficlog,"\n");
         linmin(p,xit,n,fret,func);  #endif
         for (j=1;j<=n;j++) {      } 
           xi[j][ibig]=xi[j][n];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
           xi[j][n]=xit[j];  #ifdef DEBUG
         }        int k[2],l;
 #ifdef DEBUG        k[0]=1;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        k[1]=-1;
         for(j=1;j<=n;j++)        printf("Max: %.12e",(*func)(p));
           printf(" %.12e",xit[j]);        fprintf(ficlog,"Max: %.12e",(*func)(p));
         printf("\n");        for (j=1;j<=n;j++) {
 #endif          printf(" %.12e",p[j]);
       }          fprintf(ficlog," %.12e",p[j]);
     }        }
   }        printf("\n");
 }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 /**** Prevalence limit ****************/          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 {            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          }
      matrix by transitions matrix until convergence is reached */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int i, ii,j,k;        }
   double min, max, maxmin, maxmax,sumnew=0.;  #endif
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;        free_vector(xit,1,n); 
   double agefin, delaymax=50 ; /* Max number of years to converge */        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        free_vector(pt,1,n); 
     for (j=1;j<=nlstate+ndeath;j++){        return; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      } 
     }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
    cov[1]=1.;        ptt[j]=2.0*p[j]-pt[j]; 
          xit[j]=p[j]-pt[j]; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        pt[j]=p[j]; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      } 
     newm=savm;      fptt=(*func)(ptt); 
     /* Covariates have to be included here again */      if (fptt < fp) { 
      cov[2]=agefin;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
          if (t < 0.0) { 
       for (k=1; k<=cptcovn;k++) {          linmin(p,xit,n,fret,func); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          for (j=1;j<=n;j++) { 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/            xi[j][ibig]=xi[j][n]; 
       }            xi[j][n]=xit[j]; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          }
       for (k=1; k<=cptcovprod;k++)  #ifdef DEBUG
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          for(j=1;j<=n;j++){
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/            printf(" %.12e",xit[j]);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/            fprintf(ficlog," %.12e",xit[j]);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          }
           printf("\n");
     savm=oldm;          fprintf(ficlog,"\n");
     oldm=newm;  #endif
     maxmax=0.;        }
     for(j=1;j<=nlstate;j++){      } 
       min=1.;    } 
       max=0.;  } 
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  /**** Prevalence limit (stable prevalence)  ****************/
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       }       matrix by transitions matrix until convergence is reached */
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);    int i, ii,j,k;
     }    double min, max, maxmin, maxmax,sumnew=0.;
     if(maxmax < ftolpl){    double **matprod2();
       return prlim;    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
 }  
     for (ii=1;ii<=nlstate+ndeath;ii++)
 /*************** transition probabilities ***************/      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      }
 {  
   double s1, s2;     cov[1]=1.;
   /*double t34;*/   
   int i,j,j1, nc, ii, jj;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(i=1; i<= nlstate; i++){      newm=savm;
     for(j=1; j<i;j++){      /* Covariates have to be included here again */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       cov[2]=agefin;
         /*s2 += param[i][j][nc]*cov[nc];*/    
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        for (k=1; k<=cptcovn;k++) {
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       }          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       ps[i][j]=s2;        }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }        for (k=1; k<=cptcovprod;k++)
     for(j=i+1; j<=nlstate+ndeath;j++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       ps[i][j]=s2;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     }  
   }      savm=oldm;
     /*ps[3][2]=1;*/      oldm=newm;
       maxmax=0.;
   for(i=1; i<= nlstate; i++){      for(j=1;j<=nlstate;j++){
      s1=0;        min=1.;
     for(j=1; j<i; j++)        max=0.;
       s1+=exp(ps[i][j]);        for(i=1; i<=nlstate; i++) {
     for(j=i+1; j<=nlstate+ndeath; j++)          sumnew=0;
       s1+=exp(ps[i][j]);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     ps[i][i]=1./(s1+1.);          prlim[i][j]= newm[i][j]/(1-sumnew);
     for(j=1; j<i; j++)          max=FMAX(max,prlim[i][j]);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          min=FMIN(min,prlim[i][j]);
     for(j=i+1; j<=nlstate+ndeath; j++)        }
       ps[i][j]= exp(ps[i][j])*ps[i][i];        maxmin=max-min;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        maxmax=FMAX(maxmax,maxmin);
   } /* end i */      }
       if(maxmax < ftolpl){
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        return prlim;
     for(jj=1; jj<= nlstate+ndeath; jj++){      }
       ps[ii][jj]=0;    }
       ps[ii][ii]=1;  }
     }  
   }  /*************** transition probabilities ***************/ 
   
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  {
     for(jj=1; jj<= nlstate+ndeath; jj++){    double s1, s2;
      printf("%lf ",ps[ii][jj]);    /*double t34;*/
    }    int i,j,j1, nc, ii, jj;
     printf("\n ");  
     }      for(i=1; i<= nlstate; i++){
     printf("\n ");printf("%lf ",cov[2]);*/      for(j=1; j<i;j++){
 /*        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          /*s2 += param[i][j][nc]*cov[nc];*/
   goto end;*/          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     return ps;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 }        }
         ps[i][j]=s2;
 /**************** Product of 2 matrices ******************/        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      for(j=i+1; j<=nlstate+ndeath;j++){
 {        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   /* in, b, out are matrice of pointers which should have been initialized        }
      before: only the contents of out is modified. The function returns        ps[i][j]=s2;
      a pointer to pointers identical to out */      }
   long i, j, k;    }
   for(i=nrl; i<= nrh; i++)      /*ps[3][2]=1;*/
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    for(i=1; i<= nlstate; i++){
         out[i][k] +=in[i][j]*b[j][k];       s1=0;
       for(j=1; j<i; j++)
   return out;        s1+=exp(ps[i][j]);
 }      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
 /************* Higher Matrix Product ***************/      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      for(j=i+1; j<=nlstate+ndeath; j++)
 {        ps[i][j]= exp(ps[i][j])*ps[i][i];
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
      duration (i.e. until    } /* end i */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      (typically every 2 years instead of every month which is too big).      for(jj=1; jj<= nlstate+ndeath; jj++){
      Model is determined by parameters x and covariates have to be        ps[ii][jj]=0;
      included manually here.        ps[ii][ii]=1;
       }
      */    }
   
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   double **newm;      for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
   /* Hstepm could be zero and should return the unit matrix */     }
   for (i=1;i<=nlstate+ndeath;i++)      printf("\n ");
     for (j=1;j<=nlstate+ndeath;j++){      }
       oldm[i][j]=(i==j ? 1.0 : 0.0);      printf("\n ");printf("%lf ",cov[2]);*/
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /*
     }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    goto end;*/
   for(h=1; h <=nhstepm; h++){      return ps;
     for(d=1; d <=hstepm; d++){  }
       newm=savm;  
       /* Covariates have to be included here again */  /**************** Product of 2 matrices ******************/
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
       for (k=1; k<=cptcovage;k++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for (k=1; k<=cptcovprod;k++)    /* in, b, out are matrice of pointers which should have been initialized 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
     long i, j, k;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    for(i=nrl; i<= nrh; i++)
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      for(k=ncolol; k<=ncoloh; k++)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        for(j=ncl,out[i][k]=0.; j<=nch; j++)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          out[i][k] +=in[i][j]*b[j][k];
       savm=oldm;  
       oldm=newm;    return out;
     }  }
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  /************* Higher Matrix Product ***************/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       }  {
   } /* end h */    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
   return po;       duration (i.e. until
 }       age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big).
 /*************** log-likelihood *************/       Model is determined by parameters x and covariates have to be 
 double func( double *x)       included manually here. 
 {  
   int i, ii, j, k, mi, d, kk;       */
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;    int i, j, d, h, k;
   double sw; /* Sum of weights */    double **out, cov[NCOVMAX];
   double lli; /* Individual log likelihood */    double **newm;
   long ipmx;  
   /*extern weight */    /* Hstepm could be zero and should return the unit matrix */
   /* We are differentiating ll according to initial status */    for (i=1;i<=nlstate+ndeath;i++)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      for (j=1;j<=nlstate+ndeath;j++){
   /*for(i=1;i<imx;i++)        oldm[i][j]=(i==j ? 1.0 : 0.0);
     printf(" %d\n",s[4][i]);        po[i][j][0]=(i==j ? 1.0 : 0.0);
   */      }
   cov[1]=1.;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
   for(k=1; k<=nlstate; k++) ll[k]=0.;      for(d=1; d <=hstepm; d++){
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        newm=savm;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        /* Covariates have to be included here again */
     for(mi=1; mi<= wav[i]-1; mi++){        cov[1]=1.;
       for (ii=1;ii<=nlstate+ndeath;ii++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for(d=0; d<dh[mi][i]; d++){        for (k=1; k<=cptcovage;k++)
         newm=savm;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        for (k=1; k<=cptcovprod;k++)
         for (kk=1; kk<=cptcovage;kk++) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  
                /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         savm=oldm;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         oldm=newm;        savm=oldm;
                oldm=newm;
              }
       } /* end mult */      for(i=1; i<=nlstate+ndeath; i++)
              for(j=1;j<=nlstate+ndeath;j++) {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          po[i][j][h]=newm[i][j];
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       ipmx +=1;           */
       sw += weight[i];        }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    } /* end h */
     } /* end of wave */    return po;
   } /* end of individual */  }
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  /*************** log-likelihood *************/
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  double func( double *x)
   return -l;  {
 }    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
 /*********** Maximum Likelihood Estimation ***************/    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    int s1, s2;
 {    double bbh;
   int i,j, iter;    long ipmx;
   double **xi,*delti;    /*extern weight */
   double fret;    /* We are differentiating ll according to initial status */
   xi=matrix(1,npar,1,npar);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for (i=1;i<=npar;i++)    /*for(i=1;i<imx;i++) 
     for (j=1;j<=npar;j++)      printf(" %d\n",s[4][i]);
       xi[i][j]=(i==j ? 1.0 : 0.0);    */
   printf("Powell\n");    cov[1]=1.;
   powell(p,xi,npar,ftol,&iter,&fret,func);  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    if(mle==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(mi=1; mi<= wav[i]-1; mi++){
 /**** Computes Hessian and covariance matrix ***/          for (ii=1;ii<=nlstate+ndeath;ii++)
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))            for (j=1;j<=nlstate+ndeath;j++){
 {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double  **a,**y,*x,pd;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **hess;            }
   int i, j,jk;          for(d=0; d<dh[mi][i]; d++){
   int *indx;            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double hessii(double p[], double delta, int theta, double delti[]);            for (kk=1; kk<=cptcovage;kk++) {
   double hessij(double p[], double delti[], int i, int j);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   void lubksb(double **a, int npar, int *indx, double b[]) ;            }
   void ludcmp(double **a, int npar, int *indx, double *d) ;          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   hess=matrix(1,npar,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   printf("\nCalculation of the hessian matrix. Wait...\n");            oldm=newm;
   for (i=1;i<=npar;i++){          
     printf("%d",i);fflush(stdout);          
     hess[i][i]=hessii(p,ftolhess,i,delti);          } /* end mult */
     /*printf(" %f ",p[i]);*/        
     /*printf(" %lf ",hess[i][i]);*/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   }          /* But now since version 0.9 we anticipate for bias and large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
   for (i=1;i<=npar;i++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
     for (j=1;j<=npar;j++)  {           * the nearest (and in case of equal distance, to the lowest) interval but now
       if (j>i) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         printf(".%d%d",i,j);fflush(stdout);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         hess[i][j]=hessij(p,delti,i,j);           * probability in order to take into account the bias as a fraction of the way
         hess[j][i]=hess[i][j];               * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         /*printf(" %lf ",hess[i][j]);*/           * -stepm/2 to stepm/2 .
       }           * For stepm=1 the results are the same as for previous versions of Imach.
     }           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
   printf("\n");          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          bbh=(double)bh[mi][i]/(double)stepm;
    
   a=matrix(1,npar,1,npar);          /*      lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-bbh)*out[s1][s2]));*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   ludcmp(a,npar,indx,&pd);          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   for (j=1;j<=npar;j++) {          ipmx +=1;
     for (i=1;i<=npar;i++) x[i]=0;          sw += weight[i];
     x[j]=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     lubksb(a,npar,indx,x);        } /* end of wave */
     for (i=1;i<=npar;i++){      } /* end of individual */
       matcov[i][j]=x[i];    }  else{ 
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   printf("\n#Hessian matrix#\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=1;i<=npar;i++) {            for (j=1;j<=nlstate+ndeath;j++){
     for (j=1;j<=npar;j++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("%.3e ",hess[i][j]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
     printf("\n");          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* Recompute Inverse */            for (kk=1; kk<=cptcovage;kk++) {
   for (i=1;i<=npar;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            }
   ludcmp(a,npar,indx,&pd);          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /*  printf("\n#Hessian matrix recomputed#\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   for (j=1;j<=npar;j++) {            oldm=newm;
     for (i=1;i<=npar;i++) x[i]=0;          } /* end mult */
     x[j]=1;        
     lubksb(a,npar,indx,x);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for (i=1;i<=npar;i++){          ipmx +=1;
       y[i][j]=x[i];          sw += weight[i];
       printf("%.3e ",y[i][j]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     printf("\n");      } /* end of individual */
   }    } /* End of if */
   */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   free_matrix(a,1,npar,1,npar);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   free_matrix(y,1,npar,1,npar);    return -l;
   free_vector(x,1,npar);  }
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);  
   /*********** Maximum Likelihood Estimation ***************/
   
 }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
 /*************** hessian matrix ****************/    int i,j, iter;
 double hessii( double x[], double delta, int theta, double delti[])    double **xi,*delti;
 {    double fret;
   int i;    xi=matrix(1,npar,1,npar);
   int l=1, lmax=20;    for (i=1;i<=npar;i++)
   double k1,k2;      for (j=1;j<=npar;j++)
   double p2[NPARMAX+1];        xi[i][j]=(i==j ? 1.0 : 0.0);
   double res;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double fx;  
   int k=0,kmax=10;     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   double l1;    fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];  }
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);  /**** Computes Hessian and covariance matrix ***/
     delts=delt;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for(k=1 ; k <kmax; k=k+1){  {
       delt = delta*(l1*k);    double  **a,**y,*x,pd;
       p2[theta]=x[theta] +delt;    double **hess;
       k1=func(p2)-fx;    int i, j,jk;
       p2[theta]=x[theta]-delt;    int *indx;
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double hessii(double p[], double delta, int theta, double delti[]);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    double hessij(double p[], double delti[], int i, int j);
          void lubksb(double **a, int npar, int *indx, double b[]) ;
 #ifdef DEBUG    void ludcmp(double **a, int npar, int *indx, double *d) ;
       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);  
 #endif    hess=matrix(1,npar,1,npar);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    printf("\nCalculation of the hessian matrix. Wait...\n");
         k=kmax;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       }    for (i=1;i<=npar;i++){
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      printf("%d",i);fflush(stdout);
         k=kmax; l=lmax*10.;      fprintf(ficlog,"%d",i);fflush(ficlog);
       }      hess[i][i]=hessii(p,ftolhess,i,delti);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      /*printf(" %f ",p[i]);*/
         delts=delt;      /*printf(" %lf ",hess[i][i]);*/
       }    }
     }    
   }    for (i=1;i<=npar;i++) {
   delti[theta]=delts;      for (j=1;j<=npar;j++)  {
   return res;        if (j>i) { 
            printf(".%d%d",i,j);fflush(stdout);
 }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j);
 double hessij( double x[], double delti[], int thetai,int thetaj)          hess[j][i]=hess[i][j];    
 {          /*printf(" %lf ",hess[i][j]);*/
   int i;        }
   int l=1, l1, lmax=20;      }
   double k1,k2,k3,k4,res,fx;    }
   double p2[NPARMAX+1];    printf("\n");
   int k;    fprintf(ficlog,"\n");
   
   fx=func(x);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   for (k=1; k<=2; k++) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     for (i=1;i<=npar;i++) p2[i]=x[i];    
     p2[thetai]=x[thetai]+delti[thetai]/k;    a=matrix(1,npar,1,npar);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    y=matrix(1,npar,1,npar);
     k1=func(p2)-fx;    x=vector(1,npar);
      indx=ivector(1,npar);
     p2[thetai]=x[thetai]+delti[thetai]/k;    for (i=1;i<=npar;i++)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     k2=func(p2)-fx;    ludcmp(a,npar,indx,&pd);
    
     p2[thetai]=x[thetai]-delti[thetai]/k;    for (j=1;j<=npar;j++) {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      for (i=1;i<=npar;i++) x[i]=0;
     k3=func(p2)-fx;      x[j]=1;
        lubksb(a,npar,indx,x);
     p2[thetai]=x[thetai]-delti[thetai]/k;      for (i=1;i<=npar;i++){ 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        matcov[i][j]=x[i];
     k4=func(p2)-fx;      }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    }
 #ifdef DEBUG  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    printf("\n#Hessian matrix#\n");
 #endif    fprintf(ficlog,"\n#Hessian matrix#\n");
   }    for (i=1;i<=npar;i++) { 
   return res;      for (j=1;j<=npar;j++) { 
 }        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
 /************** Inverse of matrix **************/      }
 void ludcmp(double **a, int n, int *indx, double *d)      printf("\n");
 {      fprintf(ficlog,"\n");
   int i,imax,j,k;    }
   double big,dum,sum,temp;  
   double *vv;    /* Recompute Inverse */
      for (i=1;i<=npar;i++)
   vv=vector(1,n);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   *d=1.0;    ludcmp(a,npar,indx,&pd);
   for (i=1;i<=n;i++) {  
     big=0.0;    /*  printf("\n#Hessian matrix recomputed#\n");
     for (j=1;j<=n;j++)  
       if ((temp=fabs(a[i][j])) > big) big=temp;    for (j=1;j<=npar;j++) {
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      for (i=1;i<=npar;i++) x[i]=0;
     vv[i]=1.0/big;      x[j]=1;
   }      lubksb(a,npar,indx,x);
   for (j=1;j<=n;j++) {      for (i=1;i<=npar;i++){ 
     for (i=1;i<j;i++) {        y[i][j]=x[i];
       sum=a[i][j];        printf("%.3e ",y[i][j]);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        fprintf(ficlog,"%.3e ",y[i][j]);
       a[i][j]=sum;      }
     }      printf("\n");
     big=0.0;      fprintf(ficlog,"\n");
     for (i=j;i<=n;i++) {    }
       sum=a[i][j];    */
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];    free_matrix(a,1,npar,1,npar);
       a[i][j]=sum;    free_matrix(y,1,npar,1,npar);
       if ( (dum=vv[i]*fabs(sum)) >= big) {    free_vector(x,1,npar);
         big=dum;    free_ivector(indx,1,npar);
         imax=i;    free_matrix(hess,1,npar,1,npar);
       }  
     }  
     if (j != imax) {  }
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];  /*************** hessian matrix ****************/
         a[imax][k]=a[j][k];  double hessii( double x[], double delta, int theta, double delti[])
         a[j][k]=dum;  {
       }    int i;
       *d = -(*d);    int l=1, lmax=20;
       vv[imax]=vv[j];    double k1,k2;
     }    double p2[NPARMAX+1];
     indx[j]=imax;    double res;
     if (a[j][j] == 0.0) a[j][j]=TINY;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     if (j != n) {    double fx;
       dum=1.0/(a[j][j]);    int k=0,kmax=10;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    double l1;
     }  
   }    fx=func(x);
   free_vector(vv,1,n);  /* Doesn't work */    for (i=1;i<=npar;i++) p2[i]=x[i];
 ;    for(l=0 ; l <=lmax; l++){
 }      l1=pow(10,l);
       delts=delt;
 void lubksb(double **a, int n, int *indx, double b[])      for(k=1 ; k <kmax; k=k+1){
 {        delt = delta*(l1*k);
   int i,ii=0,ip,j;        p2[theta]=x[theta] +delt;
   double sum;        k1=func(p2)-fx;
          p2[theta]=x[theta]-delt;
   for (i=1;i<=n;i++) {        k2=func(p2)-fx;
     ip=indx[i];        /*res= (k1-2.0*fx+k2)/delt/delt; */
     sum=b[ip];        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     b[ip]=b[i];        
     if (ii)  #ifdef DEBUG
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        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);
     else if (sum) ii=i;        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);
     b[i]=sum;  #endif
   }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   for (i=n;i>=1;i--) {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     sum=b[i];          k=kmax;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        }
     b[i]=sum/a[i][i];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   }          k=kmax; l=lmax*10.;
 }        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 /************ Frequencies ********************/          delts=delt;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        }
 {  /* Some frequencies */      }
      }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    delti[theta]=delts;
   double ***freq; /* Frequencies */    return res; 
   double *pp;    
   double pos, k2, dateintsum=0,k2cpt=0;  }
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  double hessij( double x[], double delti[], int thetai,int thetaj)
    {
   pp=vector(1,nlstate);    int i;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int l=1, l1, lmax=20;
   strcpy(fileresp,"p");    double k1,k2,k3,k4,res,fx;
   strcat(fileresp,fileres);    double p2[NPARMAX+1];
   if((ficresp=fopen(fileresp,"w"))==NULL) {    int k;
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);    fx=func(x);
   }    for (k=1; k<=2; k++) {
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for (i=1;i<=npar;i++) p2[i]=x[i];
   j1=0;      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   j=cptcoveff;      k1=func(p2)-fx;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    
        p2[thetai]=x[thetai]+delti[thetai]/k;
   for(k1=1; k1<=j;k1++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(i1=1; i1<=ncodemax[k1];i1++){      k2=func(p2)-fx;
       j1++;    
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      p2[thetai]=x[thetai]-delti[thetai]/k;
         scanf("%d", i);*/      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       for (i=-1; i<=nlstate+ndeath; i++)        k3=func(p2)-fx;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      
           for(m=agemin; m <= agemax+3; m++)      p2[thetai]=x[thetai]-delti[thetai]/k;
             freq[i][jk][m]=0;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
            k4=func(p2)-fx;
       dateintsum=0;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       k2cpt=0;  #ifdef DEBUG
       for (i=1; i<=imx; i++) {      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);
         bool=1;      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);
         if  (cptcovn>0) {  #endif
           for (z1=1; z1<=cptcoveff; z1++)    }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    return res;
               bool=0;  }
         }  
         if (bool==1) {  /************** Inverse of matrix **************/
           for(m=firstpass; m<=lastpass; m++){  void ludcmp(double **a, int n, int *indx, double *d) 
             k2=anint[m][i]+(mint[m][i]/12.);  { 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    int i,imax,j,k; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    double big,dum,sum,temp; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    double *vv; 
               if (m<lastpass) {   
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    vv=vector(1,n); 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    *d=1.0; 
               }    for (i=1;i<=n;i++) { 
                    big=0.0; 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      for (j=1;j<=n;j++) 
                 dateintsum=dateintsum+k2;        if ((temp=fabs(a[i][j])) > big) big=temp; 
                 k2cpt++;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
               }      vv[i]=1.0/big; 
             }    } 
           }    for (j=1;j<=n;j++) { 
         }      for (i=1;i<j;i++) { 
       }        sum=a[i][j]; 
                for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        a[i][j]=sum; 
       } 
       if  (cptcovn>0) {      big=0.0; 
         fprintf(ficresp, "\n#********** Variable ");      for (i=j;i<=n;i++) { 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        sum=a[i][j]; 
         fprintf(ficresp, "**********\n#");        for (k=1;k<j;k++) 
       }          sum -= a[i][k]*a[k][j]; 
       for(i=1; i<=nlstate;i++)        a[i][j]=sum; 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       fprintf(ficresp, "\n");          big=dum; 
                imax=i; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){        } 
         if(i==(int)agemax+3)      } 
           printf("Total");      if (j != imax) { 
         else        for (k=1;k<=n;k++) { 
           printf("Age %d", i);          dum=a[imax][k]; 
         for(jk=1; jk <=nlstate ; jk++){          a[imax][k]=a[j][k]; 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          a[j][k]=dum; 
             pp[jk] += freq[jk][m][i];        } 
         }        *d = -(*d); 
         for(jk=1; jk <=nlstate ; jk++){        vv[imax]=vv[j]; 
           for(m=-1, pos=0; m <=0 ; m++)      } 
             pos += freq[jk][m][i];      indx[j]=imax; 
           if(pp[jk]>=1.e-10)      if (a[j][j] == 0.0) a[j][j]=TINY; 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      if (j != n) { 
           else        dum=1.0/(a[j][j]); 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         }      } 
     } 
         for(jk=1; jk <=nlstate ; jk++){    free_vector(vv,1,n);  /* Doesn't work */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  ;
             pp[jk] += freq[jk][m][i];  } 
         }  
   void lubksb(double **a, int n, int *indx, double b[]) 
         for(jk=1,pos=0; jk <=nlstate ; jk++)  { 
           pos += pp[jk];    int i,ii=0,ip,j; 
         for(jk=1; jk <=nlstate ; jk++){    double sum; 
           if(pos>=1.e-5)   
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    for (i=1;i<=n;i++) { 
           else      ip=indx[i]; 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      sum=b[ip]; 
           if( i <= (int) agemax){      b[ip]=b[i]; 
             if(pos>=1.e-5){      if (ii) 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
               probs[i][jk][j1]= pp[jk]/pos;      else if (sum) ii=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]);*/      b[i]=sum; 
             }    } 
             else    for (i=n;i>=1;i--) { 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      sum=b[i]; 
           }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         }      b[i]=sum/a[i][i]; 
            } 
         for(jk=-1; jk <=nlstate+ndeath; jk++)  } 
           for(m=-1; m <=nlstate+ndeath; m++)  
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  /************ Frequencies ********************/
         if(i <= (int) agemax)  void  freqsummary(char fileres[], int agemin, int agemax, 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)
           fprintf(ficresp,"\n");  {  /* Some frequencies */
         printf("\n");    
       }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     }    int first;
   }    double ***freq; /* Frequencies */
   dateintmean=dateintsum/k2cpt;    double *pp;
      double pos, k2, dateintsum=0,k2cpt=0;
   fclose(ficresp);    FILE *ficresp;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    char fileresp[FILENAMELENGTH];
   free_vector(pp,1,nlstate);    
      pp=vector(1,nlstate);
   /* End of Freq */    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
 }    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
 /************ Prevalence ********************/    if((ficresp=fopen(fileresp,"w"))==NULL) {
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      printf("Problem with prevalence resultfile: %s\n", fileresp);
 {  /* Some frequencies */      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
        exit(0);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    }
   double ***freq; /* Frequencies */    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   double *pp;    j1=0;
   double pos, k2;    
     j=cptcoveff;
   pp=vector(1,nlstate);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
      first=1;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;    for(k1=1; k1<=j;k1++){
        for(i1=1; i1<=ncodemax[k1];i1++){
   j=cptcoveff;        j1++;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
            scanf("%d", i);*/
  for(k1=1; k1<=j;k1++){        for (i=-1; i<=nlstate+ndeath; i++)  
     for(i1=1; i1<=ncodemax[k1];i1++){          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       j1++;            for(m=agemin; m <= agemax+3; m++)
                freq[i][jk][m]=0;
       for (i=-1; i<=nlstate+ndeath; i++)          
         for (jk=-1; jk<=nlstate+ndeath; jk++)          dateintsum=0;
           for(m=agemin; m <= agemax+3; m++)        k2cpt=0;
             freq[i][jk][m]=0;        for (i=1; i<=imx; i++) {
                bool=1;
       for (i=1; i<=imx; i++) {          if  (cptcovn>0) {
         bool=1;            for (z1=1; z1<=cptcoveff; z1++) 
         if  (cptcovn>0) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           for (z1=1; z1<=cptcoveff; z1++)                bool=0;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          }
               bool=0;          if (bool==1){
         }            for(m=firstpass; m<=lastpass; m++){
         if (bool==1) {              k2=anint[m][i]+(mint[m][i]/12.);
           for(m=firstpass; m<=lastpass; m++){              if ((k2>=dateprev1) && (k2<=dateprev2)) {
             k2=anint[m][i]+(mint[m][i]/12.);                if(agev[m][i]==0) agev[m][i]=agemax+1;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {                if(agev[m][i]==1) agev[m][i]=agemax+2;
               if(agev[m][i]==0) agev[m][i]=agemax+1;                if (m<lastpass) {
               if(agev[m][i]==1) agev[m][i]=agemax+2;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */                }
             }                
           }                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
         }                  dateintsum=dateintsum+k2;
       }                  k2cpt++;
         for(i=(int)agemin; i <= (int)agemax+3; i++){                }
           for(jk=1; jk <=nlstate ; jk++){              }
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            }
               pp[jk] += freq[jk][m][i];          }
           }        }
           for(jk=1; jk <=nlstate ; jk++){         
             for(m=-1, pos=0; m <=0 ; m++)        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
             pos += freq[jk][m][i];  
         }        if  (cptcovn>0) {
                  fprintf(ficresp, "\n#********** Variable "); 
          for(jk=1; jk <=nlstate ; jk++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          fprintf(ficresp, "**********\n#");
              pp[jk] += freq[jk][m][i];        }
          }        for(i=1; i<=nlstate;i++) 
                    fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        fprintf(ficresp, "\n");
         
          for(jk=1; jk <=nlstate ; jk++){                  for(i=(int)agemin; i <= (int)agemax+3; i++){
            if( i <= (int) agemax){          if(i==(int)agemax+3){
              if(pos>=1.e-5){            fprintf(ficlog,"Total");
                probs[i][jk][j1]= pp[jk]/pos;          }else{
              }            if(first==1){
            }              first=0;
          }              printf("See log file for details...\n");
                      }
         }            fprintf(ficlog,"Age %d", i);
     }          }
   }          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                pp[jk] += freq[jk][m][i]; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          }
   free_vector(pp,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pos=0; m <=0 ; m++)
 }  /* End of Freq */              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
 /************* Waves Concatenation ***************/              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)              }
 {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            }else{
      Death is a valid wave (if date is known).              if(first==1)
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      and mw[mi+1][i]. dh depends on stepm.            }
      */          }
   
   int i, mi, m;          for(jk=1; jk <=nlstate ; jk++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
      double sum=0., jmean=0.;*/              pp[jk] += freq[jk][m][i];
           }
   int j, k=0,jk, ju, jl;  
   double sum=0.;          for(jk=1,pos=0; jk <=nlstate ; jk++)
   jmin=1e+5;            pos += pp[jk];
   jmax=-1;          for(jk=1; jk <=nlstate ; jk++){
   jmean=0.;            if(pos>=1.e-5){
   for(i=1; i<=imx; i++){              if(first==1)
     mi=0;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     m=firstpass;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     while(s[m][i] <= nlstate){            }else{
       if(s[m][i]>=1)              if(first==1)
         mw[++mi][i]=m;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       if(m >=lastpass)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         break;            }
       else            if( i <= (int) agemax){
         m++;              if(pos>=1.e-5){
     }/* end while */                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
     if (s[m][i] > nlstate){                probs[i][jk][j1]= pp[jk]/pos;
       mi++;     /* Death is another wave */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       /* if(mi==0)  never been interviewed correctly before death */              }
          /* Only death is a correct wave */              else
       mw[mi][i]=m;                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
     }            }
           }
     wav[i]=mi;          
     if(mi==0)          for(jk=-1; jk <=nlstate+ndeath; jk++)
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            for(m=-1; m <=nlstate+ndeath; m++)
   }              if(freq[jk][m][i] !=0 ) {
               if(first==1)
   for(i=1; i<=imx; i++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(mi=1; mi<wav[i];mi++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       if (stepm <=0)              }
         dh[mi][i]=1;          if(i <= (int) agemax)
       else{            fprintf(ficresp,"\n");
         if (s[mw[mi+1][i]][i] > nlstate) {          if(first==1)
           if (agedc[i] < 2*AGESUP) {            printf("Others in log...\n");
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          fprintf(ficlog,"\n");
           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;    dateintmean=dateintsum/k2cpt; 
           sum=sum+j;   
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    fclose(ficresp);
           }    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
         }    free_vector(pp,1,nlstate);
         else{    
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    /* End of Freq */
           k=k+1;  }
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;  /************ Prevalence ********************/
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
           sum=sum+j;  {  /* Some frequencies */
         }   
         jk= j/stepm;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         jl= j -jk*stepm;    double ***freq; /* Frequencies */
         ju= j -(jk+1)*stepm;    double *pp;
         if(jl <= -ju)    double pos, k2;
           dh[mi][i]=jk;  
         else    pp=vector(1,nlstate);
           dh[mi][i]=jk+1;    
         if(dh[mi][i]==0)    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
           dh[mi][i]=1; /* At least one step */    j1=0;
       }    
     }    j=cptcoveff;
   }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   jmean=sum/k;    
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    for(k1=1; k1<=j;k1++){
  }      for(i1=1; i1<=ncodemax[k1];i1++){
 /*********** Tricode ****************************/        j1++;
 void tricode(int *Tvar, int **nbcode, int imx)        
 {        for (i=-1; i<=nlstate+ndeath; i++)  
   int Ndum[20],ij=1, k, j, i;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   int cptcode=0;            for(m=agemin; m <= agemax+3; m++)
   cptcoveff=0;              freq[i][jk][m]=0;
         
   for (k=0; k<19; k++) Ndum[k]=0;        for (i=1; i<=imx; i++) {
   for (k=1; k<=7; k++) ncodemax[k]=0;          bool=1;
           if  (cptcovn>0) {
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            for (z1=1; z1<=cptcoveff; z1++) 
     for (i=1; i<=imx; i++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       ij=(int)(covar[Tvar[j]][i]);                bool=0;
       Ndum[ij]++;          } 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          if (bool==1) { 
       if (ij > cptcode) cptcode=ij;            for(m=firstpass; m<=lastpass; m++){
     }              k2=anint[m][i]+(mint[m][i]/12.);
               if ((k2>=dateprev1) && (k2<=dateprev2)) {
     for (i=0; i<=cptcode; i++) {                if(agev[m][i]==0) agev[m][i]=agemax+1;
       if(Ndum[i]!=0) ncodemax[j]++;                if(agev[m][i]==1) agev[m][i]=agemax+2;
     }                if (m<lastpass) {
     ij=1;                  if (calagedate>0) 
                     freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
                   else
     for (i=1; i<=ncodemax[j]; i++) {                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       for (k=0; k<=19; k++) {                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
         if (Ndum[k] != 0) {                }
           nbcode[Tvar[j]][ij]=k;              }
                      }
           ij++;          }
         }        }
         if (ij > ncodemax[j]) break;        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
       }            for(jk=1; jk <=nlstate ; jk++){
     }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   }                pp[jk] += freq[jk][m][i]; 
           }
  for (k=0; k<19; k++) Ndum[k]=0;          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
  for (i=1; i<=ncovmodel-2; i++) {              pos += freq[jk][m][i];
       ij=Tvar[i];          }
       Ndum[ij]++;          
     }          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
  ij=1;              pp[jk] += freq[jk][m][i];
  for (i=1; i<=10; i++) {          }
    if((Ndum[i]!=0) && (i<=ncovcol)){          
      Tvaraff[ij]=i;          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
      ij++;          
    }          for(jk=1; jk <=nlstate ; jk++){    
  }            if( i <= (int) agemax){
                if(pos>=1.e-5){
     cptcoveff=ij-1;                probs[i][jk][j1]= pp[jk]/pos;
 }              }
             }
 /*********** Health Expectancies ****************/          }/* end jk */
         }/* end i */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)      } /* end i1 */
 {    } /* end k1 */
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm;    
   double age, agelim, hf;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   double ***p3mat;    free_vector(pp,1,nlstate);
      
   fprintf(ficreseij,"# Health expectancies\n");  }  /* End of Freq */
   fprintf(ficreseij,"# Age");  
   for(i=1; i<=nlstate;i++)  /************* Waves Concatenation ***************/
     for(j=1; j<=nlstate;j++)  
       fprintf(ficreseij," %1d-%1d",i,j);  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   fprintf(ficreseij,"\n");  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   if(estepm < stepm){       Death is a valid wave (if date is known).
     printf ("Problem %d lower than %d\n",estepm, stepm);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   else  hstepm=estepm;         and mw[mi+1][i]. dh depends on stepm.
   /* We compute the life expectancy from trapezoids spaced every estepm months       */
    * 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    int i, mi, m;
    * we are calculating an estimate of the Life Expectancy assuming a linear    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
    * progression inbetween and thus overestimating or underestimating according       double sum=0., jmean=0.;*/
    * to the curvature of the survival function. If, for the same date, we    int first;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    int j, k=0,jk, ju, jl;
    * to compare the new estimate of Life expectancy with the same linear    double sum=0.;
    * hypothesis. A more precise result, taking into account a more precise    first=0;
    * curvature will be obtained if estepm is as small as stepm. */    jmin=1e+5;
     jmax=-1;
   /* For example we decided to compute the life expectancy with the smallest unit */    jmean=0.;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    for(i=1; i<=imx; i++){
      nhstepm is the number of hstepm from age to agelim      mi=0;
      nstepm is the number of stepm from age to agelin.      m=firstpass;
      Look at hpijx to understand the reason of that which relies in memory size      while(s[m][i] <= nlstate){
      and note for a fixed period like estepm months */        if(s[m][i]>=1)
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          mw[++mi][i]=m;
      survival function given by stepm (the optimization length). Unfortunately it        if(m >=lastpass)
      means that if the survival funtion is printed only each two years of age and if          break;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        else
      results. So we changed our mind and took the option of the best precision.          m++;
   */      }/* end while */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
   agelim=AGESUP;        /* if(mi==0)  never been interviewed correctly before death */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */           /* Only death is a correct wave */
     /* nhstepm age range expressed in number of stepm */        mw[mi][i]=m;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  
     /* if (stepm >= YEARM) hstepm=1;*/      wav[i]=mi;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      if(mi==0){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if(first==0){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          first=1;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          }
          if(first==1){
     /*for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++) printf("%f %.5f\n", age*12+h, p3mat[1][1][h]);*/          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
         }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      } /* end mi==0 */
     for(i=1; i<=nlstate;i++)    }
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    for(i=1; i<=imx; i++){
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      for(mi=1; mi<wav[i];mi++){
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/        if (stepm <=0)
         }          dh[mi][i]=1;
     fprintf(ficreseij,"%3.0f",age );        else{
     for(i=1; i<=nlstate;i++)          if (s[mw[mi+1][i]][i] > nlstate) {
       for(j=1; j<=nlstate;j++){            if (agedc[i] < 2*AGESUP) {
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       }            if(j==0) j=1;  /* Survives at least one month after exam */
     fprintf(ficreseij,"\n");            k=k+1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if (j >= jmax) jmax=j;
   }            if (j <= jmin) jmin=j;
 }            sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i); */
 /************ Variance ******************/            }
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)          }
 {          else{
   /* Variance of health expectancies */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            k=k+1;
   double **newm;            if (j >= jmax) jmax=j;
   double **dnewm,**doldm;            else if (j <= jmin)jmin=j;
   int i, j, nhstepm, hstepm, h, nstepm ;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   int k, cptcode;            sum=sum+j;
   double *xp;          }
   double **gp, **gm;          jk= j/stepm;
   double ***gradg, ***trgradg;          jl= j -jk*stepm;
   double ***p3mat;          ju= j -(jk+1)*stepm;
   double age,agelim, hf;          if(jl <= -ju){
   int theta;            dh[mi][i]=jk;
             bh[mi][i]=jl;
    fprintf(ficresvij,"# Covariances of life expectancies\n");          }
   fprintf(ficresvij,"# Age");          else{
   for(i=1; i<=nlstate;i++)            dh[mi][i]=jk+1;
     for(j=1; j<=nlstate;j++)            bh[mi][i]=ju;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          }
   fprintf(ficresvij,"\n");          if(dh[mi][i]==0){
             dh[mi][i]=1; /* At least one step */
   xp=vector(1,npar);            bh[mi][i]=ju; /* At least one step */
   dnewm=matrix(1,nlstate,1,npar);            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);
   doldm=matrix(1,nlstate,1,nlstate);          }
            if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);
   if(estepm < stepm){        }
     printf ("Problem %d lower than %d\n",estepm, stepm);      }
   }    }
   else  hstepm=estepm;      jmean=sum/k;
   /* For example we decided to compute the life expectancy with the smallest unit */    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      nhstepm is the number of hstepm from age to agelim   }
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size  /*********** Tricode ****************************/
      and note for a fixed period like k years */  void tricode(int *Tvar, int **nbcode, int imx)
   /* 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    
      means that if the survival funtion is printed only each two years of age and if    int Ndum[20],ij=1, k, j, i, maxncov=19;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    int cptcode=0;
      results. So we changed our mind and took the option of the best precision.    cptcoveff=0; 
   */   
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for (k=0; k<maxncov; k++) Ndum[k]=0;
   agelim = AGESUP;    for (k=1; k<=7; k++) ncodemax[k]=0;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                 modality*/ 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     gp=matrix(0,nhstepm,1,nlstate);        Ndum[ij]++; /*store the modality */
     gm=matrix(0,nhstepm,1,nlstate);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     for(theta=1; theta <=npar; theta++){                                         Tvar[j]. If V=sex and male is 0 and 
       for(i=1; i<=npar; i++){ /* Computes gradient */                                         female is 1, then  cptcode=1.*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      }
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (i=0; i<=cptcode; i++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        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 */
       }
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)      ij=1; 
           prlim[i][i]=probs[(int)age][i][ij];      for (i=1; i<=ncodemax[j]; i++) {
       }        for (k=0; k<= maxncov; k++) {
            if (Ndum[k] != 0) {
       for(j=1; j<= nlstate; j++){            nbcode[Tvar[j]][ij]=k; 
         for(h=0; h<=nhstepm; h++){            /* 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; */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            ij++;
         }          }
       }          if (ij > ncodemax[j]) break; 
            }  
       for(i=1; i<=npar; i++) /* Computes gradient */      } 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);   for (k=0; k< maxncov; k++) Ndum[k]=0;
    
       if (popbased==1) {   for (i=1; i<=ncovmodel-2; i++) { 
         for(i=1; i<=nlstate;i++)     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           prlim[i][i]=probs[(int)age][i][ij];     ij=Tvar[i];
       }     Ndum[ij]++;
    }
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){   ij=1;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)   for (i=1; i<= maxncov; i++) {
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];     if((Ndum[i]!=0) && (i<=ncovcol)){
         }       Tvaraff[ij]=i; /*For printing */
       }       ij++;
      }
       for(j=1; j<= nlstate; j++)   }
         for(h=0; h<=nhstepm; h++){   
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];   cptcoveff=ij-1; /*Number of simple covariates*/
         }  }
     } /* End theta */  
   /*********** Health Expectancies ****************/
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  
   void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
     for(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)  {
         for(theta=1; theta <=npar; theta++)    /* Health expectancies */
           trgradg[h][j][theta]=gradg[h][theta][j];    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    double ***p3mat,***varhe;
     for(i=1;i<=nlstate;i++)    double **dnewm,**doldm;
       for(j=1;j<=nlstate;j++)    double *xp;
         vareij[i][j][(int)age] =0.;    double **gp, **gm;
     double ***gradg, ***trgradg;
     for(h=0;h<=nhstepm;h++){    int theta;
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    xp=vector(1,npar);
         for(i=1;i<=nlstate;i++)    dnewm=matrix(1,nlstate*2,1,npar);
           for(j=1;j<=nlstate;j++)    doldm=matrix(1,nlstate*2,1,nlstate*2);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    
       }    fprintf(ficreseij,"# Health expectancies\n");
     }    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
     fprintf(ficresvij,"%.0f ",age );      for(j=1; j<=nlstate;j++)
     for(i=1; i<=nlstate;i++)        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       for(j=1; j<=nlstate;j++){    fprintf(ficreseij,"\n");
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  
       }    if(estepm < stepm){
     fprintf(ficresvij,"\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_matrix(gp,0,nhstepm,1,nlstate);    }
     free_matrix(gm,0,nhstepm,1,nlstate);    else  hstepm=estepm;   
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    /* We compute the life expectancy from trapezoids spaced every estepm months
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);     * This is mainly to measure the difference between two models: for example
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * if stepm=24 months pijx are given only every 2 years and by summing them
   } /* End age */     * we are calculating an estimate of the Life Expectancy assuming a linear 
       * progression inbetween and thus overestimating or underestimating according
   free_vector(xp,1,npar);     * to the curvature of the survival function. If, for the same date, we 
   free_matrix(doldm,1,nlstate,1,npar);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   free_matrix(dnewm,1,nlstate,1,nlstate);     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
 }     * curvature will be obtained if estepm is as small as stepm. */
   
 /************ Variance of prevlim ******************/    /* For example we decided to compute the life expectancy with the smallest unit */
 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)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 {       nhstepm is the number of hstepm from age to agelim 
   /* Variance of prevalence limit */       nstepm is the number of stepm from age to agelin. 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       Look at hpijx to understand the reason of that which relies in memory size
   double **newm;       and note for a fixed period like estepm months */
   double **dnewm,**doldm;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   int i, j, nhstepm, hstepm;       survival function given by stepm (the optimization length). Unfortunately it
   int k, cptcode;       means that if the survival funtion is printed only each two years of age and if
   double *xp;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double *gp, *gm;       results. So we changed our mind and took the option of the best precision.
   double **gradg, **trgradg;    */
   double age,agelim;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   int theta;  
        agelim=AGESUP;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fprintf(ficresvpl,"# Age");      /* nhstepm age range expressed in number of stepm */
   for(i=1; i<=nlstate;i++)      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       fprintf(ficresvpl," %1d-%1d",i,i);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fprintf(ficresvpl,"\n");      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   xp=vector(1,npar);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   dnewm=matrix(1,nlstate,1,npar);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   doldm=matrix(1,nlstate,1,nlstate);      gp=matrix(0,nhstepm,1,nlstate*2);
        gm=matrix(0,nhstepm,1,nlstate*2);
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   agelim = AGESUP;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);      /* Computing Variances of health expectancies */
     gm=vector(1,nlstate);  
        for(theta=1; theta <=npar; theta++){
     for(theta=1; theta <=npar; theta++){        for(i=1; i<=npar; i++){ 
       for(i=1; i<=npar; i++){ /* Computes gradient */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        }
       }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    
       for(i=1;i<=nlstate;i++)        cptj=0;
         gp[i] = prlim[i][i];        for(j=1; j<= nlstate; j++){
              for(i=1; i<=nlstate; i++){
       for(i=1; i<=npar; i++) /* Computes gradient */            cptj=cptj+1;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       for(i=1;i<=nlstate;i++)            }
         gm[i] = prlim[i][i];          }
         }
       for(i=1;i<=nlstate;i++)       
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       
     } /* End theta */        for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
     trgradg =matrix(1,nlstate,1,npar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         
     for(j=1; j<=nlstate;j++)        cptj=0;
       for(theta=1; theta <=npar; theta++)        for(j=1; j<= nlstate; j++){
         trgradg[j][theta]=gradg[theta][j];          for(i=1;i<=nlstate;i++){
             cptj=cptj+1;
     for(i=1;i<=nlstate;i++)            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       varpl[i][(int)age] =0.;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          }
     for(i=1;i<=nlstate;i++)        }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        for(j=1; j<= nlstate*2; j++)
           for(h=0; h<=nhstepm-1; h++){
     fprintf(ficresvpl,"%.0f ",age );            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for(i=1; i<=nlstate;i++)          }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));       } 
     fprintf(ficresvpl,"\n");     
     free_vector(gp,1,nlstate);  /* End theta */
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*2;j++)
   free_vector(xp,1,npar);          for(theta=1; theta <=npar; theta++)
   free_matrix(doldm,1,nlstate,1,npar);            trgradg[h][j][theta]=gradg[h][theta][j];
   free_matrix(dnewm,1,nlstate,1,nlstate);       
   
 }       for(i=1;i<=nlstate*2;i++)
         for(j=1;j<=nlstate*2;j++)
 /************ Variance of one-step probabilities  ******************/          varhe[i][j][(int)age] =0.;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)  
 {       printf("%d|",(int)age);fflush(stdout);
   int i, j, i1, k1, j1, z1;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   int k=0, cptcode;       for(h=0;h<=nhstepm-1;h++){
   double **dnewm,**doldm;        for(k=0;k<=nhstepm-1;k++){
   double *xp;          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
   double *gp, *gm;          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
   double **gradg, **trgradg;          for(i=1;i<=nlstate*2;i++)
   double age,agelim, cov[NCOVMAX];            for(j=1;j<=nlstate*2;j++)
   int theta;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   char fileresprob[FILENAMELENGTH];        }
       }
   strcpy(fileresprob,"prob");      /* Computing expectancies */
   strcat(fileresprob,fileres);      for(i=1; i<=nlstate;i++)
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        for(j=1; j<=nlstate;j++)
     printf("Problem with resultfile: %s\n", fileresprob);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);            
    /* 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]);*/
   
   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));      fprintf(ficreseij,"%3.0f",age );
        cptj=0;
   cov[1]=1;      for(i=1; i<=nlstate;i++)
   j=cptcoveff;        for(j=1; j<=nlstate;j++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          cptj++;
   j1=0;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   for(k1=1; k1<=1;k1++){        }
     for(i1=1; i1<=ncodemax[k1];i1++){      fprintf(ficreseij,"\n");
     j1++;     
       free_matrix(gm,0,nhstepm,1,nlstate*2);
     if  (cptcovn>0) {      free_matrix(gp,0,nhstepm,1,nlstate*2);
       fprintf(ficresprob, "\n#********** Variable ");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
       fprintf(ficresprob, "**********\n#");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    }
        printf("\n");
       for (age=bage; age<=fage; age ++){    fprintf(ficlog,"\n");
         cov[2]=age;  
         for (k=1; k<=cptcovn;k++) {    free_vector(xp,1,npar);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    free_matrix(dnewm,1,nlstate*2,1,npar);
              free_matrix(doldm,1,nlstate*2,1,nlstate*2);
         }    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  }
         for (k=1; k<=cptcovprod;k++)  
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /************ 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)
         gradg=matrix(1,npar,1,9);  {
         trgradg=matrix(1,9,1,npar);    /* Variance of health expectancies */
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    /* double **newm;*/
        double **dnewm,**doldm;
         for(theta=1; theta <=npar; theta++){    double **dnewmp,**doldmp;
           for(i=1; i<=npar; i++)    int i, j, nhstepm, hstepm, h, nstepm ;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    int k, cptcode;
              double *xp;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    double **gp, **gm;  /* for var eij */
              double ***gradg, ***trgradg; /*for var eij */
           k=0;    double **gradgp, **trgradgp; /* for var p point j */
           for(i=1; i<= (nlstate+ndeath); i++){    double *gpp, *gmp; /* for var p point j */
             for(j=1; j<=(nlstate+ndeath);j++){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
               k=k+1;    double ***p3mat;
               gp[k]=pmmij[i][j];    double age,agelim, hf;
             }    double ***mobaverage;
           }    int theta;
              char digit[4];
           for(i=1; i<=npar; i++)    char digitp[25];
             xp[i] = x[i] - (i==theta ?delti[theta]:0);  
        char fileresprobmorprev[FILENAMELENGTH];
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
           k=0;    if(popbased==1){
           for(i=1; i<=(nlstate+ndeath); i++){      if(mobilav!=0)
             for(j=1; j<=(nlstate+ndeath);j++){        strcpy(digitp,"-populbased-mobilav-");
               k=k+1;      else strcpy(digitp,"-populbased-nomobil-");
               gm[k]=pmmij[i][j];    }
             }    else 
           }      strcpy(digitp,"-stablbased-");
        
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    if (mobilav!=0) {
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        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);
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           for(theta=1; theta <=npar; theta++)      }
             trgradg[j][theta]=gradg[theta][j];    }
          
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    strcpy(fileresprobmorprev,"prmorprev"); 
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    sprintf(digit,"%-d",ij);
            /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         pmij(pmmij,cov,ncovmodel,x,nlstate);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
            strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         k=0;    strcat(fileresprobmorprev,fileres);
         for(i=1; i<=(nlstate+ndeath); i++){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           for(j=1; j<=(nlstate+ndeath);j++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
             k=k+1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
             gm[k]=pmmij[i][j];    }
           }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
          fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
      /*printf("\n%d ",(int)age);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      fprintf(ficresprobmorprev," p.%-d SE",j);
      }*/      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         fprintf(ficresprob,"\n%d ",(int)age);    }  
     fprintf(ficresprobmorprev,"\n");
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],doldm[i][i]);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
        fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       }      exit(0);
     }    }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    else{
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      fprintf(ficgp,"\n# Routine varevsij");
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   }      printf("Problem with html file: %s\n", optionfilehtm);
   free_vector(xp,1,npar);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   fclose(ficresprob);      exit(0);
      }
 }    else{
       fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
 /******************* Printing html file ***********/      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    }
  int lastpass, int stepm, int weightopt, char model[],\    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \  
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    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");
  char version[], int popforecast, int estepm ){    fprintf(ficresvij,"# Age");
   int jj1, k1, i1, cpt;    for(i=1; i<=nlstate;i++)
   FILE *fichtm;      for(j=1; j<=nlstate;j++)
   /*char optionfilehtm[FILENAMELENGTH];*/        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficresvij,"\n");
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");    xp=vector(1,npar);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    dnewm=matrix(1,nlstate,1,npar);
     printf("Problem with %s \n",optionfilehtm), exit(0);    doldm=matrix(1,nlstate,1,nlstate);
   }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  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    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
 \n    gpp=vector(nlstate+1,nlstate+ndeath);
 Total number of observations=%d <br>\n    gmp=vector(nlstate+1,nlstate+ndeath);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 <hr  size=\"2\" color=\"#EC5E5E\">    
  <ul><li>Outputs files<br>\n    if(estepm < stepm){
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      printf ("Problem %d lower than %d\n",estepm, stepm);
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    }
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    else  hstepm=estepm;   
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    /* For example we decided to compute the life expectancy with the smallest unit */
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
  fprintf(fichtm,"\n       Look at hpijx to understand the reason of that which relies in memory size
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n       and note for a fixed period like k years */
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n       survival function given by stepm (the optimization length). Unfortunately it
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  if(popforecast==1) fprintf(fichtm,"\n       results. So we changed our mind and took the option of the best precision.
  - 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    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         <br>",fileres,fileres,fileres,fileres);    agelim = AGESUP;
  else    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
    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);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 fprintf(fichtm," <li>Graphs</li><p>");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  m=cptcoveff;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
  jj1=0;  
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){      for(theta=1; theta <=npar; theta++){
        jj1++;        for(i=1; i<=npar; i++){ /* Computes gradient */
        if (cptcovn > 0) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        }
          for (cpt=1; cpt<=cptcoveff;cpt++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }        if (popbased==1) {
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          if(mobilav ==0){
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                for(i=1; i<=nlstate;i++)
        for(cpt=1; cpt<nlstate;cpt++){              prlim[i][i]=probs[(int)age][i][ij];
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          }else{ /* mobilav */ 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for(i=1; i<=nlstate;i++)
        }              prlim[i][i]=mobaverage[(int)age][i][ij];
     for(cpt=1; cpt<=nlstate;cpt++) {          }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        }
 interval) in state (%d): v%s%d%d.gif <br>    
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(j=1; j<= nlstate; j++){
      }          for(h=0; h<=nhstepm; h++){
      for(cpt=1; cpt<=nlstate;cpt++) {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          }
      }        }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        /* This for computing forces of mortality (h=1)as a weighted average */
 health expectancies in states (1) and (2): e%s%d.gif<br>        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          for(i=1; i<= nlstate; i++)
 fprintf(fichtm,"\n</body>");            gpp[j] += prlim[i][i]*p3mat[i][j][1];
    }        }    
    }        /* end force of mortality */
 fclose(fichtm);  
 }        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
 /******************* Gnuplot file **************/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        if (popbased==1) {
           if(mobilav ==0){
   strcpy(optionfilegnuplot,optionfilefiname);            for(i=1; i<=nlstate;i++)
   strcat(optionfilegnuplot,".gp.txt");              prlim[i][i]=probs[(int)age][i][ij];
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          }else{ /* mobilav */ 
     printf("Problem with file %s",optionfilegnuplot);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
 #ifdef windows        }
     fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif        for(j=1; j<= nlstate; j++){
 m=pow(2,cptcoveff);          for(h=0; h<=nhstepm; h++){
              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
  /* 1eme*/              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   for (cpt=1; cpt<= nlstate ; cpt ++) {          }
    for (k1=1; k1<= m ; k1 ++) {        }
         /* This for computing force of mortality (h=1)as a weighted average */
 #ifdef windows        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
     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",ageminpar,fage,fileres,k1-1,k1-1);          for(i=1; i<= nlstate; i++)
 #endif            gmp[j] += prlim[i][i]*p3mat[i][j][1];
 #ifdef unix        }    
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        /* end force of mortality */
 #endif  
         for(j=1; j<= nlstate; j++) /* vareij */
 for (i=1; i<= nlstate ; i ++) {          for(h=0; h<=nhstepm; h++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     for (i=1; i<= nlstate ; i ++) {        }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      } /* End theta */
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for(h=0; h<=nhstepm; h++) /* veij */
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<=nlstate;j++)
 }            for(theta=1; theta <=npar; theta++)
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            trgradg[h][j][theta]=gradg[h][theta][j];
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
 #endif        for(theta=1; theta <=npar; theta++)
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          trgradgp[j][theta]=gradgp[theta][j];
    }  
   }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   /*2 eme*/      for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
   for (k1=1; k1<= m ; k1 ++) {          vareij[i][j][(int)age] =0.;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);  
          for(h=0;h<=nhstepm;h++){
     for (i=1; i<= nlstate+1 ; i ++) {        for(k=0;k<=nhstepm;k++){
       k=2*i;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       for (j=1; j<= nlstate+1 ; j ++) {          for(i=1;i<=nlstate;i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(j=1;j<=nlstate;j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
 }          }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      /* pptj */
       for (j=1; j<= nlstate+1 ; j ++) {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
         else fprintf(ficgp," \%%*lf (\%%*lf)");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
 }          for(i=nlstate+1;i<=nlstate+ndeath;i++)
       fprintf(ficgp,"\" t\"\" w l 0,");          varppt[j][i]=doldmp[j][i];
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      /* end ppptj */
       for (j=1; j<= nlstate+1 ; j ++) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }        if (popbased==1) {
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        if(mobilav ==0){
       else fprintf(ficgp,"\" t\"\" w l 0,");          for(i=1; i<=nlstate;i++)
     }            prlim[i][i]=probs[(int)age][i][ij];
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        }else{ /* mobilav */ 
   }          for(i=1; i<=nlstate;i++)
              prlim[i][i]=mobaverage[(int)age][i][ij];
   /*3eme*/        }
       }
   for (k1=1; k1<= m ; k1 ++) {      
     for (cpt=1; cpt<= nlstate ; cpt ++) {      /* This for computing force of mortality (h=1)as a weighted average */
       k=2+nlstate*(cpt-1);      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
       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",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        for(i=1; i<= nlstate; i++)
       for (i=1; i< nlstate ; i ++) {          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         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);      }    
       }      /* end force of mortality */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }      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]));
   /* CV preval stat */        for(i=1; i<=nlstate;i++){
     for (k1=1; k1<= m ; k1 ++) {          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     for (cpt=1; cpt<nlstate ; cpt ++) {        }
       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",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      fprintf(ficresprobmorprev,"\n");
   
       for (i=1; i< nlstate ; i ++)      fprintf(ficresvij,"%.0f ",age );
         fprintf(ficgp,"+$%d",k+i+1);      for(i=1; i<=nlstate;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        for(j=1; j<=nlstate;j++){
                fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       l=3+(nlstate+ndeath)*cpt;        }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      fprintf(ficresvij,"\n");
       for (i=1; i< nlstate ; i ++) {      free_matrix(gp,0,nhstepm,1,nlstate);
         l=3+(nlstate+ndeath)*cpt;      free_matrix(gm,0,nhstepm,1,nlstate);
         fprintf(ficgp,"+$%d",l+i+1);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    } /* End age */
     }    free_vector(gpp,nlstate+1,nlstate+ndeath);
   }      free_vector(gmp,nlstate+1,nlstate+ndeath);
      free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   /* proba elementaires */    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     for(k=1; k <=(nlstate+ndeath); k++){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       if (k != i) {    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         for(j=1; j <=ncovmodel; j++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
            fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
           jk++;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
           fprintf(ficgp,"\n");    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
         }    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       }  */
     }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
     }  
     free_vector(xp,1,npar);
     for(jk=1; jk <=m; jk++) {    free_matrix(doldm,1,nlstate,1,nlstate);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    free_matrix(dnewm,1,nlstate,1,npar);
    i=1;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    for(k2=1; k2<=nlstate; k2++) {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      k3=i;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      for(k=1; k<=(nlstate+ndeath); k++) {    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (k != k2){    fclose(ficresprobmorprev);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    fclose(ficgp);
 ij=1;    fclose(fichtm);
         for(j=3; j <=ncovmodel; j++) {  }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  /************ Variance of prevlim ******************/
             ij++;  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)
           }  {
           else    /* Variance of prevalence limit */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         }    double **newm;
           fprintf(ficgp,")/(1");    double **dnewm,**doldm;
            int i, j, nhstepm, hstepm;
         for(k1=1; k1 <=nlstate; k1++){      int k, cptcode;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    double *xp;
 ij=1;    double *gp, *gm;
           for(j=3; j <=ncovmodel; j++){    double **gradg, **trgradg;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double age,agelim;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    int theta;
             ij++;     
           }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
           else    fprintf(ficresvpl,"# Age");
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    for(i=1; i<=nlstate;i++)
           }        fprintf(ficresvpl," %1d-%1d",i,i);
           fprintf(ficgp,")");    fprintf(ficresvpl,"\n");
         }  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    xp=vector(1,npar);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    dnewm=matrix(1,nlstate,1,npar);
         i=i+ncovmodel;    doldm=matrix(1,nlstate,1,nlstate);
        }    
      }    hstepm=1*YEARM; /* Every year of age */
    }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    agelim = AGESUP;
    }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
          nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   fclose(ficgp);      if (stepm >= YEARM) hstepm=1;
 }  /* end gnuplot */      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
 /*************** Moving average **************/      gm=vector(1,nlstate);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  
       for(theta=1; theta <=npar; theta++){
   int i, cpt, cptcod;        for(i=1; i<=npar; i++){ /* Computes gradient */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for (i=1; i<=nlstate;i++)        }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           mobaverage[(int)agedeb][i][cptcod]=0.;        for(i=1;i<=nlstate;i++)
              gp[i] = prlim[i][i];
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      
       for (i=1; i<=nlstate;i++){        for(i=1; i<=npar; i++) /* Computes gradient */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           for (cpt=0;cpt<=4;cpt++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        for(i=1;i<=nlstate;i++)
           }          gm[i] = prlim[i][i];
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }        for(i=1;i<=nlstate;i++)
       }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     }      } /* End theta */
      
 }      trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
 /************** Forecasting ******************/        for(theta=1; theta <=npar; theta++)
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){          trgradg[j][theta]=gradg[theta][j];
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      for(i=1;i<=nlstate;i++)
   int *popage;        varpl[i][(int)age] =0.;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   double *popeffectif,*popcount;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   double ***p3mat;      for(i=1;i<=nlstate;i++)
   char fileresf[FILENAMELENGTH];        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
  agelim=AGESUP;      fprintf(ficresvpl,"%.0f ",age );
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      fprintf(ficresvpl,"\n");
        free_vector(gp,1,nlstate);
        free_vector(gm,1,nlstate);
   strcpy(fileresf,"f");      free_matrix(gradg,1,npar,1,nlstate);
   strcat(fileresf,fileres);      free_matrix(trgradg,1,nlstate,1,npar);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    } /* End age */
     printf("Problem with forecast resultfile: %s\n", fileresf);  
   }    free_vector(xp,1,npar);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
   }
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /************ Variance of one-step probabilities  ******************/
     movingaverage(agedeb, fage, ageminpar, mobaverage);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   }  {
     int i, j=0,  i1, k1, l1, t, tj;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int k2, l2, j1,  z1;
   if (stepm<=12) stepsize=1;    int k=0,l, cptcode;
      int first=1, first1;
   agelim=AGESUP;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      double **dnewm,**doldm;
   hstepm=1;    double *xp;
   hstepm=hstepm/stepm;    double *gp, *gm;
   yp1=modf(dateintmean,&yp);    double **gradg, **trgradg;
   anprojmean=yp;    double **mu;
   yp2=modf((yp1*12),&yp);    double age,agelim, cov[NCOVMAX];
   mprojmean=yp;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   yp1=modf((yp2*30.5),&yp);    int theta;
   jprojmean=yp;    char fileresprob[FILENAMELENGTH];
   if(jprojmean==0) jprojmean=1;    char fileresprobcov[FILENAMELENGTH];
   if(mprojmean==0) jprojmean=1;    char fileresprobcor[FILENAMELENGTH];
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    double ***varpij;
    
   for(cptcov=1;cptcov<=i2;cptcov++){    strcpy(fileresprob,"prob"); 
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    strcat(fileresprob,fileres);
       k=k+1;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       fprintf(ficresf,"\n#******");      printf("Problem with resultfile: %s\n", fileresprob);
       for(j=1;j<=cptcoveff;j++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
       }    strcpy(fileresprobcov,"probcov"); 
       fprintf(ficresf,"******\n");    strcat(fileresprobcov,fileres);
       fprintf(ficresf,"# StartingAge FinalAge");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      printf("Problem with resultfile: %s\n", fileresprobcov);
            fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
          }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    strcpy(fileresprobcor,"probcor"); 
         fprintf(ficresf,"\n");    strcat(fileresprobcor,fileres);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    }
           nhstepm = nhstepm/hstepm;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
              fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           oldm=oldms;savm=savms;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
            fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           for (h=0; h<=nhstepm; h++){    
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    fprintf(ficresprob,"# Age");
             }    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
             for(j=1; j<=nlstate+ndeath;j++) {    fprintf(ficresprobcov,"# Age");
               kk1=0.;kk2=0;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
               for(i=1; i<=nlstate;i++) {                  fprintf(ficresprobcov,"# Age");
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {    for(i=1; i<=nlstate;i++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for(j=1; j<=(nlstate+ndeath);j++){
                 }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
                        fprintf(ficresprobcov," p%1d-%1d ",i,j);
               }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
               if (h==(int)(calagedate+12*cpt)){      }  
                 fprintf(ficresf," %.3f", kk1);    fprintf(ficresprob,"\n");
                            fprintf(ficresprobcov,"\n");
               }    fprintf(ficresprobcor,"\n");
             }    xp=vector(1,npar);
           }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       }    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     }    first=1;
   }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
              printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
   fclose(ficresf);    }
 }    else{
 /************** Forecasting ******************/      fprintf(ficgp,"\n# Routine varprob");
 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){    }
      if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      printf("Problem with html file: %s\n", optionfilehtm);
   int *popage;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      exit(0);
   double *popeffectif,*popcount;    }
   double ***p3mat,***tabpop,***tabpopprev;    else{
   char filerespop[FILENAMELENGTH];      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(fichtm,"\n");
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   agelim=AGESUP;      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");
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      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");
    
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    }
    
      cov[1]=1;
   strcpy(filerespop,"pop");    tj=cptcoveff;
   strcat(filerespop,fileres);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    j1=0;
     printf("Problem with forecast resultfile: %s\n", filerespop);    for(t=1; t<=tj;t++){
   }      for(i1=1; i1<=ncodemax[t];i1++){ 
   printf("Computing forecasting: result on file '%s' \n", filerespop);        j1++;
         if  (cptcovn>0) {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (mobilav==1) {          fprintf(ficresprob, "**********\n#");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficresprobcov, "\n#********** Variable "); 
     movingaverage(agedeb, fage, ageminpar, mobaverage);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprobcov, "**********\n#");
           
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficgp, "\n#********** Variable "); 
   if (stepm<=12) stepsize=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficgp, "**********\n#");
   agelim=AGESUP;          
            
   hstepm=1;          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   hstepm=hstepm/stepm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   if (popforecast==1) {          
     if((ficpop=fopen(popfile,"r"))==NULL) {          fprintf(ficresprobcor, "\n#********** Variable ");    
       printf("Problem with population file : %s\n",popfile);exit(0);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficgp, "**********\n#");    
     popage=ivector(0,AGESUP);        }
     popeffectif=vector(0,AGESUP);        
     popcount=vector(0,AGESUP);        for (age=bage; age<=fage; age ++){ 
              cov[2]=age;
     i=1;            for (k=1; k<=cptcovn;k++) {
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
              }
     imx=i;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          for (k=1; k<=cptcovprod;k++)
   }            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
   for(cptcov=1;cptcov<=i2;cptcov++){          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       k=k+1;          gp=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficrespop,"\n#******");          gm=vector(1,(nlstate)*(nlstate+ndeath));
       for(j=1;j<=cptcoveff;j++) {      
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(theta=1; theta <=npar; theta++){
       }            for(i=1; i<=npar; i++)
       fprintf(ficrespop,"******\n");              xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficrespop,"# Age");            
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       if (popforecast==1)  fprintf(ficrespop," [Population]");            
                  k=0;
       for (cpt=0; cpt<=0;cpt++) {            for(i=1; i<= (nlstate); i++){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                for(j=1; j<=(nlstate+ndeath);j++){
                        k=k+1;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                gp[k]=pmmij[i][j];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              }
           nhstepm = nhstepm/hstepm;            }
                      
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(i=1; i<=npar; i++)
           oldm=oldms;savm=savms;              xp[i] = x[i] - (i==theta ?delti[theta]:0);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        
                    pmij(pmmij,cov,ncovmodel,xp,nlstate);
           for (h=0; h<=nhstepm; h++){            k=0;
             if (h==(int) (calagedate+YEARM*cpt)) {            for(i=1; i<=(nlstate); i++){
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              for(j=1; j<=(nlstate+ndeath);j++){
             }                k=k+1;
             for(j=1; j<=nlstate+ndeath;j++) {                gm[k]=pmmij[i][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];            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                 else {              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          }
                 }  
               }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
               if (h==(int)(calagedate+12*cpt)){            for(theta=1; theta <=npar; theta++)
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;              trgradg[j][theta]=gradg[theta][j];
                   /*fprintf(ficrespop," %.3f", kk1);          
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+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));
             for(i=1; i<=nlstate;i++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
               kk1=0.;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                 for(j=1; j<=nlstate;j++){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  
                 }          pmij(pmmij,cov,ncovmodel,x,nlstate);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          
             }          k=0;
           for(i=1; i<=(nlstate); i++){
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)            for(j=1; j<=(nlstate+ndeath);j++){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);              k=k+1;
           }              mu[k][(int) age]=pmmij[i][j];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
         }          }
       }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
              for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   /******/              varpij[i][j][(int)age] = doldm[i][j];
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          /*printf("\n%d ",(int)age);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           nhstepm = nhstepm/hstepm;            }*/
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprob,"\n%d ",(int)age);
           oldm=oldms;savm=savms;          fprintf(ficresprobcov,"\n%d ",(int)age);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(ficresprobcor,"\n%d ",(int)age);
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
             }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             for(j=1; j<=nlstate+ndeath;j++) {            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
               kk1=0.;kk2=0;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
               for(i=1; i<=nlstate;i++) {                        }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              i=0;
               }          for (k=1; k<=(nlstate);k++){
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            for (l=1; l<=(nlstate+ndeath);l++){ 
             }              i=i++;
           }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
         }              for (j=1; j<=i;j++){
       }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
    }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   }              }
              }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }/* end of loop for state */
         } /* end of loop for age */
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);        /* Confidence intervalle of pij  */
     free_vector(popeffectif,0,AGESUP);        /*
     free_vector(popcount,0,AGESUP);          fprintf(ficgp,"\nset noparametric;unset label");
   }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          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);
   fclose(ficrespop);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
 }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
 /***********************************************/        */
 /**************** Main Program *****************/  
 /***********************************************/        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
 int main(int argc, char *argv[])        for (k2=1; k2<=(nlstate);k2++){
 {          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            j=(k2-1)*(nlstate+ndeath)+l2;
   double agedeb, agefin,hf;            for (k1=1; k1<=(nlstate);k1++){
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
   double fret;                i=(k1-1)*(nlstate+ndeath)+l1;
   double **xi,tmp,delta;                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
   double dum; /* Dummy variable */                  if ((int)age %5==0){
   double ***p3mat;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   int *indx;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   char line[MAXLINE], linepar[MAXLINE];                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   char title[MAXLINE];                    mu1=mu[i][(int) age]/stepm*YEARM ;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];                    mu2=mu[j][(int) age]/stepm*YEARM;
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];                    c12=cv12/sqrt(v1*v2);
                      /* Computing eigen value of matrix of covariance */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   char filerest[FILENAMELENGTH];                    /* Eigen vectors */
   char fileregp[FILENAMELENGTH];                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   char popfile[FILENAMELENGTH];                    /*v21=sqrt(1.-v11*v11); *//* error */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                    v21=(lc1-v1)/cv12*v11;
   int firstobs=1, lastobs=10;                    v12=-v21;
   int sdeb, sfin; /* Status at beginning and end */                    v22=v11;
   int c,  h , cpt,l;                    tnalp=v21/v11;
   int ju,jl, mi;                    if(first1==1){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                      first1=0;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                      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);
   int mobilav=0,popforecast=0;                    }
   int hstepm, nhstepm;                    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);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;                    /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   double bage, fage, age, agelim, agebase;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   double ftolpl=FTOL;                    if(first==1){
   double **prlim;                      first=0;
   double *severity;                      fprintf(ficgp,"\nset parametric;unset label");
   double ***param; /* Matrix of parameters */                      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);
   double  *p;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   double **matcov; /* Matrix of covariance */                      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);
   double ***delti3; /* Scale */                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   double *delti; /* Scale */                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   double ***eij, ***vareij;                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   double **varpl; /* Variances of prevalence limits by age */                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   double *epj, vepp;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   double kk1, kk2;                      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",\
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";                      first=0;
   char *alph[]={"a","a","b","c","d","e"}, str[4];                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   char z[1]="c", occ;                      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",\
 #include <sys/time.h>                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
 #include <time.h>                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                    }/* if first */
                    } /* age mod 5 */
   /* long total_usecs;                } /* end loop age */
   struct timeval start_time, end_time;                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                  first=1;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */              } /*l12 */
   getcwd(pathcd, size);            } /* k12 */
           } /*l1 */
   printf("\n%s",version);        }/* k1 */
   if(argc <=1){      } /* loop covariates */
     printf("\nEnter the parameter file name: ");    }
     scanf("%s",pathtot);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   else{    free_vector(xp,1,npar);
     strcpy(pathtot,argv[1]);    fclose(ficresprob);
   }    fclose(ficresprobcov);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    fclose(ficresprobcor);
   /*cygwin_split_path(pathtot,path,optionfile);    fclose(ficgp);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    fclose(fichtm);
   /* 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);  /******************* Printing html file ***********/
   chdir(path);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   replace(pathc,path);                    int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
 /*-------- arguments in the command line --------*/                    int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
   strcpy(fileres,"r");                    double jprev2, double mprev2,double anprev2){
   strcat(fileres, optionfilefiname);    int jj1, k1, i1, cpt;
   strcat(fileres,".txt");    /* Other files have txt extension */    /*char optionfilehtm[FILENAMELENGTH];*/
     if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   /*---------arguments file --------*/      printf("Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    }
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   }   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
    - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   strcpy(filereso,"o");   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   strcat(filereso,fileres);   - Life expectancies by age and initial health status (estepm=%2d months): 
   if((ficparo=fopen(filereso,"w"))==NULL) {     <a href=\"e%s\">e%s</a> <br>\n</li>", \
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   }  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){   m=cptcoveff;
     ungetc(c,ficpar);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     fgets(line, MAXLINE, ficpar);  
     puts(line);   jj1=0;
     fputs(line,ficparo);   for(k1=1; k1<=m;k1++){
   }     for(i1=1; i1<=ncodemax[k1];i1++){
   ungetc(c,ficpar);       jj1++;
        if (cptcovn > 0) {
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   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);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
 while((c=getc(ficpar))=='#' && c!= EOF){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     ungetc(c,ficpar);       }
     fgets(line, MAXLINE, ficpar);       /* Pij */
     puts(line);       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>
     fputs(line,ficparo);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
   }       /* Quasi-incidences */
   ungetc(c,ficpar);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
    <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
             /* Stable prevalence in each health state */
   covar=matrix(0,NCOVMAX,1,n);         for(cpt=1; cpt<nlstate;cpt++){
   cptcovn=0;           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
   ncovmodel=2+cptcovn;       for(cpt=1; cpt<=nlstate;cpt++) {
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
    <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   /* Read guess parameters */       }
   /* Reads comments: lines beginning with '#' */       fprintf(fichtm,"\n<br>- Total life expectancy by age and
   while((c=getc(ficpar))=='#' && c!= EOF){  health expectancies in states (1) and (2): e%s%d.png<br>
     ungetc(c,ficpar);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     fgets(line, MAXLINE, ficpar);     } /* end i1 */
     puts(line);   }/* End k1 */
     fputs(line,ficparo);   fprintf(fichtm,"</ul>");
   }  
   ungetc(c,ficpar);  
     fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     for(i=1; i <=nlstate; i++)   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     for(j=1; j <=nlstate+ndeath-1; j++){   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
       fscanf(ficpar,"%1d%1d",&i1,&j1);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
       fprintf(ficparo,"%1d%1d",i1,j1);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
       printf("%1d%1d",i,j);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
       for(k=1; k<=ncovmodel;k++){   - 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);
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);   if(popforecast==1) fprintf(fichtm,"\n
         fprintf(ficparo," %lf",param[i][j][k]);   - 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
       fscanf(ficpar,"\n");          <br>",fileres,fileres,fileres,fileres);
       printf("\n");   else 
       fprintf(ficparo,"\n");     fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
     }  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   p=param[1][1];  
     jj1=0;
   /* Reads comments: lines beginning with '#' */   for(k1=1; k1<=m;k1++){
   while((c=getc(ficpar))=='#' && c!= EOF){     for(i1=1; i1<=ncodemax[k1];i1++){
     ungetc(c,ficpar);       jj1++;
     fgets(line, MAXLINE, ficpar);       if (cptcovn > 0) {
     puts(line);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fputs(line,ficparo);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   ungetc(c,ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       for(cpt=1; cpt<=nlstate;cpt++) {
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   for(i=1; i <=nlstate; i++){  interval) in state (%d): v%s%d%d.png <br>
     for(j=1; j <=nlstate+ndeath-1; j++){  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
       fscanf(ficpar,"%1d%1d",&i1,&j1);       }
       printf("%1d%1d",i,j);     } /* end i1 */
       fprintf(ficparo,"%1d%1d",i1,j1);   }/* End k1 */
       for(k=1; k<=ncovmodel;k++){   fprintf(fichtm,"</ul>");
         fscanf(ficpar,"%le",&delti3[i][j][k]);  fclose(fichtm);
         printf(" %le",delti3[i][j][k]);  }
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }  /******************* Gnuplot file **************/
       fscanf(ficpar,"\n");  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
       printf("\n");  
       fprintf(ficparo,"\n");    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     }    int ng;
   }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   delti=delti3[1][1];      printf("Problem with file %s",optionfilegnuplot);
        fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    /*#ifdef windows */
     fgets(line, MAXLINE, ficpar);      fprintf(ficgp,"cd \"%s\" \n",pathc);
     puts(line);      /*#endif */
     fputs(line,ficparo);  m=pow(2,cptcoveff);
   }    
   ungetc(c,ficpar);   /* 1eme*/
      for (cpt=1; cpt<= nlstate ; cpt ++) {
   matcov=matrix(1,npar,1,npar);     for (k1=1; k1<= m ; k1 ++) {
   for(i=1; i <=npar; i++){       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     fscanf(ficpar,"%s",&str);       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);
     printf("%s",str);  
     fprintf(ficparo,"%s",str);       for (i=1; i<= nlstate ; i ++) {
     for(j=1; j <=i; j++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       fscanf(ficpar," %le",&matcov[i][j]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf(" %.5le",matcov[i][j]);       }
       fprintf(ficparo," %.5le",matcov[i][j]);       fprintf(ficgp,"\" t\"Stable 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 ++) {
     fscanf(ficpar,"\n");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     printf("\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
     fprintf(ficparo,"\n");       } 
   }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
   for(i=1; i <=npar; i++)       for (i=1; i<= nlstate ; i ++) {
     for(j=i+1;j<=npar;j++)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       matcov[i][j]=matcov[j][i];         else fprintf(ficgp," \%%*lf (\%%*lf)");
           }  
   printf("\n");       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*-------- Rewriting paramater file ----------*/    /*2 eme*/
      strcpy(rfileres,"r");    /* "Rparameterfile */    
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    for (k1=1; k1<= m ; k1 ++) { 
      strcat(rfileres,".");    /* */      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     if((ficres =fopen(rfileres,"w"))==NULL) {      
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      for (i=1; i<= nlstate+1 ; i ++) {
     }        k=2*i;
     fprintf(ficres,"#%s\n",version);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
            for (j=1; j<= nlstate+1 ; j ++) {
     /*-------- data file ----------*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     if((fic=fopen(datafile,"r"))==NULL)    {          else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf("Problem with datafile: %s\n", datafile);goto end;        }   
     }        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     n= lastobs;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
     severity = vector(1,maxwav);        for (j=1; j<= nlstate+1 ; j ++) {
     outcome=imatrix(1,maxwav+1,1,n);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     num=ivector(1,n);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     moisnais=vector(1,n);        }   
     annais=vector(1,n);        fprintf(ficgp,"\" t\"\" w l 0,");
     moisdc=vector(1,n);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
     andc=vector(1,n);        for (j=1; j<= nlstate+1 ; j ++) {
     agedc=vector(1,n);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     cod=ivector(1,n);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     weight=vector(1,n);        }   
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     mint=matrix(1,maxwav,1,n);        else fprintf(ficgp,"\" t\"\" w l 0,");
     anint=matrix(1,maxwav,1,n);      }
     s=imatrix(1,maxwav+1,1,n);    }
     adl=imatrix(1,maxwav+1,1,n);        
     tab=ivector(1,NCOVMAX);    /*3eme*/
     ncodemax=ivector(1,8);    
     for (k1=1; k1<= m ; k1 ++) { 
     i=1;      for (cpt=1; cpt<= nlstate ; cpt ++) {
     while (fgets(line, MAXLINE, fic) != NULL)    {        k=2+nlstate*(2*cpt-2);
       if ((i >= firstobs) && (i <=lastobs)) {        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
                fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         for (j=maxwav;j>=1;j--){        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           strcpy(line,stra);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                  
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
         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);    /* CV preval stat */
         }    for (k1=1; k1<= m ; k1 ++) { 
         num[i]=atol(stra);      for (cpt=1; cpt<nlstate ; cpt ++) {
                k=3;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           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;}*/        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);
         
         i=i+1;        for (i=1; i< nlstate ; i ++)
       }          fprintf(ficgp,"+$%d",k+i+1);
     }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     /* printf("ii=%d", ij);        
        scanf("%d",i);*/        l=3+(nlstate+ndeath)*cpt;
   imx=i-1; /* Number of individuals */        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
   /* for (i=1; i<=imx; i++){          l=3+(nlstate+ndeath)*cpt;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          fprintf(ficgp,"+$%d",l+i+1);
     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;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     }*/      } 
    /*  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]));}*/    /* proba elementaires */
      for(i=1,jk=1; i <=nlstate; i++){
        for(k=1; k <=(nlstate+ndeath); k++){
   /* Calculation of the number of parameter from char model*/        if (k != i) {
   Tvar=ivector(1,15);          for(j=1; j <=ncovmodel; j++){
   Tprod=ivector(1,15);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   Tvaraff=ivector(1,15);            jk++; 
   Tvard=imatrix(1,15,1,2);            fprintf(ficgp,"\n");
   Tage=ivector(1,15);                }
            }
   if (strlen(model) >1){      }
     j=0, j1=0, k1=1, k2=1;     }
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     cptcovn=j+1;       for(jk=1; jk <=m; jk++) {
     cptcovprod=j1;         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
             if (ng==2)
     strcpy(modelsav,model);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){         else
       printf("Error. Non available option model=%s ",model);           fprintf(ficgp,"\nset title \"Probability\"\n");
       goto end;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     }         i=1;
             for(k2=1; k2<=nlstate; k2++) {
     for(i=(j+1); i>=1;i--){           k3=i;
       cutv(stra,strb,modelsav,'+');           for(k=1; k<=(nlstate+ndeath); k++) {
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);             if (k != k2){
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/               if(ng==2)
       /*scanf("%d",i);*/                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
       if (strchr(strb,'*')) {               else
         cutv(strd,strc,strb,'*');                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
         if (strcmp(strc,"age")==0) {               ij=1;
           cptcovprod--;               for(j=3; j <=ncovmodel; j++) {
           cutv(strb,stre,strd,'V');                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           Tvar[i]=atoi(stre);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           cptcovage++;                   ij++;
             Tage[cptcovage]=i;                 }
             /*printf("stre=%s ", stre);*/                 else
         }                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         else if (strcmp(strd,"age")==0) {               }
           cptcovprod--;               fprintf(ficgp,")/(1");
           cutv(strb,stre,strc,'V');               
           Tvar[i]=atoi(stre);               for(k1=1; k1 <=nlstate; k1++){   
           cptcovage++;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
           Tage[cptcovage]=i;                 ij=1;
         }                 for(j=3; j <=ncovmodel; j++){
         else {                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           cutv(strb,stre,strc,'V');                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           Tvar[i]=ncovcol+k1;                     ij++;
           cutv(strb,strc,strd,'V');                   }
           Tprod[k1]=i;                   else
           Tvard[k1][1]=atoi(strc);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           Tvard[k1][2]=atoi(stre);                 }
           Tvar[cptcovn+k2]=Tvard[k1][1];                 fprintf(ficgp,")");
           Tvar[cptcovn+k2+1]=Tvard[k1][2];               }
           for (k=1; k<=lastobs;k++)               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           k1++;               i=i+ncovmodel;
           k2=k2+2;             }
         }           } /* end k */
       }         } /* end k2 */
       else {       } /* end jk */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/     } /* end ng */
        /*  scanf("%d",i);*/     fclose(ficgp); 
       cutv(strd,strc,strb,'V');  }  /* end gnuplot */
       Tvar[i]=atoi(strc);  
       }  
       strcpy(modelsav,stra);    /*************** Moving average **************/
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
         scanf("%d",i);*/  
     }    int i, cpt, cptcod;
 }    int modcovmax =1;
      int mobilavrange, mob;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    double age;
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
     fclose(fic);                             a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       for(i=1;i<=n;i++) weight[i]=1.0;      if(mobilav==1) mobilavrange=5; /* default */
     }      else mobilavrange=mobilav;
     /*-calculation of age at interview from date of interview and age at death -*/      for (age=bage; age<=fage; age++)
     agev=matrix(1,maxwav,1,imx);        for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
     for (i=1; i<=imx; i++) {            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       for(m=2; (m<= maxwav); m++) {      /* We keep the original values on the extreme ages bage, fage and for 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          anint[m][i]=9999;         we use a 5 terms etc. until the borders are no more concerned. 
          s[m][i]=-1;      */ 
        }      for (mob=3;mob <=mobilavrange;mob=mob+2){
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
       }          for (i=1; i<=nlstate;i++){
     }            for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
     for (i=1; i<=imx; i++)  {                for (cpt=1;cpt<=(mob-1)/2;cpt++){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       for(m=1; (m<= maxwav); m++){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
         if(s[m][i] >0){                }
           if (s[m][i] >= nlstate+1) {              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             if(agedc[i]>0)            }
               if(moisdc[i]!=99 && andc[i]!=9999)          }
                 agev[m][i]=agedc[i];        }/* end age */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      }/* end mob */
            else {    }else return -1;
               if (andc[i]!=9999){    return 0;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  }/* End movingaverage */
               agev[m][i]=-1;  
               }  
             }  /************** Forecasting ******************/
           }  prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
           else if(s[m][i] !=9){ /* Should no more exist */    
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
             if(mint[m][i]==99 || anint[m][i]==9999)    int *popage;
               agev[m][i]=1;    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
             else if(agev[m][i] <agemin){    double *popeffectif,*popcount;
               agemin=agev[m][i];    double ***p3mat;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    double ***mobaverage;
             }    char fileresf[FILENAMELENGTH];
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];   agelim=AGESUP;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
             /*   agev[m][i] = age[i]+2*m;*/   
           }   
           else { /* =9 */    strcpy(fileresf,"f"); 
             agev[m][i]=1;    strcat(fileresf,fileres);
             s[m][i]=-1;    if((ficresf=fopen(fileresf,"w"))==NULL) {
           }      printf("Problem with forecast resultfile: %s\n", fileresf);
         }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
         else /*= 0 Unknown */    }
           agev[m][i]=1;    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;
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){    if (mobilav!=0) {
         if (s[m][i] > (nlstate+ndeath)) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           printf("Error: Wrong value in nlstate or ndeath\n");        if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
           goto end;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }      }
     }    }
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     free_vector(severity,1,maxwav);    
     free_imatrix(outcome,1,maxwav+1,1,n);    agelim=AGESUP;
     free_vector(moisnais,1,n);    
     free_vector(annais,1,n);    hstepm=1;
     /* free_matrix(mint,1,maxwav,1,n);    hstepm=hstepm/stepm; 
        free_matrix(anint,1,maxwav,1,n);*/    yp1=modf(dateintmean,&yp);
     free_vector(moisdc,1,n);    anprojmean=yp;
     free_vector(andc,1,n);    yp2=modf((yp1*12),&yp);
     mprojmean=yp;
        yp1=modf((yp2*30.5),&yp);
     wav=ivector(1,imx);    jprojmean=yp;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    if(jprojmean==0) jprojmean=1;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    if(mprojmean==0) jprojmean=1;
        
     /* Concatenates waves */    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    
     for(cptcov=1;cptcov<=i2;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       Tcode=ivector(1,100);        k=k+1;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        fprintf(ficresf,"\n#******");
       ncodemax[1]=1;        for(j=1;j<=cptcoveff;j++) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
              }
    codtab=imatrix(1,100,1,10);        fprintf(ficresf,"******\n");
    h=0;        fprintf(ficresf,"# StartingAge FinalAge");
    m=pow(2,cptcoveff);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
          
    for(k=1;k<=cptcoveff; k++){        
      for(i=1; i <=(m/pow(2,k));i++){        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
        for(j=1; j <= ncodemax[k]; j++){          fprintf(ficresf,"\n");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
            h++;  
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
          }            nhstepm = nhstepm/hstepm; 
        }            
      }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }            oldm=oldms;savm=savms;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
       codtab[1][2]=1;codtab[2][2]=2; */          
    /* for(i=1; i <=m ;i++){            for (h=0; h<=nhstepm; h++){
       for(k=1; k <=cptcovn; k++){              if (h==(int) (calagedate+YEARM*cpt)) {
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
       }              } 
       printf("\n");              for(j=1; j<=nlstate+ndeath;j++) {
       }                kk1=0.;kk2=0;
       scanf("%d",i);*/                for(i=1; i<=nlstate;i++) {              
                      if (mobilav==1) 
    /* Calculates basic frequencies. Computes observed prevalence at single age                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
        and prints on file fileres'p'. */                  else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                      }
                      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if (h==(int)(calagedate+12*cpt)){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  fprintf(ficresf," %.3f", kk1);
     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] */            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          }
         }
     if(mle==1){      }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    }
     }         
        if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     /*--------- results files --------------*/  
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);    fclose(ficresf);
    }
   /************** Forecasting ******************/
    jk=1;  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){
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
    for(i=1,jk=1; i <=nlstate; i++){    int *popage;
      for(k=1; k <=(nlstate+ndeath); k++){    double calagedate, agelim, kk1, kk2;
        if (k != i)    double *popeffectif,*popcount;
          {    double ***p3mat,***tabpop,***tabpopprev;
            printf("%d%d ",i,k);    double ***mobaverage;
            fprintf(ficres,"%1d%1d ",i,k);    char filerespop[FILENAMELENGTH];
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
              fprintf(ficres,"%f ",p[jk]);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
              jk++;    agelim=AGESUP;
            }    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
            printf("\n");    
            fprintf(ficres,"\n");    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
          }    
      }    
    }    strcpy(filerespop,"pop"); 
  if(mle==1){    strcat(filerespop,fileres);
     /* Computing hessian and covariance matrix */    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     ftolhess=ftol; /* Usually correct */      printf("Problem with forecast resultfile: %s\n", filerespop);
     hesscov(matcov, p, npar, delti, ftolhess, func);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
  }    }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    printf("Computing forecasting: result on file '%s' \n", filerespop);
     printf("# Scales (for hessian or gradient estimation)\n");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
         if (j!=i) {  
           fprintf(ficres,"%1d%1d",i,j);    if (mobilav!=0) {
           printf("%1d%1d",i,j);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           for(k=1; k<=ncovmodel;k++){      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
             printf(" %.5e",delti[jk]);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             fprintf(ficres," %.5e",delti[jk]);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             jk++;      }
           }    }
           printf("\n");  
           fprintf(ficres,"\n");    stepsize=(int) (stepm+YEARM-1)/YEARM;
         }    if (stepm<=12) stepsize=1;
       }    
      }    agelim=AGESUP;
        
     k=1;    hstepm=1;
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    hstepm=hstepm/stepm; 
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    
     for(i=1;i<=npar;i++){    if (popforecast==1) {
       /*  if (k>nlstate) k=1;      if((ficpop=fopen(popfile,"r"))==NULL) {
       i1=(i-1)/(ncovmodel*nlstate)+1;        printf("Problem with population file : %s\n",popfile);exit(0);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       printf("%s%d%d",alph[k],i1,tab[i]);*/      } 
       fprintf(ficres,"%3d",i);      popage=ivector(0,AGESUP);
       printf("%3d",i);      popeffectif=vector(0,AGESUP);
       for(j=1; j<=i;j++){      popcount=vector(0,AGESUP);
         fprintf(ficres," %.5e",matcov[i][j]);      
         printf(" %.5e",matcov[i][j]);      i=1;   
       }      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
       fprintf(ficres,"\n");     
       printf("\n");      imx=i;
       k++;      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }    }
      
     while((c=getc(ficpar))=='#' && c!= EOF){    for(cptcov=1;cptcov<=i2;cptcov++){
       ungetc(c,ficpar);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       fgets(line, MAXLINE, ficpar);        k=k+1;
       puts(line);        fprintf(ficrespop,"\n#******");
       fputs(line,ficparo);        for(j=1;j<=cptcoveff;j++) {
     }          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     ungetc(c,ficpar);        }
     estepm=0;        fprintf(ficrespop,"******\n");
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);        fprintf(ficrespop,"# Age");
     if (estepm==0 || estepm < stepm) estepm=stepm;        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     if (fage <= 2) {        if (popforecast==1)  fprintf(ficrespop," [Population]");
       bage = ageminpar;        
       fage = agemaxpar;        for (cpt=0; cpt<=0;cpt++) { 
     }          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
              
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);            nhstepm = nhstepm/hstepm; 
              
     while((c=getc(ficpar))=='#' && c!= EOF){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     ungetc(c,ficpar);            oldm=oldms;savm=savms;
     fgets(line, MAXLINE, ficpar);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     puts(line);          
     fputs(line,ficparo);            for (h=0; h<=nhstepm; h++){
   }              if (h==(int) (calagedate+YEARM*cpt)) {
   ungetc(c,ficpar);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                } 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);              for(j=1; j<=nlstate+ndeath;j++) {
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                kk1=0.;kk2=0;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                for(i=1; i<=nlstate;i++) {              
                        if (mobilav==1) 
   while((c=getc(ficpar))=='#' && c!= EOF){                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
     ungetc(c,ficpar);                  else {
     fgets(line, MAXLINE, ficpar);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     puts(line);                  }
     fputs(line,ficparo);                }
   }                if (h==(int)(calagedate+12*cpt)){
   ungetc(c,ficpar);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                      /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                }
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              }
               for(i=1; i<=nlstate;i++){
   fscanf(ficpar,"pop_based=%d\n",&popbased);                kk1=0.;
   fprintf(ficparo,"pop_based=%d\n",popbased);                    for(j=1; j<=nlstate;j++){
   fprintf(ficres,"pop_based=%d\n",popbased);                      kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                    }
   while((c=getc(ficpar))=='#' && c!= EOF){                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
     ungetc(c,ficpar);              }
     fgets(line, MAXLINE, ficpar);  
     puts(line);              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
     fputs(line,ficparo);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   }            }
   ungetc(c,ficpar);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);        }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);   
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     ungetc(c,ficpar);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
     fgets(line, MAXLINE, ficpar);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     puts(line);            nhstepm = nhstepm/hstepm; 
     fputs(line,ficparo);            
   }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   ungetc(c,ficpar);            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            for (h=0; h<=nhstepm; h++){
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);              if (h==(int) (calagedate+YEARM*cpt)) {
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
 /*------------ gnuplot -------------*/                for(i=1; i<=nlstate;i++) {              
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                  }
 /*------------ free_vector  -------------*/                if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
  chdir(path);              }
              }
  free_ivector(wav,1,imx);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  free_imatrix(dh,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,1,NCOVMAX,1,n);*/   
  fclose(ficparo);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  fclose(ficres);  
     if (popforecast==1) {
 /*--------- index.htm --------*/      free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);      free_vector(popcount,0,AGESUP);
     }
      free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*--------------- Prevalence limit --------------*/    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fclose(ficrespop);
   strcpy(filerespl,"pl");  }
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  /***********************************************/
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  /**************** Main Program *****************/
   }  /***********************************************/
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");  int main(int argc, char *argv[])
   fprintf(ficrespl,"#Age ");  {
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   fprintf(ficrespl,"\n");    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
      double agedeb, agefin,hf;
   prlim=matrix(1,nlstate,1,nlstate);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double fret;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double **xi,tmp,delta;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double dum; /* Dummy variable */
   k=0;    double ***p3mat;
   agebase=ageminpar;    double ***mobaverage;
   agelim=agemaxpar;    int *indx;
   ftolpl=1.e-10;    char line[MAXLINE], linepar[MAXLINE];
   i1=cptcoveff;    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
   if (cptcovn < 1){i1=1;}    int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
   for(cptcov=1;cptcov<=i1;cptcov++){    int c,  h , cpt,l;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int ju,jl, mi;
         k=k+1;    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
         fprintf(ficrespl,"\n#******");    int mobilav=0,popforecast=0;
         for(j=1;j<=cptcoveff;j++)    int hstepm, nhstepm;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
         fprintf(ficrespl,"******\n");  
            double bage, fage, age, agelim, agebase;
         for (age=agebase; age<=agelim; age++){    double ftolpl=FTOL;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double **prlim;
           fprintf(ficrespl,"%.0f",age );    double *severity;
           for(i=1; i<=nlstate;i++)    double ***param; /* Matrix of parameters */
           fprintf(ficrespl," %.5f", prlim[i][i]);    double  *p;
           fprintf(ficrespl,"\n");    double **matcov; /* Matrix of covariance */
         }    double ***delti3; /* Scale */
       }    double *delti; /* Scale */
     }    double ***eij, ***vareij;
   fclose(ficrespl);    double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   /*------------- h Pij x at various ages ------------*/    double kk1, kk2;
      double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    char *alph[]={"a","a","b","c","d","e"}, str[4];
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);    char z[1]="c", occ;
    #include <sys/time.h>
   stepsize=(int) (stepm+YEARM-1)/YEARM;  #include <time.h>
   /*if (stepm<=24) stepsize=2;*/    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
   agelim=AGESUP;    /* long total_usecs;
   hstepm=stepsize*YEARM; /* Every year of age */       struct timeval start_time, end_time;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    
         gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   k=0;    getcwd(pathcd, size);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    printf("\n%s",version);
       k=k+1;    if(argc <=1){
         fprintf(ficrespij,"\n#****** ");      printf("\nEnter the parameter file name: ");
         for(j=1;j<=cptcoveff;j++)      scanf("%s",pathtot);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
         fprintf(ficrespij,"******\n");    else{
              strcpy(pathtot,argv[1]);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    /*cygwin_split_path(pathtot,path,optionfile);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
           oldm=oldms;savm=savms;    /* cutv(path,optionfile,pathtot,'\\');*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
           for(i=1; i<=nlstate;i++)    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
             for(j=1; j<=nlstate+ndeath;j++)    chdir(path);
               fprintf(ficrespij," %1d-%1d",i,j);    replace(pathc,path);
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){    /*-------- arguments in the command line --------*/
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)    /* Log file */
               for(j=1; j<=nlstate+ndeath;j++)    strcat(filelog, optionfilefiname);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    strcat(filelog,".log");    /* */
             fprintf(ficrespij,"\n");    if((ficlog=fopen(filelog,"w"))==NULL)    {
           }      printf("Problem with logfile %s\n",filelog);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      goto end;
           fprintf(ficrespij,"\n");    }
         }    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);
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    fflush(ficlog);
   
   fclose(ficrespij);    /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
   /*---------- Forecasting ------------------*/    strcat(fileres,".txt");    /* Other files have txt extension */
   if((stepm == 1) && (strcmp(model,".")==0)){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    /*---------arguments file --------*/
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
     free_matrix(mint,1,maxwav,1,n);    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      printf("Problem with optionfile %s\n",optionfile);
     free_vector(weight,1,n);}      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
   else{      goto end;
     erreur=108;    }
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);  
   }    strcpy(filereso,"o");
      strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
   /*---------- Health expectancies and variances ------------*/      printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
   strcpy(filerest,"t");      goto end;
   strcat(filerest,fileres);    }
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    /* Reads comments: lines beginning with '#' */
   }    while((c=getc(ficpar))=='#' && c!= EOF){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
   strcpy(filerese,"e");      fputs(line,ficparo);
   strcat(filerese,fileres);    }
   if((ficreseij=fopen(filerese,"w"))==NULL) {    ungetc(c,ficpar);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    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);
  strcpy(fileresv,"v");    while((c=getc(ficpar))=='#' && c!= EOF){
   strcat(fileresv,fileres);      ungetc(c,ficpar);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      fgets(line, MAXLINE, ficpar);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      puts(line);
   }      fputs(line,ficparo);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    }
     ungetc(c,ficpar);
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){     
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    covar=matrix(0,NCOVMAX,1,n); 
       k=k+1;    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
       fprintf(ficrest,"\n#****** ");    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
       fprintf(ficrest,"******\n");    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
       fprintf(ficreseij,"\n#****** ");    /* Read guess parameters */
       for(j=1;j<=cptcoveff;j++)    /* Reads comments: lines beginning with '#' */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    while((c=getc(ficpar))=='#' && c!= EOF){
       fprintf(ficreseij,"******\n");      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       fprintf(ficresvij,"\n#****** ");      puts(line);
       for(j=1;j<=cptcoveff;j++)      fputs(line,ficparo);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
       fprintf(ficresvij,"******\n");    ungetc(c,ficpar);
     
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       oldm=oldms;savm=savms;    for(i=1; i <=nlstate; i++)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);        for(j=1; j <=nlstate+ndeath-1; j++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fscanf(ficpar,"%1d%1d",&i1,&j1);
       oldm=oldms;savm=savms;        fprintf(ficparo,"%1d%1d",i1,j1);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        if(mle==1)
              printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
          for(k=1; k<=ncovmodel;k++){
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          fscanf(ficpar," %lf",&param[i][j][k]);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          if(mle==1){
       fprintf(ficrest,"\n");            printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
       epj=vector(1,nlstate+1);          }
       for(age=bage; age <=fage ;age++){          else
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            fprintf(ficlog," %lf",param[i][j][k]);
         if (popbased==1) {          fprintf(ficparo," %lf",param[i][j][k]);
           for(i=1; i<=nlstate;i++)        }
             prlim[i][i]=probs[(int)age][i][k];        fscanf(ficpar,"\n");
         }        if(mle==1)
                  printf("\n");
         fprintf(ficrest," %4.0f",age);        fprintf(ficlog,"\n");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        fprintf(ficparo,"\n");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      }
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    
           }    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
           epj[nlstate+1] +=epj[j];  
         }    p=param[1][1];
         for(i=1, vepp=0.;i <=nlstate;i++)    
           for(j=1;j <=nlstate;j++)    /* Reads comments: lines beginning with '#' */
             vepp += vareij[i][j][(int)age];    while((c=getc(ficpar))=='#' && c!= EOF){
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));      ungetc(c,ficpar);
         for(j=1;j <=nlstate;j++){      fgets(line, MAXLINE, ficpar);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));      puts(line);
         }      fputs(line,ficparo);
         fprintf(ficrest,"\n");    }
       }    ungetc(c,ficpar);
     }  
   }    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
   fclose(ficreseij);    for(i=1; i <=nlstate; i++){
   fclose(ficresvij);      for(j=1; j <=nlstate+ndeath-1; j++){
   fclose(ficrest);        fscanf(ficpar,"%1d%1d",&i1,&j1);
   fclose(ficpar);        printf("%1d%1d",i,j);
   free_vector(epj,1,nlstate+1);        fprintf(ficparo,"%1d%1d",i1,j1);
          for(k=1; k<=ncovmodel;k++){
   /*------- Variance limit prevalence------*/            fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
   strcpy(fileresvpl,"vpl");          fprintf(ficparo," %le",delti3[i][j][k]);
   strcat(fileresvpl,fileres);        }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        fscanf(ficpar,"\n");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        printf("\n");
     exit(0);        fprintf(ficparo,"\n");
   }      }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    }
     delti=delti3[1][1];
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    /* Reads comments: lines beginning with '#' */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    while((c=getc(ficpar))=='#' && c!= EOF){
       k=k+1;      ungetc(c,ficpar);
       fprintf(ficresvpl,"\n#****** ");      fgets(line, MAXLINE, ficpar);
       for(j=1;j<=cptcoveff;j++)      puts(line);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fputs(line,ficparo);
       fprintf(ficresvpl,"******\n");    }
          ungetc(c,ficpar);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    
       oldm=oldms;savm=savms;    matcov=matrix(1,npar,1,npar);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    for(i=1; i <=npar; i++){
     }      fscanf(ficpar,"%s",&str);
  }      if(mle==1)
         printf("%s",str);
   fclose(ficresvpl);      fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
   /*---------- End : free ----------------*/      for(j=1; j <=i; j++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        fscanf(ficpar," %le",&matcov[i][j]);
          if(mle==1){
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          printf(" %.5le",matcov[i][j]);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          fprintf(ficlog," %.5le",matcov[i][j]);
          }
          else
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficlog," %.5le",matcov[i][j]);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficparo," %.5le",matcov[i][j]);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      fscanf(ficpar,"\n");
        if(mle==1)
   free_matrix(matcov,1,npar,1,npar);        printf("\n");
   free_vector(delti,1,npar);      fprintf(ficlog,"\n");
   free_matrix(agev,1,maxwav,1,imx);      fprintf(ficparo,"\n");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    }
     for(i=1; i <=npar; i++)
   if(erreur >0)      for(j=i+1;j<=npar;j++)
     printf("End of Imach with error or warning %d\n",erreur);        matcov[i][j]=matcov[j][i];
   else   printf("End of Imach\n");     
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    if(mle==1)
        printf("\n");
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    fprintf(ficlog,"\n");
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/  
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
  end:    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
 #ifdef windows    strcat(rfileres,".");    /* */
   /* chdir(pathcd);*/    strcat(rfileres,optionfilext);    /* Other files have txt extension */
 #endif    if((ficres =fopen(rfileres,"w"))==NULL) {
  /*system("wgnuplot graph.plt");*/      printf("Problem writing new parameter file: %s\n", fileres);goto end;
  /*system("../gp37mgw/wgnuplot graph.plt");*/      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
  /*system("cd ../gp37mgw");*/    }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    fprintf(ficres,"#%s\n",version);
  strcpy(plotcmd,GNUPLOTPROGRAM);      
  strcat(plotcmd," ");    /*-------- data file ----------*/
  strcat(plotcmd,optionfilegnuplot);    if((fic=fopen(datafile,"r"))==NULL)    {
  system(plotcmd);      printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
 #ifdef windows    }
   while (z[0] != 'q') {  
     /* chdir(path); */    n= lastobs;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    severity = vector(1,maxwav);
     scanf("%s",z);    outcome=imatrix(1,maxwav+1,1,n);
     if (z[0] == 'c') system("./imach");    num=ivector(1,n);
     else if (z[0] == 'e') system(optionfilehtm);    moisnais=vector(1,n);
     else if (z[0] == 'g') system(plotcmd);    annais=vector(1,n);
     else if (z[0] == 'q') exit(0);    moisdc=vector(1,n);
   }    andc=vector(1,n);
 #endif    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]));}*/
     
    
     /* 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 ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=1; (m<= maxwav); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (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){ /* Should no more exist */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || 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=1; (m<= maxwav); 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;
         }
       }
     }
   
     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);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+mprev1/12.+jprev1/365.;
     dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     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,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
     fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
     fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
   
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   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,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(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*/
   
     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,"# Age");
           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 %f %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, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     if((stepm == 1) && (strcmp(model,".")==0)){
       prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
       if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     } 
     else{
       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);
   
     calagedate=-1;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   
     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(matcov,1,npar,1,npar);
     free_vector(delti,1,npar);
     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_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);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     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: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#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.1.39  
changed lines
  Added in v.1.63


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