Diff for /imach/src/imach.c between versions 1.49 and 1.62

version 1.49, 2002/06/20 14:03:39 version 1.62, 2002/11/20 07:56:21
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 "gnuplot"  #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  #ifdef windows
 #define DIRSEPARATOR '\\'  #define DIRSEPARATOR '\\'
 #else  #define ODIRSEPARATOR '/'
 #define DIRSEPARATOR '/'  #else
 #endif  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";  #endif
 int erreur; /* Error number */  
 int nvar;  char version[80]="Imach version 0.9, November 2002, INED-EUROREVES ";
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  int erreur; /* Error number */
 int npar=NPARMAX;  int nvar;
 int nlstate=2; /* Number of live states */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int ndeath=1; /* Number of dead states */  int npar=NPARMAX;
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int nlstate=2; /* Number of live states */
 int popbased=0;  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int *wav; /* Number of waves for this individuual 0 is possible */  int popbased=0;
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */  int *wav; /* Number of waves for this individuual 0 is possible */
 int mle, weightopt;  int maxwav; /* Maxim number of waves */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int jmin, jmax; /* min, max spacing between 2 waves */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int mle, weightopt;
 double jmean; /* Mean space between 2 waves */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  double jmean; /* Mean space between 2 waves */
 FILE *fichtm; /* Html File */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 FILE *ficreseij;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 char filerese[FILENAMELENGTH];  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE  *ficresvij;  FILE *ficlog;
 char fileresv[FILENAMELENGTH];  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 FILE  *ficresvpl;  FILE *ficresprobmorprev;
 char fileresvpl[FILENAMELENGTH];  FILE *fichtm; /* Html File */
 char title[MAXLINE];  FILE *ficreseij;
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  char filerese[FILENAMELENGTH];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 char filerest[FILENAMELENGTH];  char title[MAXLINE];
 char fileregp[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 char popfile[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 #define NR_END 1  char filerest[FILENAMELENGTH];
 #define FREE_ARG char*  char fileregp[FILENAMELENGTH];
 #define FTOL 1.0e-10  char popfile[FILENAMELENGTH];
   
 #define NRANSI  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define ITMAX 200  
   #define NR_END 1
 #define TOL 2.0e-4  #define FREE_ARG char*
   #define FTOL 1.0e-10
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10  #define NRANSI 
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define ITMAX 200 
   
 #define GOLD 1.618034  #define TOL 2.0e-4 
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 static double maxarg1,maxarg2;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define GOLD 1.618034 
    #define GLIMIT 100.0 
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define TINY 1.0e-20 
 #define rint(a) floor(a+0.5)  
   static double maxarg1,maxarg2;
 static double sqrarg;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 int imx;  #define rint(a) floor(a+0.5)
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 int estepm;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
   int imx; 
 int m,nb;  int stepm;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  /* Stepm, step in month: minimum step interpolation*/
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;  int estepm;
 double dateintmean=0;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 double *weight;  int m,nb;
 int **s; /* Status */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double *agedc, **covar, idx;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  double **pmmij, ***probs;
   double dateintmean=0;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  double *weight;
   int **s; /* Status */
 /**************** split *************************/  double *agedc, **covar, idx;
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 {  
    char *s;                             /* pointer */  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
    int  l1, l2;                         /* length counters */  double ftolhess; /* Tolerance for computing hessian */
   
    l1 = strlen( path );                 /* length of path */  /**************** split *************************/
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */  {
    if ( s == NULL ) {                   /* no directory, so use current */    char  *ss;                            /* pointer */
 #if     defined(__bsd__)                /* get current working directory */    int   l1, l2;                         /* length counters */
       extern char       *getwd( );  
     l1 = strlen(path );                   /* length of path */
       if ( getwd( dirc ) == NULL ) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 #else    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       extern char       *getcwd( );    if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #endif  #if     defined(__bsd__)                /* get current working directory */
          return( GLOCK_ERROR_GETCWD );      extern char *getwd( );
       }  
       strcpy( name, path );             /* we've got it */      if ( getwd( dirc ) == NULL ) {
    } else {                             /* strip direcotry from path */  #else
       s++;                              /* after this, the filename */      extern char *getcwd( );
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       strcpy( name, s );                /* save file name */  #endif
       strncpy( dirc, path, l1 - l2 );   /* now the directory */        return( GLOCK_ERROR_GETCWD );
       dirc[l1-l2] = 0;                  /* add zero */      }
    }      strcpy( name, path );               /* we've got it */
    l1 = strlen( dirc );                 /* length of directory */    } else {                              /* strip direcotry from path */
 #ifdef windows      ss++;                               /* after this, the filename */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }      l2 = strlen( ss );                  /* length of filename */
 #else      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }      strcpy( name, ss );         /* save file name */
 #endif      strncpy( dirc, path, l1 - l2 );     /* now the directory */
    s = strrchr( name, '.' );            /* find last / */      dirc[l1-l2] = 0;                    /* add zero */
    s++;    }
    strcpy(ext,s);                       /* save extension */    l1 = strlen( dirc );                  /* length of directory */
    l1= strlen( name);  #ifdef windows
    l2= strlen( s)+1;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
    strncpy( finame, name, l1-l2);  #else
    finame[l1-l2]= 0;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
    return( 0 );                         /* we're done */  #endif
 }    ss = strrchr( name, '.' );            /* find last / */
     ss++;
     strcpy(ext,ss);                       /* save extension */
 /******************************************/    l1= strlen( name);
     l2= strlen(ss)+1;
 void replace(char *s, char*t)    strncpy( finame, name, l1-l2);
 {    finame[l1-l2]= 0;
   int i;    return( 0 );                          /* we're done */
   int lg=20;  }
   i=0;  
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  /******************************************/
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';  void replace(char *s, char*t)
   }  {
 }    int i;
     int lg=20;
 int nbocc(char *s, char occ)    i=0;
 {    lg=strlen(t);
   int i,j=0;    for(i=0; i<= lg; i++) {
   int lg=20;      (s[i] = t[i]);
   i=0;      if (t[i]== '\\') s[i]='/';
   lg=strlen(s);    }
   for(i=0; i<= lg; i++) {  }
   if  (s[i] == occ ) j++;  
   }  int nbocc(char *s, char occ)
   return j;  {
 }    int i,j=0;
     int lg=20;
 void cutv(char *u,char *v, char*t, char occ)    i=0;
 {    lg=strlen(s);
   int i,lg,j,p=0;    for(i=0; i<= lg; i++) {
   i=0;    if  (s[i] == occ ) j++;
   for(j=0; j<=strlen(t)-1; j++) {    }
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    return j;
   }  }
   
   lg=strlen(t);  void cutv(char *u,char *v, char*t, char occ)
   for(j=0; j<p; j++) {  {
     (u[j] = t[j]);    /* cuts string t into u and v where u is ended by char occ excluding it
   }       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
      u[p]='\0';       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
    for(j=0; j<= lg; j++) {    i=0;
     if (j>=(p+1))(v[j-p-1] = t[j]);    for(j=0; j<=strlen(t)-1; j++) {
   }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 }    }
   
 /********************** nrerror ********************/    lg=strlen(t);
     for(j=0; j<p; j++) {
 void nrerror(char error_text[])      (u[j] = t[j]);
 {    }
   fprintf(stderr,"ERREUR ...\n");       u[p]='\0';
   fprintf(stderr,"%s\n",error_text);  
   exit(1);     for(j=0; j<= lg; j++) {
 }      if (j>=(p+1))(v[j-p-1] = t[j]);
 /*********************** vector *******************/    }
 double *vector(int nl, int nh)  }
 {  
   double *v;  /********************** nrerror ********************/
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  void nrerror(char error_text[])
   return v-nl+NR_END;  {
 }    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 /************************ free vector ******************/    exit(EXIT_FAILURE);
 void free_vector(double*v, int nl, int nh)  }
 {  /*********************** vector *******************/
   free((FREE_ARG)(v+nl-NR_END));  double *vector(int nl, int nh)
 }  {
     double *v;
 /************************ivector *******************************/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 int *ivector(long nl,long nh)    if (!v) nrerror("allocation failure in vector");
 {    return v-nl+NR_END;
   int *v;  }
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  /************************ free vector ******************/
   return v-nl+NR_END;  void free_vector(double*v, int nl, int nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /******************free ivector **************************/  }
 void free_ivector(int *v, long nl, long nh)  
 {  /************************ivector *******************************/
   free((FREE_ARG)(v+nl-NR_END));  int *ivector(long nl,long nh)
 }  {
     int *v;
 /******************* imatrix *******************************/    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 int **imatrix(long nrl, long nrh, long ncl, long nch)    if (!v) nrerror("allocation failure in ivector");
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    return v-nl+NR_END;
 {  }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  /******************free ivector **************************/
    void free_ivector(int *v, long nl, long nh)
   /* allocate pointers to rows */  {
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    free((FREE_ARG)(v+nl-NR_END));
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   m += NR_END;  
   m -= nrl;  /******************* imatrix *******************************/
    int **imatrix(long nrl, long nrh, long ncl, long nch) 
         /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   /* allocate rows and set pointers to them */  { 
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    int **m; 
   m[nrl] += NR_END;    
   m[nrl] -= ncl;    /* allocate pointers to rows */ 
      m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    if (!m) nrerror("allocation failure 1 in matrix()"); 
      m += NR_END; 
   /* return pointer to array of pointers to rows */    m -= nrl; 
   return m;    
 }    
     /* allocate rows and set pointers to them */ 
 /****************** free_imatrix *************************/    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 void free_imatrix(m,nrl,nrh,ncl,nch)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       int **m;    m[nrl] += NR_END; 
       long nch,ncl,nrh,nrl;    m[nrl] -= ncl; 
      /* free an int matrix allocated by imatrix() */    
 {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    
   free((FREE_ARG) (m+nrl-NR_END));    /* return pointer to array of pointers to rows */ 
 }    return m; 
   } 
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  /****************** free_imatrix *************************/
 {  void free_imatrix(m,nrl,nrh,ncl,nch)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;        int **m;
   double **m;        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  { 
   if (!m) nrerror("allocation failure 1 in matrix()");    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   m += NR_END;    free((FREE_ARG) (m+nrl-NR_END)); 
   m -= nrl;  } 
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /******************* matrix *******************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double **matrix(long nrl, long nrh, long ncl, long nch)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /*************************free matrix ************************/    m -= nrl;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /******************* ma3x *******************************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    return m;
 {  }
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   m += NR_END;    free((FREE_ARG)(m+nrl-NR_END));
   m -= nrl;  }
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /******************* ma3x *******************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    if (!m) nrerror("allocation failure 1 in matrix()");
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    m += NR_END;
   m[nrl][ncl] += NR_END;    m -= nrl;
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     m[nrl][j]=m[nrl][j-1]+nlay;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      m[nrl] += NR_END;
   for (i=nrl+1; i<=nrh; i++) {    m[nrl] -= ncl;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       m[i][j]=m[i][j-1]+nlay;  
   }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   return m;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 }    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
 /*************************free ma3x ************************/    for (j=ncl+1; j<=nch; j++) 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)      m[nrl][j]=m[nrl][j-1]+nlay;
 {    
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    for (i=nrl+1; i<=nrh; i++) {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   free((FREE_ARG)(m+nrl-NR_END));      for (j=ncl+1; j<=nch; j++) 
 }        m[i][j]=m[i][j-1]+nlay;
     }
 /***************** f1dim *************************/    return m;
 extern int ncom;  }
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  /*************************free ma3x ************************/
    void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 double f1dim(double x)  {
 {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   int j;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double f;    free((FREE_ARG)(m+nrl-NR_END));
   double *xt;  }
    
   xt=vector(1,ncom);  /***************** f1dim *************************/
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  extern int ncom; 
   f=(*nrfunc)(xt);  extern double *pcom,*xicom;
   free_vector(xt,1,ncom);  extern double (*nrfunc)(double []); 
   return f;   
 }  double f1dim(double x) 
   { 
 /*****************brent *************************/    int j; 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    double f;
 {    double *xt; 
   int iter;   
   double a,b,d,etemp;    xt=vector(1,ncom); 
   double fu,fv,fw,fx;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double ftemp;    f=(*nrfunc)(xt); 
   double p,q,r,tol1,tol2,u,v,w,x,xm;    free_vector(xt,1,ncom); 
   double e=0.0;    return f; 
    } 
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  /*****************brent *************************/
   x=w=v=bx;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   fw=fv=fx=(*f)(x);  { 
   for (iter=1;iter<=ITMAX;iter++) {    int iter; 
     xm=0.5*(a+b);    double a,b,d,etemp;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    double fu,fv,fw,fx;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    double ftemp;
     printf(".");fflush(stdout);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
 #ifdef DEBUG    double e=0.0; 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);   
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    a=(ax < cx ? ax : cx); 
 #endif    b=(ax > cx ? ax : cx); 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    x=w=v=bx; 
       *xmin=x;    fw=fv=fx=(*f)(x); 
       return fx;    for (iter=1;iter<=ITMAX;iter++) { 
     }      xm=0.5*(a+b); 
     ftemp=fu;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     if (fabs(e) > tol1) {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       r=(x-w)*(fx-fv);      printf(".");fflush(stdout);
       q=(x-v)*(fx-fw);      fprintf(ficlog,".");fflush(ficlog);
       p=(x-v)*q-(x-w)*r;  #ifdef DEBUG
       q=2.0*(q-r);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       if (q > 0.0) p = -p;      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);
       q=fabs(q);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       etemp=e;  #endif
       e=d;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))        *xmin=x; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));        return fx; 
       else {      } 
         d=p/q;      ftemp=fu;
         u=x+d;      if (fabs(e) > tol1) { 
         if (u-a < tol2 || b-u < tol2)        r=(x-w)*(fx-fv); 
           d=SIGN(tol1,xm-x);        q=(x-v)*(fx-fw); 
       }        p=(x-v)*q-(x-w)*r; 
     } else {        q=2.0*(q-r); 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));        etemp=e; 
     fu=(*f)(u);        e=d; 
     if (fu <= fx) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       if (u >= x) a=x; else b=x;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       SHFT(v,w,x,u)        else { 
         SHFT(fv,fw,fx,fu)          d=p/q; 
         } else {          u=x+d; 
           if (u < x) a=u; else b=u;          if (u-a < tol2 || b-u < tol2) 
           if (fu <= fw || w == x) {            d=SIGN(tol1,xm-x); 
             v=w;        } 
             w=u;      } else { 
             fv=fw;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             fw=fu;      } 
           } else if (fu <= fv || v == x || v == w) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
             v=u;      fu=(*f)(u); 
             fv=fu;      if (fu <= fx) { 
           }        if (u >= x) a=x; else b=x; 
         }        SHFT(v,w,x,u) 
   }          SHFT(fv,fw,fx,fu) 
   nrerror("Too many iterations in brent");          } else { 
   *xmin=x;            if (u < x) a=u; else b=u; 
   return fx;            if (fu <= fw || w == x) { 
 }              v=w; 
               w=u; 
 /****************** mnbrak ***********************/              fv=fw; 
               fw=fu; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,            } else if (fu <= fv || v == x || v == w) { 
             double (*func)(double))              v=u; 
 {              fv=fu; 
   double ulim,u,r,q, dum;            } 
   double fu;          } 
      } 
   *fa=(*func)(*ax);    nrerror("Too many iterations in brent"); 
   *fb=(*func)(*bx);    *xmin=x; 
   if (*fb > *fa) {    return fx; 
     SHFT(dum,*ax,*bx,dum)  } 
       SHFT(dum,*fb,*fa,dum)  
       }  /****************** mnbrak ***********************/
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   while (*fb > *fc) {              double (*func)(double)) 
     r=(*bx-*ax)*(*fb-*fc);  { 
     q=(*bx-*cx)*(*fb-*fa);    double ulim,u,r,q, dum;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    double fu; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));   
     ulim=(*bx)+GLIMIT*(*cx-*bx);    *fa=(*func)(*ax); 
     if ((*bx-u)*(u-*cx) > 0.0) {    *fb=(*func)(*bx); 
       fu=(*func)(u);    if (*fb > *fa) { 
     } else if ((*cx-u)*(u-ulim) > 0.0) {      SHFT(dum,*ax,*bx,dum) 
       fu=(*func)(u);        SHFT(dum,*fb,*fa,dum) 
       if (fu < *fc) {        } 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    *cx=(*bx)+GOLD*(*bx-*ax); 
           SHFT(*fb,*fc,fu,(*func)(u))    *fc=(*func)(*cx); 
           }    while (*fb > *fc) { 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      r=(*bx-*ax)*(*fb-*fc); 
       u=ulim;      q=(*bx-*cx)*(*fb-*fa); 
       fu=(*func)(u);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     } else {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       u=(*cx)+GOLD*(*cx-*bx);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       fu=(*func)(u);      if ((*bx-u)*(u-*cx) > 0.0) { 
     }        fu=(*func)(u); 
     SHFT(*ax,*bx,*cx,u)      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       SHFT(*fa,*fb,*fc,fu)        fu=(*func)(u); 
       }        if (fu < *fc) { 
 }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
 /*************** linmin ************************/            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 int ncom;        u=ulim; 
 double *pcom,*xicom;        fu=(*func)(u); 
 double (*nrfunc)(double []);      } else { 
          u=(*cx)+GOLD*(*cx-*bx); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        fu=(*func)(u); 
 {      } 
   double brent(double ax, double bx, double cx,      SHFT(*ax,*bx,*cx,u) 
                double (*f)(double), double tol, double *xmin);        SHFT(*fa,*fb,*fc,fu) 
   double f1dim(double x);        } 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  } 
               double *fc, double (*func)(double));  
   int j;  /*************** linmin ************************/
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  int ncom; 
    double *pcom,*xicom;
   ncom=n;  double (*nrfunc)(double []); 
   pcom=vector(1,n);   
   xicom=vector(1,n);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   nrfunc=func;  { 
   for (j=1;j<=n;j++) {    double brent(double ax, double bx, double cx, 
     pcom[j]=p[j];                 double (*f)(double), double tol, double *xmin); 
     xicom[j]=xi[j];    double f1dim(double x); 
   }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   ax=0.0;                double *fc, double (*func)(double)); 
   xx=1.0;    int j; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double xx,xmin,bx,ax; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    double fx,fb,fa;
 #ifdef DEBUG   
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    ncom=n; 
 #endif    pcom=vector(1,n); 
   for (j=1;j<=n;j++) {    xicom=vector(1,n); 
     xi[j] *= xmin;    nrfunc=func; 
     p[j] += xi[j];    for (j=1;j<=n;j++) { 
   }      pcom[j]=p[j]; 
   free_vector(xicom,1,n);      xicom[j]=xi[j]; 
   free_vector(pcom,1,n);    } 
 }    ax=0.0; 
     xx=1.0; 
 /*************** powell ************************/    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
             double (*func)(double []))  #ifdef DEBUG
 {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   void linmin(double p[], double xi[], int n, double *fret,    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
               double (*func)(double []));  #endif
   int i,ibig,j;    for (j=1;j<=n;j++) { 
   double del,t,*pt,*ptt,*xit;      xi[j] *= xmin; 
   double fp,fptt;      p[j] += xi[j]; 
   double *xits;    } 
   pt=vector(1,n);    free_vector(xicom,1,n); 
   ptt=vector(1,n);    free_vector(pcom,1,n); 
   xit=vector(1,n);  } 
   xits=vector(1,n);  
   *fret=(*func)(p);  /*************** powell ************************/
   for (j=1;j<=n;j++) pt[j]=p[j];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   for (*iter=1;;++(*iter)) {              double (*func)(double [])) 
     fp=(*fret);  { 
     ibig=0;    void linmin(double p[], double xi[], int n, double *fret, 
     del=0.0;                double (*func)(double [])); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    int i,ibig,j; 
     for (i=1;i<=n;i++)    double del,t,*pt,*ptt,*xit;
       printf(" %d %.12f",i, p[i]);    double fp,fptt;
     printf("\n");    double *xits;
     for (i=1;i<=n;i++) {    pt=vector(1,n); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    ptt=vector(1,n); 
       fptt=(*fret);    xit=vector(1,n); 
 #ifdef DEBUG    xits=vector(1,n); 
       printf("fret=%lf \n",*fret);    *fret=(*func)(p); 
 #endif    for (j=1;j<=n;j++) pt[j]=p[j]; 
       printf("%d",i);fflush(stdout);    for (*iter=1;;++(*iter)) { 
       linmin(p,xit,n,fret,func);      fp=(*fret); 
       if (fabs(fptt-(*fret)) > del) {      ibig=0; 
         del=fabs(fptt-(*fret));      del=0.0; 
         ibig=i;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 #ifdef DEBUG      for (i=1;i<=n;i++) 
       printf("%d %.12e",i,(*fret));        printf(" %d %.12f",i, p[i]);
       for (j=1;j<=n;j++) {      fprintf(ficlog," %d %.12f",i, p[i]);
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      printf("\n");
         printf(" x(%d)=%.12e",j,xit[j]);      fprintf(ficlog,"\n");
       }      for (i=1;i<=n;i++) { 
       for(j=1;j<=n;j++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         printf(" p=%.12e",p[j]);        fptt=(*fret); 
       printf("\n");  #ifdef DEBUG
 #endif        printf("fret=%lf \n",*fret);
     }        fprintf(ficlog,"fret=%lf \n",*fret);
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #endif
 #ifdef DEBUG        printf("%d",i);fflush(stdout);
       int k[2],l;        fprintf(ficlog,"%d",i);fflush(ficlog);
       k[0]=1;        linmin(p,xit,n,fret,func); 
       k[1]=-1;        if (fabs(fptt-(*fret)) > del) { 
       printf("Max: %.12e",(*func)(p));          del=fabs(fptt-(*fret)); 
       for (j=1;j<=n;j++)          ibig=i; 
         printf(" %.12e",p[j]);        } 
       printf("\n");  #ifdef DEBUG
       for(l=0;l<=1;l++) {        printf("%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {        fprintf(ficlog,"%d %.12e",i,(*fret));
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        for (j=1;j<=n;j++) {
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         }          printf(" x(%d)=%.12e",j,xit[j]);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
 #endif        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
       free_vector(xit,1,n);        }
       free_vector(xits,1,n);        printf("\n");
       free_vector(ptt,1,n);        fprintf(ficlog,"\n");
       free_vector(pt,1,n);  #endif
       return;      } 
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #ifdef DEBUG
     for (j=1;j<=n;j++) {        int k[2],l;
       ptt[j]=2.0*p[j]-pt[j];        k[0]=1;
       xit[j]=p[j]-pt[j];        k[1]=-1;
       pt[j]=p[j];        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
     fptt=(*func)(ptt);        for (j=1;j<=n;j++) {
     if (fptt < fp) {          printf(" %.12e",p[j]);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);          fprintf(ficlog," %.12e",p[j]);
       if (t < 0.0) {        }
         linmin(p,xit,n,fret,func);        printf("\n");
         for (j=1;j<=n;j++) {        fprintf(ficlog,"\n");
           xi[j][ibig]=xi[j][n];        for(l=0;l<=1;l++) {
           xi[j][n]=xit[j];          for (j=1;j<=n;j++) {
         }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 #ifdef DEBUG            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         for(j=1;j<=n;j++)          }
           printf(" %.12e",xit[j]);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         printf("\n");          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 #endif        }
       }  #endif
     }  
   }  
 }        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
 /**** Prevalence limit ****************/        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        return; 
 {      } 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
      matrix by transitions matrix until convergence is reached */      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
   int i, ii,j,k;        xit[j]=p[j]-pt[j]; 
   double min, max, maxmin, maxmax,sumnew=0.;        pt[j]=p[j]; 
   double **matprod2();      } 
   double **out, cov[NCOVMAX], **pmij();      fptt=(*func)(ptt); 
   double **newm;      if (fptt < fp) { 
   double agefin, delaymax=50 ; /* Max number of years to converge */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
   for (ii=1;ii<=nlstate+ndeath;ii++)          linmin(p,xit,n,fret,func); 
     for (j=1;j<=nlstate+ndeath;j++){          for (j=1;j<=n;j++) { 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);            xi[j][ibig]=xi[j][n]; 
     }            xi[j][n]=xit[j]; 
           }
    cov[1]=1.;  #ifdef DEBUG
            printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){          for(j=1;j<=n;j++){
     newm=savm;            printf(" %.12e",xit[j]);
     /* Covariates have to be included here again */            fprintf(ficlog," %.12e",xit[j]);
      cov[2]=agefin;          }
            printf("\n");
       for (k=1; k<=cptcovn;k++) {          fprintf(ficlog,"\n");
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #endif
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/        }
       }      } 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    } 
       for (k=1; k<=cptcovprod;k++)  } 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   /**** Prevalence limit (stable prevalence)  ****************/
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  {
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
     savm=oldm;  
     oldm=newm;    int i, ii,j,k;
     maxmax=0.;    double min, max, maxmin, maxmax,sumnew=0.;
     for(j=1;j<=nlstate;j++){    double **matprod2();
       min=1.;    double **out, cov[NCOVMAX], **pmij();
       max=0.;    double **newm;
       for(i=1; i<=nlstate; i++) {    double agefin, delaymax=50 ; /* Max number of years to converge */
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    for (ii=1;ii<=nlstate+ndeath;ii++)
         prlim[i][j]= newm[i][j]/(1-sumnew);      for (j=1;j<=nlstate+ndeath;j++){
         max=FMAX(max,prlim[i][j]);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         min=FMIN(min,prlim[i][j]);      }
       }  
       maxmin=max-min;     cov[1]=1.;
       maxmax=FMAX(maxmax,maxmin);   
     }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     if(maxmax < ftolpl){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       return prlim;      newm=savm;
     }      /* Covariates have to be included here again */
   }       cov[2]=agefin;
 }    
         for (k=1; k<=cptcovn;k++) {
 /*************** transition probabilities ***************/          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]]);*/
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        }
 {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double s1, s2;        for (k=1; k<=cptcovprod;k++)
   /*double t34;*/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   int i,j,j1, nc, ii, jj;  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for(i=1; i<= nlstate; i++){        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for(j=1; j<i;j++){        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      savm=oldm;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      oldm=newm;
       }      maxmax=0.;
       ps[i][j]=s2;      for(j=1;j<=nlstate;j++){
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        min=1.;
     }        max=0.;
     for(j=i+1; j<=nlstate+ndeath;j++){        for(i=1; i<=nlstate; i++) {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          sumnew=0;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          prlim[i][j]= newm[i][j]/(1-sumnew);
       }          max=FMAX(max,prlim[i][j]);
       ps[i][j]=s2;          min=FMIN(min,prlim[i][j]);
     }        }
   }        maxmin=max-min;
     /*ps[3][2]=1;*/        maxmax=FMAX(maxmax,maxmin);
       }
   for(i=1; i<= nlstate; i++){      if(maxmax < ftolpl){
      s1=0;        return prlim;
     for(j=1; j<i; j++)      }
       s1+=exp(ps[i][j]);    }
     for(j=i+1; j<=nlstate+ndeath; j++)  }
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);  /*************** transition probabilities ***************/ 
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for(j=i+1; j<=nlstate+ndeath; j++)  {
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double s1, s2;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    /*double t34;*/
   } /* end i */    int i,j,j1, nc, ii, jj;
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      for(i=1; i<= nlstate; i++){
     for(jj=1; jj<= nlstate+ndeath; jj++){      for(j=1; j<i;j++){
       ps[ii][jj]=0;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       ps[ii][ii]=1;          /*s2 += param[i][j][nc]*cov[nc];*/
     }          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   }          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
         ps[i][j]=s2;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
     for(jj=1; jj<= nlstate+ndeath; jj++){      }
      printf("%lf ",ps[ii][jj]);      for(j=i+1; j<=nlstate+ndeath;j++){
    }        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     printf("\n ");          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     }          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     printf("\n ");printf("%lf ",cov[2]);*/        }
 /*        ps[i][j]=s2;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      }
   goto end;*/    }
     return ps;      /*ps[3][2]=1;*/
 }  
     for(i=1; i<= nlstate; i++){
 /**************** Product of 2 matrices ******************/       s1=0;
       for(j=1; j<i; j++)
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        s1+=exp(ps[i][j]);
 {      for(j=i+1; j<=nlstate+ndeath; j++)
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        s1+=exp(ps[i][j]);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      ps[i][i]=1./(s1+1.);
   /* in, b, out are matrice of pointers which should have been initialized      for(j=1; j<i; j++)
      before: only the contents of out is modified. The function returns        ps[i][j]= exp(ps[i][j])*ps[i][i];
      a pointer to pointers identical to out */      for(j=i+1; j<=nlstate+ndeath; j++)
   long i, j, k;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   for(i=nrl; i<= nrh; i++)      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     for(k=ncolol; k<=ncoloh; k++)    } /* end i */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
   return out;        ps[ii][jj]=0;
 }        ps[ii][ii]=1;
       }
     }
 /************* Higher Matrix Product ***************/  
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
 {      for(jj=1; jj<= nlstate+ndeath; jj++){
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month       printf("%lf ",ps[ii][jj]);
      duration (i.e. until     }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      printf("\n ");
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      }
      (typically every 2 years instead of every month which is too big).      printf("\n ");printf("%lf ",cov[2]);*/
      Model is determined by parameters x and covariates have to be  /*
      included manually here.    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     goto end;*/
      */      return ps;
   }
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  /**************** Product of 2 matrices ******************/
   double **newm;  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   /* Hstepm could be zero and should return the unit matrix */  {
   for (i=1;i<=nlstate+ndeath;i++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     for (j=1;j<=nlstate+ndeath;j++){       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       oldm[i][j]=(i==j ? 1.0 : 0.0);    /* in, b, out are matrice of pointers which should have been initialized 
       po[i][j][0]=(i==j ? 1.0 : 0.0);       before: only the contents of out is modified. The function returns
     }       a pointer to pointers identical to out */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    long i, j, k;
   for(h=1; h <=nhstepm; h++){    for(i=nrl; i<= nrh; i++)
     for(d=1; d <=hstepm; d++){      for(k=ncolol; k<=ncoloh; k++)
       newm=savm;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       /* Covariates have to be included here again */          out[i][k] +=in[i][j]*b[j][k];
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    return out;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  }
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /************* Higher Matrix Product ***************/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/       duration (i.e. until
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,       age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       savm=oldm;       (typically every 2 years instead of every month which is too big).
       oldm=newm;       Model is determined by parameters x and covariates have to be 
     }       included manually here. 
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {       */
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    int i, j, d, h, k;
          */    double **out, cov[NCOVMAX];
       }    double **newm;
   } /* end h */  
   return po;    /* Hstepm could be zero and should return the unit matrix */
 }    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
 /*************** log-likelihood *************/        po[i][j][0]=(i==j ? 1.0 : 0.0);
 double func( double *x)      }
 {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int i, ii, j, k, mi, d, kk;    for(h=1; h <=nhstepm; h++){
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      for(d=1; d <=hstepm; d++){
   double **out;        newm=savm;
   double sw; /* Sum of weights */        /* Covariates have to be included here again */
   double lli; /* Individual log likelihood */        cov[1]=1.;
   long ipmx;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   /*extern weight */        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   /* We are differentiating ll according to initial status */        for (k=1; k<=cptcovage;k++)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /*for(i=1;i<imx;i++)        for (k=1; k<=cptcovprod;k++)
     printf(" %d\n",s[4][i]);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   */  
   cov[1]=1.;  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   for(k=1; k<=nlstate; k++) ll[k]=0.;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(mi=1; mi<= wav[i]-1; mi++){        savm=oldm;
       for (ii=1;ii<=nlstate+ndeath;ii++)        oldm=newm;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      }
       for(d=0; d<dh[mi][i]; d++){      for(i=1; i<=nlstate+ndeath; i++)
         newm=savm;        for(j=1;j<=nlstate+ndeath;j++) {
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          po[i][j][h]=newm[i][j];
         for (kk=1; kk<=cptcovage;kk++) {          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];           */
         }        }
            } /* end h */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    return po;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  }
         savm=oldm;  
         oldm=newm;  
          /*************** log-likelihood *************/
          double func( double *x)
       } /* end mult */  {
          int i, ii, j, k, mi, d, kk;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double **out;
       ipmx +=1;    double sw; /* Sum of weights */
       sw += weight[i];    double lli; /* Individual log likelihood */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    int s1, s2;
     } /* end of wave */    double bbh;
   } /* end of individual */    long ipmx;
     /*extern weight */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    /* We are differentiating ll according to initial status */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    /*for(i=1;i<imx;i++) 
   return -l;      printf(" %d\n",s[4][i]);
 }    */
     cov[1]=1.;
   
 /*********** Maximum Likelihood Estimation ***************/    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    if(mle==1){
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i,j, iter;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **xi,*delti;        for(mi=1; mi<= wav[i]-1; mi++){
   double fret;          for (ii=1;ii<=nlstate+ndeath;ii++)
   xi=matrix(1,npar,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   for (i=1;i<=npar;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=1;j<=npar;j++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       xi[i][j]=(i==j ? 1.0 : 0.0);            }
   printf("Powell\n");          for(d=0; d<dh[mi][i]; d++){
   powell(p,xi,npar,ftol,&iter,&fret,func);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));            for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /**** Computes Hessian and covariance matrix ***/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))            savm=oldm;
 {            oldm=newm;
   double  **a,**y,*x,pd;          
   double **hess;          
   int i, j,jk;          } /* end mult */
   int *indx;        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double hessii(double p[], double delta, int theta, double delti[]);          /* But now since version 0.9 we anticipate for bias and large stepm.
   double hessij(double p[], double delti[], int i, int j);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   void lubksb(double **a, int npar, int *indx, double b[]) ;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   void ludcmp(double **a, int npar, int *indx, double *d) ;           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
   hess=matrix(1,npar,1,npar);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
   printf("\nCalculation of the hessian matrix. Wait...\n");           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for (i=1;i<=npar;i++){           * -stepm/2 to stepm/2 .
     printf("%d",i);fflush(stdout);           * For stepm=1 the results are the same as for previous versions of Imach.
     hess[i][i]=hessii(p,ftolhess,i,delti);           * For stepm > 1 the results are less biased than in previous versions. 
     /*printf(" %f ",p[i]);*/           */
     /*printf(" %lf ",hess[i][i]);*/          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm;
   for (i=1;i<=npar;i++) {          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]));
     for (j=1;j<=npar;j++)  {          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-bbh)*out[s1][s2]));*/
       if (j>i) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         printf(".%d%d",i,j);fflush(stdout);          /*if(lli ==000.0)*/
         hess[i][j]=hessij(p,delti,i,j);          /*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); */
         hess[j][i]=hess[i][j];              ipmx +=1;
         /*printf(" %lf ",hess[i][j]);*/          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
   }      } /* end of individual */
   printf("\n");    }  else{ 
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   a=matrix(1,npar,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   y=matrix(1,npar,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   x=vector(1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   indx=ivector(1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++)            }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          for(d=0; d<dh[mi][i]; d++){
   ludcmp(a,npar,indx,&pd);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (j=1;j<=npar;j++) {            for (kk=1; kk<=cptcovage;kk++) {
     for (i=1;i<=npar;i++) x[i]=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     x[j]=1;            }
     lubksb(a,npar,indx,x);          
     for (i=1;i<=npar;i++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       matcov[i][j]=x[i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
   }            oldm=newm;
           } /* end mult */
   printf("\n#Hessian matrix#\n");        
   for (i=1;i<=npar;i++) {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for (j=1;j<=npar;j++) {          ipmx +=1;
       printf("%.3e ",hess[i][j]);          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     printf("\n");        } /* end of wave */
   }      } /* end of individual */
     } /* End of if */
   /* Recompute Inverse */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   for (i=1;i<=npar;i++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   ludcmp(a,npar,indx,&pd);    return -l;
   }
   /*  printf("\n#Hessian matrix recomputed#\n");  
   
   for (j=1;j<=npar;j++) {  /*********** Maximum Likelihood Estimation ***************/
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     lubksb(a,npar,indx,x);  {
     for (i=1;i<=npar;i++){    int i,j, iter;
       y[i][j]=x[i];    double **xi,*delti;
       printf("%.3e ",y[i][j]);    double fret;
     }    xi=matrix(1,npar,1,npar);
     printf("\n");    for (i=1;i<=npar;i++)
   }      for (j=1;j<=npar;j++)
   */        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
   free_matrix(a,1,npar,1,npar);    powell(p,xi,npar,ftol,&iter,&fret,func);
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   free_ivector(indx,1,npar);    fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   free_matrix(hess,1,npar,1,npar);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
   }
 }  
   /**** Computes Hessian and covariance matrix ***/
 /*************** hessian matrix ****************/  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 double hessii( double x[], double delta, int theta, double delti[])  {
 {    double  **a,**y,*x,pd;
   int i;    double **hess;
   int l=1, lmax=20;    int i, j,jk;
   double k1,k2;    int *indx;
   double p2[NPARMAX+1];  
   double res;    double hessii(double p[], double delta, int theta, double delti[]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double hessij(double p[], double delti[], int i, int j);
   double fx;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   int k=0,kmax=10;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double l1;  
     hess=matrix(1,npar,1,npar);
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];    printf("\nCalculation of the hessian matrix. Wait...\n");
   for(l=0 ; l <=lmax; l++){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     l1=pow(10,l);    for (i=1;i<=npar;i++){
     delts=delt;      printf("%d",i);fflush(stdout);
     for(k=1 ; k <kmax; k=k+1){      fprintf(ficlog,"%d",i);fflush(ficlog);
       delt = delta*(l1*k);      hess[i][i]=hessii(p,ftolhess,i,delti);
       p2[theta]=x[theta] +delt;      /*printf(" %f ",p[i]);*/
       k1=func(p2)-fx;      /*printf(" %lf ",hess[i][i]);*/
       p2[theta]=x[theta]-delt;    }
       k2=func(p2)-fx;    
       /*res= (k1-2.0*fx+k2)/delt/delt; */    for (i=1;i<=npar;i++) {
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      for (j=1;j<=npar;j++)  {
              if (j>i) { 
 #ifdef DEBUG          printf(".%d%d",i,j);fflush(stdout);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 #endif          hess[i][j]=hessij(p,delti,i,j);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          hess[j][i]=hess[i][j];    
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /*printf(" %lf ",hess[i][j]);*/
         k=kmax;        }
       }      }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    }
         k=kmax; l=lmax*10.;    printf("\n");
       }    fprintf(ficlog,"\n");
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     }    
   }    a=matrix(1,npar,1,npar);
   delti[theta]=delts;    y=matrix(1,npar,1,npar);
   return res;    x=vector(1,npar);
      indx=ivector(1,npar);
 }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 double hessij( double x[], double delti[], int thetai,int thetaj)    ludcmp(a,npar,indx,&pd);
 {  
   int i;    for (j=1;j<=npar;j++) {
   int l=1, l1, lmax=20;      for (i=1;i<=npar;i++) x[i]=0;
   double k1,k2,k3,k4,res,fx;      x[j]=1;
   double p2[NPARMAX+1];      lubksb(a,npar,indx,x);
   int k;      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
   fx=func(x);      }
   for (k=1; k<=2; k++) {    }
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;    printf("\n#Hessian matrix#\n");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    fprintf(ficlog,"\n#Hessian matrix#\n");
     k1=func(p2)-fx;    for (i=1;i<=npar;i++) { 
        for (j=1;j<=npar;j++) { 
     p2[thetai]=x[thetai]+delti[thetai]/k;        printf("%.3e ",hess[i][j]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        fprintf(ficlog,"%.3e ",hess[i][j]);
     k2=func(p2)-fx;      }
        printf("\n");
     p2[thetai]=x[thetai]-delti[thetai]/k;      fprintf(ficlog,"\n");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    }
     k3=func(p2)-fx;  
      /* Recompute Inverse */
     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]=matcov[i][j];
     k4=func(p2)-fx;    ludcmp(a,npar,indx,&pd);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG    /*  printf("\n#Hessian matrix recomputed#\n");
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
   return res;      x[j]=1;
 }      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
 /************** Inverse of matrix **************/        y[i][j]=x[i];
 void ludcmp(double **a, int n, int *indx, double *d)        printf("%.3e ",y[i][j]);
 {        fprintf(ficlog,"%.3e ",y[i][j]);
   int i,imax,j,k;      }
   double big,dum,sum,temp;      printf("\n");
   double *vv;      fprintf(ficlog,"\n");
      }
   vv=vector(1,n);    */
   *d=1.0;  
   for (i=1;i<=n;i++) {    free_matrix(a,1,npar,1,npar);
     big=0.0;    free_matrix(y,1,npar,1,npar);
     for (j=1;j<=n;j++)    free_vector(x,1,npar);
       if ((temp=fabs(a[i][j])) > big) big=temp;    free_ivector(indx,1,npar);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    free_matrix(hess,1,npar,1,npar);
     vv[i]=1.0/big;  
   }  
   for (j=1;j<=n;j++) {  }
     for (i=1;i<j;i++) {  
       sum=a[i][j];  /*************** hessian matrix ****************/
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  double hessii( double x[], double delta, int theta, double delti[])
       a[i][j]=sum;  {
     }    int i;
     big=0.0;    int l=1, lmax=20;
     for (i=j;i<=n;i++) {    double k1,k2;
       sum=a[i][j];    double p2[NPARMAX+1];
       for (k=1;k<j;k++)    double res;
         sum -= a[i][k]*a[k][j];    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       a[i][j]=sum;    double fx;
       if ( (dum=vv[i]*fabs(sum)) >= big) {    int k=0,kmax=10;
         big=dum;    double l1;
         imax=i;  
       }    fx=func(x);
     }    for (i=1;i<=npar;i++) p2[i]=x[i];
     if (j != imax) {    for(l=0 ; l <=lmax; l++){
       for (k=1;k<=n;k++) {      l1=pow(10,l);
         dum=a[imax][k];      delts=delt;
         a[imax][k]=a[j][k];      for(k=1 ; k <kmax; k=k+1){
         a[j][k]=dum;        delt = delta*(l1*k);
       }        p2[theta]=x[theta] +delt;
       *d = -(*d);        k1=func(p2)-fx;
       vv[imax]=vv[j];        p2[theta]=x[theta]-delt;
     }        k2=func(p2)-fx;
     indx[j]=imax;        /*res= (k1-2.0*fx+k2)/delt/delt; */
     if (a[j][j] == 0.0) a[j][j]=TINY;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     if (j != n) {        
       dum=1.0/(a[j][j]);  #ifdef DEBUG
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   }  #endif
   free_vector(vv,1,n);  /* Doesn't work */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 ;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 }          k=kmax;
         }
 void lubksb(double **a, int n, int *indx, double b[])        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 {          k=kmax; l=lmax*10.;
   int i,ii=0,ip,j;        }
   double sum;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
            delts=delt;
   for (i=1;i<=n;i++) {        }
     ip=indx[i];      }
     sum=b[ip];    }
     b[ip]=b[i];    delti[theta]=delts;
     if (ii)    return res; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    
     else if (sum) ii=i;  }
     b[i]=sum;  
   }  double hessij( double x[], double delti[], int thetai,int thetaj)
   for (i=n;i>=1;i--) {  {
     sum=b[i];    int i;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    int l=1, l1, lmax=20;
     b[i]=sum/a[i][i];    double k1,k2,k3,k4,res,fx;
   }    double p2[NPARMAX+1];
 }    int k;
   
 /************ Frequencies ********************/    fx=func(x);
 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)    for (k=1; k<=2; k++) {
 {  /* Some frequencies */      for (i=1;i<=npar;i++) p2[i]=x[i];
        p2[thetai]=x[thetai]+delti[thetai]/k;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double ***freq; /* Frequencies */      k1=func(p2)-fx;
   double *pp;    
   double pos, k2, dateintsum=0,k2cpt=0;      p2[thetai]=x[thetai]+delti[thetai]/k;
   FILE *ficresp;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   char fileresp[FILENAMELENGTH];      k2=func(p2)-fx;
      
   pp=vector(1,nlstate);      p2[thetai]=x[thetai]-delti[thetai]/k;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   strcpy(fileresp,"p");      k3=func(p2)-fx;
   strcat(fileresp,fileres);    
   if((ficresp=fopen(fileresp,"w"))==NULL) {      p2[thetai]=x[thetai]-delti[thetai]/k;
     printf("Problem with prevalence resultfile: %s\n", fileresp);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     exit(0);      k4=func(p2)-fx;
   }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  #ifdef DEBUG
   j1=0;      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
        fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   j=cptcoveff;  #endif
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    }
      return res;
   for(k1=1; k1<=j;k1++){  }
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;  /************** Inverse of matrix **************/
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  void ludcmp(double **a, int n, int *indx, double *d) 
         scanf("%d", i);*/  { 
       for (i=-1; i<=nlstate+ndeath; i++)      int i,imax,j,k; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double big,dum,sum,temp; 
           for(m=agemin; m <= agemax+3; m++)    double *vv; 
             freq[i][jk][m]=0;   
          vv=vector(1,n); 
       dateintsum=0;    *d=1.0; 
       k2cpt=0;    for (i=1;i<=n;i++) { 
       for (i=1; i<=imx; i++) {      big=0.0; 
         bool=1;      for (j=1;j<=n;j++) 
         if  (cptcovn>0) {        if ((temp=fabs(a[i][j])) > big) big=temp; 
           for (z1=1; z1<=cptcoveff; z1++)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      vv[i]=1.0/big; 
               bool=0;    } 
         }    for (j=1;j<=n;j++) { 
         if (bool==1) {      for (i=1;i<j;i++) { 
           for(m=firstpass; m<=lastpass; m++){        sum=a[i][j]; 
             k2=anint[m][i]+(mint[m][i]/12.);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        a[i][j]=sum; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;      } 
               if(agev[m][i]==1) agev[m][i]=agemax+2;      big=0.0; 
               if (m<lastpass) {      for (i=j;i<=n;i++) { 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        sum=a[i][j]; 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        for (k=1;k<j;k++) 
               }          sum -= a[i][k]*a[k][j]; 
                      a[i][j]=sum; 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
                 dateintsum=dateintsum+k2;          big=dum; 
                 k2cpt++;          imax=i; 
               }        } 
             }      } 
           }      if (j != imax) { 
         }        for (k=1;k<=n;k++) { 
       }          dum=a[imax][k]; 
                  a[imax][k]=a[j][k]; 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          a[j][k]=dum; 
         } 
       if  (cptcovn>0) {        *d = -(*d); 
         fprintf(ficresp, "\n#********** Variable ");        vv[imax]=vv[j]; 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      } 
         fprintf(ficresp, "**********\n#");      indx[j]=imax; 
       }      if (a[j][j] == 0.0) a[j][j]=TINY; 
       for(i=1; i<=nlstate;i++)      if (j != n) { 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        dum=1.0/(a[j][j]); 
       fprintf(ficresp, "\n");        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
            } 
       for(i=(int)agemin; i <= (int)agemax+3; i++){    } 
         if(i==(int)agemax+3)    free_vector(vv,1,n);  /* Doesn't work */
           printf("Total");  ;
         else  } 
           printf("Age %d", i);  
         for(jk=1; jk <=nlstate ; jk++){  void lubksb(double **a, int n, int *indx, double b[]) 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  { 
             pp[jk] += freq[jk][m][i];    int i,ii=0,ip,j; 
         }    double sum; 
         for(jk=1; jk <=nlstate ; jk++){   
           for(m=-1, pos=0; m <=0 ; m++)    for (i=1;i<=n;i++) { 
             pos += freq[jk][m][i];      ip=indx[i]; 
           if(pp[jk]>=1.e-10)      sum=b[ip]; 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      b[ip]=b[i]; 
           else      if (ii) 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         }      else if (sum) ii=i; 
       b[i]=sum; 
         for(jk=1; jk <=nlstate ; jk++){    } 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    for (i=n;i>=1;i--) { 
             pp[jk] += freq[jk][m][i];      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,pos=0; jk <=nlstate ; jk++)    } 
           pos += pp[jk];  } 
         for(jk=1; jk <=nlstate ; jk++){  
           if(pos>=1.e-5)  /************ Frequencies ********************/
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  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)
           else  {  /* Some frequencies */
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    
           if( i <= (int) agemax){    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
             if(pos>=1.e-5){    int first;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    double ***freq; /* Frequencies */
               probs[i][jk][j1]= pp[jk]/pos;    double *pp;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    double pos, k2, dateintsum=0,k2cpt=0;
             }    FILE *ficresp;
             else    char fileresp[FILENAMELENGTH];
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    
           }    pp=vector(1,nlstate);
         }    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
            strcpy(fileresp,"p");
         for(jk=-1; jk <=nlstate+ndeath; jk++)    strcat(fileresp,fileres);
           for(m=-1; m <=nlstate+ndeath; m++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      printf("Problem with prevalence resultfile: %s\n", fileresp);
         if(i <= (int) agemax)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           fprintf(ficresp,"\n");      exit(0);
         printf("\n");    }
       }    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
     }    j1=0;
   }    
   dateintmean=dateintsum/k2cpt;    j=cptcoveff;
      if (cptcovn<1) {j=1;ncodemax[1]=1;}
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    first=1;
   free_vector(pp,1,nlstate);  
      for(k1=1; k1<=j;k1++){
   /* End of Freq */      for(i1=1; i1<=ncodemax[k1];i1++){
 }        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 /************ Prevalence ********************/          scanf("%d", 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)        for (i=-1; i<=nlstate+ndeath; i++)  
 {  /* Some frequencies */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
              for(m=agemin; m <= agemax+3; m++)
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;              freq[i][jk][m]=0;
   double ***freq; /* Frequencies */        
   double *pp;        dateintsum=0;
   double pos, k2;        k2cpt=0;
         for (i=1; i<=imx; i++) {
   pp=vector(1,nlstate);          bool=1;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   j1=0;                bool=0;
            }
   j=cptcoveff;          if (bool==1){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            for(m=firstpass; m<=lastpass; m++){
                k2=anint[m][i]+(mint[m][i]/12.);
   for(k1=1; k1<=j;k1++){              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     for(i1=1; i1<=ncodemax[k1];i1++){                if(agev[m][i]==0) agev[m][i]=agemax+1;
       j1++;                if(agev[m][i]==1) agev[m][i]=agemax+2;
                      if (m<lastpass) {
       for (i=-1; i<=nlstate+ndeath; i++)                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         for (jk=-1; jk<=nlstate+ndeath; jk++)                    freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
           for(m=agemin; m <= agemax+3; m++)                }
             freq[i][jk][m]=0;                
                      if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
       for (i=1; i<=imx; i++) {                  dateintsum=dateintsum+k2;
         bool=1;                  k2cpt++;
         if  (cptcovn>0) {                }
           for (z1=1; z1<=cptcoveff; z1++)              }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            }
               bool=0;          }
         }        }
         if (bool==1) {         
           for(m=firstpass; m<=lastpass; m++){        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        if  (cptcovn>0) {
               if(agev[m][i]==0) agev[m][i]=agemax+1;          fprintf(ficresp, "\n#********** Variable "); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               if (m<lastpass) {          fprintf(ficresp, "**********\n#");
                 if (calagedate>0)        }
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        for(i=1; i<=nlstate;i++) 
                 else          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        fprintf(ficresp, "\n");
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];        
               }        for(i=(int)agemin; i <= (int)agemax+3; i++){
             }          if(i==(int)agemax+3){
           }            fprintf(ficlog,"Total");
         }          }else{
       }            if(first==1){
       for(i=(int)agemin; i <= (int)agemax+3; i++){              first=0;
         for(jk=1; jk <=nlstate ; jk++){              printf("See log file for details...\n");
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            }
             pp[jk] += freq[jk][m][i];            fprintf(ficlog,"Age %d", i);
         }          }
         for(jk=1; jk <=nlstate ; jk++){          for(jk=1; jk <=nlstate ; jk++){
           for(m=-1, pos=0; m <=0 ; m++)            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
             pos += freq[jk][m][i];              pp[jk] += freq[jk][m][i]; 
         }          }
                  for(jk=1; jk <=nlstate ; jk++){
         for(jk=1; jk <=nlstate ; jk++){            for(m=-1, pos=0; m <=0 ; m++)
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              pos += freq[jk][m][i];
             pp[jk] += freq[jk][m][i];            if(pp[jk]>=1.e-10){
         }              if(first==1){
                      printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];              }
                      fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for(jk=1; jk <=nlstate ; jk++){                }else{
           if( i <= (int) agemax){              if(first==1)
             if(pos>=1.e-5){                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               probs[i][jk][j1]= pp[jk]/pos;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }            }
           }          }
         }  
                  for(jk=1; jk <=nlstate ; jk++){
       }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     }              pp[jk] += freq[jk][m][i];
   }          }
   
            for(jk=1,pos=0; jk <=nlstate ; jk++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            pos += pp[jk];
   free_vector(pp,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
              if(pos>=1.e-5){
 }  /* End of Freq */              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 /************* Waves Concatenation ***************/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)              if(first==1)
 {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      Death is a valid wave (if date is known).            }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            if( i <= (int) agemax){
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]              if(pos>=1.e-5){
      and mw[mi+1][i]. dh depends on stepm.                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
      */                probs[i][jk][j1]= pp[jk]/pos;
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   int i, mi, m;              }
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;              else
      double sum=0., jmean=0.;*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
             }
   int j, k=0,jk, ju, jl;          }
   double sum=0.;          
   jmin=1e+5;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   jmax=-1;            for(m=-1; m <=nlstate+ndeath; m++)
   jmean=0.;              if(freq[jk][m][i] !=0 ) {
   for(i=1; i<=imx; i++){              if(first==1)
     mi=0;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     m=firstpass;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     while(s[m][i] <= nlstate){              }
       if(s[m][i]>=1)          if(i <= (int) agemax)
         mw[++mi][i]=m;            fprintf(ficresp,"\n");
       if(m >=lastpass)          if(first==1)
         break;            printf("Others in log...\n");
       else          fprintf(ficlog,"\n");
         m++;        }
     }/* end while */      }
     if (s[m][i] > nlstate){    }
       mi++;     /* Death is another wave */    dateintmean=dateintsum/k2cpt; 
       /* if(mi==0)  never been interviewed correctly before death */   
          /* Only death is a correct wave */    fclose(ficresp);
       mw[mi][i]=m;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     }    free_vector(pp,1,nlstate);
     
     wav[i]=mi;    /* End of Freq */
     if(mi==0)  }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  
   }  /************ Prevalence ********************/
   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)
   for(i=1; i<=imx; i++){  {  /* Some frequencies */
     for(mi=1; mi<wav[i];mi++){   
       if (stepm <=0)    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         dh[mi][i]=1;    double ***freq; /* Frequencies */
       else{    double *pp;
         if (s[mw[mi+1][i]][i] > nlstate) {    double pos, k2;
           if (agedc[i] < 2*AGESUP) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    pp=vector(1,nlstate);
           if(j==0) j=1;  /* Survives at least one month after exam */    
           k=k+1;    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
           if (j >= jmax) jmax=j;    j1=0;
           if (j <= jmin) jmin=j;    
           sum=sum+j;    j=cptcoveff;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           }    
         }    for(k1=1; k1<=j;k1++){
         else{      for(i1=1; i1<=ncodemax[k1];i1++){
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        j1++;
           k=k+1;        
           if (j >= jmax) jmax=j;        for (i=-1; i<=nlstate+ndeath; i++)  
           else if (j <= jmin)jmin=j;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            for(m=agemin; m <= agemax+3; m++)
           sum=sum+j;              freq[i][jk][m]=0;
         }       
         jk= j/stepm;        for (i=1; i<=imx; i++) {
         jl= j -jk*stepm;          bool=1;
         ju= j -(jk+1)*stepm;          if  (cptcovn>0) {
         if(jl <= -ju)            for (z1=1; z1<=cptcoveff; z1++) 
           dh[mi][i]=jk;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         else                bool=0;
           dh[mi][i]=jk+1;          } 
         if(dh[mi][i]==0)          if (bool==1) { 
           dh[mi][i]=1; /* At least one step */            for(m=firstpass; m<=lastpass; m++){
       }              k2=anint[m][i]+(mint[m][i]/12.);
     }              if ((k2>=dateprev1) && (k2<=dateprev2)) {
   }                if(agev[m][i]==0) agev[m][i]=agemax+1;
   jmean=sum/k;                if(agev[m][i]==1) agev[m][i]=agemax+2;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);                if (m<lastpass) {
  }                  if (calagedate>0) 
 /*********** Tricode ****************************/                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
 void tricode(int *Tvar, int **nbcode, int imx)                  else
 {                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   int Ndum[20],ij=1, k, j, i;                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
   int cptcode=0;                }
   cptcoveff=0;              }
              }
   for (k=0; k<19; k++) Ndum[k]=0;          }
   for (k=1; k<=7; k++) ncodemax[k]=0;        }
         for(i=(int)agemin; i <= (int)agemax+3; i++){ 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          for(jk=1; jk <=nlstate ; jk++){
     for (i=1; i<=imx; i++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       ij=(int)(covar[Tvar[j]][i]);              pp[jk] += freq[jk][m][i]; 
       Ndum[ij]++;          }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          for(jk=1; jk <=nlstate ; jk++){
       if (ij > cptcode) cptcode=ij;            for(m=-1, pos=0; m <=0 ; m++)
     }              pos += freq[jk][m][i];
           }
     for (i=0; i<=cptcode; i++) {          
       if(Ndum[i]!=0) ncodemax[j]++;          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<=ncodemax[j]; i++) {          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
       for (k=0; k<=19; k++) {          
         if (Ndum[k] != 0) {          for(jk=1; jk <=nlstate ; jk++){    
           nbcode[Tvar[j]][ij]=k;            if( i <= (int) agemax){
                        if(pos>=1.e-5){
           ij++;                probs[i][jk][j1]= pp[jk]/pos;
         }              }
         if (ij > ncodemax[j]) break;            }
       }            }/* end jk */
     }        }/* end i */
   }        } /* end i1 */
     } /* end k1 */
  for (k=0; k<19; k++) Ndum[k]=0;  
     
  for (i=1; i<=ncovmodel-2; i++) {    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
       ij=Tvar[i];    free_vector(pp,1,nlstate);
       Ndum[ij]++;    
     }  }  /* End of Freq */
   
  ij=1;  /************* Waves Concatenation ***************/
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncovcol)){  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)
      Tvaraff[ij]=i;  {
      ij++;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
    }       Death is a valid wave (if date is known).
  }       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]
     cptcoveff=ij-1;       and mw[mi+1][i]. dh depends on stepm.
 }       */
   
 /*********** Health Expectancies ****************/    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )       double sum=0., jmean=0.;*/
     int first;
 {    int j, k=0,jk, ju, jl;
   /* Health expectancies */    double sum=0.;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    first=0;
   double age, agelim, hf;    jmin=1e+5;
   double ***p3mat,***varhe;    jmax=-1;
   double **dnewm,**doldm;    jmean=0.;
   double *xp;    for(i=1; i<=imx; i++){
   double **gp, **gm;      mi=0;
   double ***gradg, ***trgradg;      m=firstpass;
   int theta;      while(s[m][i] <= nlstate){
         if(s[m][i]>=1)
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          mw[++mi][i]=m;
   xp=vector(1,npar);        if(m >=lastpass)
   dnewm=matrix(1,nlstate*2,1,npar);          break;
   doldm=matrix(1,nlstate*2,1,nlstate*2);        else
            m++;
   fprintf(ficreseij,"# Health expectancies\n");      }/* end while */
   fprintf(ficreseij,"# Age");      if (s[m][i] > nlstate){
   for(i=1; i<=nlstate;i++)        mi++;     /* Death is another wave */
     for(j=1; j<=nlstate;j++)        /* if(mi==0)  never been interviewed correctly before death */
       fprintf(ficreseij," %1d-%1d (SE)",i,j);           /* Only death is a correct wave */
   fprintf(ficreseij,"\n");        mw[mi][i]=m;
       }
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);      wav[i]=mi;
   }      if(mi==0){
   else  hstepm=estepm;          if(first==0){
   /* We compute the life expectancy from trapezoids spaced every estepm months          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
    * This is mainly to measure the difference between two models: for example          first=1;
    * if stepm=24 months pijx are given only every 2 years and by summing them        }
    * we are calculating an estimate of the Life Expectancy assuming a linear        if(first==1){
    * progression inbetween and thus overestimating or underestimating according          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
    * to the curvature of the survival function. If, for the same date, we        }
    * estimate the model with stepm=1 month, we can keep estepm to 24 months      } /* end mi==0 */
    * 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. */    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
   /* For example we decided to compute the life expectancy with the smallest unit */        if (stepm <=0)
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          dh[mi][i]=1;
      nhstepm is the number of hstepm from age to agelim        else{
      nstepm is the number of stepm from age to agelin.          if (s[mw[mi+1][i]][i] > nlstate) {
      Look at hpijx to understand the reason of that which relies in memory size            if (agedc[i] < 2*AGESUP) {
      and note for a fixed period like estepm months */            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            if(j==0) j=1;  /* Survives at least one month after exam */
      survival function given by stepm (the optimization length). Unfortunately it            k=k+1;
      means that if the survival funtion is printed only each two years of age and if            if (j >= jmax) jmax=j;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            if (j <= jmin) jmin=j;
      results. So we changed our mind and took the option of the best precision.            sum=sum+j;
   */            /*if (j<0) printf("j=%d num=%d \n",j,i); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            }
           }
   agelim=AGESUP;          else{
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     /* nhstepm age range expressed in number of stepm */            k=k+1;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);            if (j >= jmax) jmax=j;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            else if (j <= jmin)jmin=j;
     /* if (stepm >= YEARM) hstepm=1;*/            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            sum=sum+j;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          jk= j/stepm;
     gp=matrix(0,nhstepm,1,nlstate*2);          jl= j -jk*stepm;
     gm=matrix(0,nhstepm,1,nlstate*2);          ju= j -(jk+1)*stepm;
           if(jl <= -ju){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            dh[mi][i]=jk;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            bh[mi][i]=jl;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            }
            else{
             dh[mi][i]=jk+1;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            bh[mi][i]=ju;
           }
     /* Computing Variances of health expectancies */          if(dh[mi][i]==0){
             dh[mi][i]=1; /* At least one step */
      for(theta=1; theta <=npar; theta++){            bh[mi][i]=ju; /* At least one step */
       for(i=1; i<=npar; i++){            printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
       }          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);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
        }
       cptj=0;    }
       for(j=1; j<= nlstate; j++){    jmean=sum/k;
         for(i=1; i<=nlstate; i++){    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           cptj=cptj+1;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){   }
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  /*********** Tricode ****************************/
         }  void tricode(int *Tvar, int **nbcode, int imx)
       }  {
          
          int Ndum[20],ij=1, k, j, i, maxncov=19;
       for(i=1; i<=npar; i++)    int cptcode=0;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    cptcoveff=0; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     
          for (k=0; k<maxncov; k++) Ndum[k]=0;
       cptj=0;    for (k=1; k<=7; k++) ncodemax[k]=0;
       for(j=1; j<= nlstate; j++){  
         for(i=1;i<=nlstate;i++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
           cptj=cptj+1;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){                                 modality*/ 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
           }        Ndum[ij]++; /*store the modality */
         }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       for(j=1; j<= nlstate*2; j++)                                         Tvar[j]. If V=sex and male is 0 and 
         for(h=0; h<=nhstepm-1; h++){                                         female is 1, then  cptcode=1.*/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      }
         }  
      }      for (i=0; i<=cptcode; i++) {
            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 */
 /* End theta */      }
   
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
      for(h=0; h<=nhstepm-1; h++)        for (k=0; k<= maxncov; k++) {
       for(j=1; j<=nlstate*2;j++)          if (Ndum[k] != 0) {
         for(theta=1; theta <=npar; theta++)            nbcode[Tvar[j]][ij]=k; 
           trgradg[h][j][theta]=gradg[h][theta][j];            /* 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; */
                  
             ij++;
      for(i=1;i<=nlstate*2;i++)          }
       for(j=1;j<=nlstate*2;j++)          if (ij > ncodemax[j]) break; 
         varhe[i][j][(int)age] =0.;        }  
       } 
      printf("%d|",(int)age);fflush(stdout);    }  
      for(h=0;h<=nhstepm-1;h++){  
       for(k=0;k<=nhstepm-1;k++){   for (k=0; k< maxncov; k++) Ndum[k]=0;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);   for (i=1; i<=ncovmodel-2; i++) { 
         for(i=1;i<=nlstate*2;i++)     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           for(j=1;j<=nlstate*2;j++)     ij=Tvar[i];
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;     Ndum[ij]++;
       }   }
     }  
     /* Computing expectancies */   ij=1;
     for(i=1; i<=nlstate;i++)   for (i=1; i<= maxncov; i++) {
       for(j=1; j<=nlstate;j++)     if((Ndum[i]!=0) && (i<=ncovcol)){
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){       Tvaraff[ij]=i; /*For printing */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;       ij++;
               }
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/   }
    
         }   cptcoveff=ij-1; /*Number of simple covariates*/
   }
     fprintf(ficreseij,"%3.0f",age );  
     cptj=0;  /*********** Health Expectancies ****************/
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
         cptj++;  
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );  {
       }    /* Health expectancies */
     fprintf(ficreseij,"\n");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
        double age, agelim, hf;
     free_matrix(gm,0,nhstepm,1,nlstate*2);    double ***p3mat,***varhe;
     free_matrix(gp,0,nhstepm,1,nlstate*2);    double **dnewm,**doldm;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    double *xp;
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    double **gp, **gm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double ***gradg, ***trgradg;
   }    int theta;
   printf("\n");  
     varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
   free_vector(xp,1,npar);    xp=vector(1,npar);
   free_matrix(dnewm,1,nlstate*2,1,npar);    dnewm=matrix(1,nlstate*2,1,npar);
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    doldm=matrix(1,nlstate*2,1,nlstate*2);
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    
 }    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
 /************ Variance ******************/    for(i=1; i<=nlstate;i++)
 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)      for(j=1; j<=nlstate;j++)
 {        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   /* Variance of health expectancies */    fprintf(ficreseij,"\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;    if(estepm < stepm){
   double **dnewm,**doldm;      printf ("Problem %d lower than %d\n",estepm, stepm);
   int i, j, nhstepm, hstepm, h, nstepm ;    }
   int k, cptcode;    else  hstepm=estepm;   
   double *xp;    /* We compute the life expectancy from trapezoids spaced every estepm months
   double **gp, **gm;     * This is mainly to measure the difference between two models: for example
   double ***gradg, ***trgradg;     * if stepm=24 months pijx are given only every 2 years and by summing them
   double ***p3mat;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   double age,agelim, hf;     * progression inbetween and thus overestimating or underestimating according
   int theta;     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
   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");     * to compare the new estimate of Life expectancy with the same linear 
   fprintf(ficresvij,"# Age");     * hypothesis. A more precise result, taking into account a more precise
   for(i=1; i<=nlstate;i++)     * curvature will be obtained if estepm is as small as stepm. */
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    /* For example we decided to compute the life expectancy with the smallest unit */
   fprintf(ficresvij,"\n");    /* 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 
   xp=vector(1,npar);       nstepm is the number of stepm from age to agelin. 
   dnewm=matrix(1,nlstate,1,npar);       Look at hpijx to understand the reason of that which relies in memory size
   doldm=matrix(1,nlstate,1,nlstate);       and note for a fixed period like estepm months */
      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if(estepm < stepm){       survival function given by stepm (the optimization length). Unfortunately it
     printf ("Problem %d lower than %d\n",estepm, stepm);       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 
   else  hstepm=estepm;         results. So we changed our mind and took the option of the best precision.
   /* For example we decided to compute the life expectancy with the smallest unit */    */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.    agelim=AGESUP;
      Look at hpijx to understand the reason of that which relies in memory size    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      and note for a fixed period like k years */      /* nhstepm age range expressed in number of stepm */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
      survival function given by stepm (the optimization length). Unfortunately it      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      means that if the survival funtion is printed only each two years of age and if      /* if (stepm >= YEARM) hstepm=1;*/
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      results. So we changed our mind and took the option of the best precision.      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      gp=matrix(0,nhstepm,1,nlstate*2);
   agelim = AGESUP;      gm=matrix(0,nhstepm,1,nlstate*2);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);   
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
     for(theta=1; theta <=npar; theta++){      /* Computing Variances of health expectancies */
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);       for(theta=1; theta <=npar; theta++){
       }        for(i=1; i<=npar; i++){ 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            xp[i] = x[i] + (i==theta ?delti[theta]:0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       if (popbased==1) {    
         for(i=1; i<=nlstate;i++)        cptj=0;
           prlim[i][i]=probs[(int)age][i][ij];        for(j=1; j<= nlstate; j++){
       }          for(i=1; i<=nlstate; i++){
              cptj=cptj+1;
       for(j=1; j<= nlstate; j++){            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         for(h=0; h<=nhstepm; h++){              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          }
         }        }
       }       
           
       for(i=1; i<=npar; i++) /* Computes gradient */        for(i=1; i<=npar; i++) 
         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);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        
          cptj=0;
       if (popbased==1) {        for(j=1; j<= nlstate; j++){
         for(i=1; i<=nlstate;i++)          for(i=1;i<=nlstate;i++){
           prlim[i][i]=probs[(int)age][i][ij];            cptj=cptj+1;
       }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       for(j=1; j<= nlstate; j++){            }
         for(h=0; h<=nhstepm; h++){          }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        for(j=1; j<= nlstate*2; j++)
         }          for(h=0; h<=nhstepm-1; h++){
       }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
       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];  /* End theta */
         }  
     } /* End theta */       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*2;j++)
     for(h=0; h<=nhstepm; h++)          for(theta=1; theta <=npar; theta++)
       for(j=1; j<=nlstate;j++)            trgradg[h][j][theta]=gradg[h][theta][j];
         for(theta=1; theta <=npar; theta++)       
           trgradg[h][j][theta]=gradg[h][theta][j];  
        for(i=1;i<=nlstate*2;i++)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        for(j=1;j<=nlstate*2;j++)
     for(i=1;i<=nlstate;i++)          varhe[i][j][(int)age] =0.;
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     for(h=0;h<=nhstepm;h++){       for(h=0;h<=nhstepm-1;h++){
       for(k=0;k<=nhstepm;k++){        for(k=0;k<=nhstepm-1;k++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
         for(i=1;i<=nlstate;i++)          for(i=1;i<=nlstate*2;i++)
           for(j=1;j<=nlstate;j++)            for(j=1;j<=nlstate*2;j++)
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
     }      }
       /* Computing expectancies */
     fprintf(ficresvij,"%.0f ",age );      for(i=1; i<=nlstate;i++)
     for(i=1; i<=nlstate;i++)        for(j=1; j<=nlstate;j++)
       for(j=1; j<=nlstate;j++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       }            
     fprintf(ficresvij,"\n");  /* 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]);*/
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);          }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      fprintf(ficreseij,"%3.0f",age );
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      cptj=0;
   } /* End age */      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
   free_vector(xp,1,npar);          cptj++;
   free_matrix(doldm,1,nlstate,1,npar);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   free_matrix(dnewm,1,nlstate,1,nlstate);        }
       fprintf(ficreseij,"\n");
 }     
       free_matrix(gm,0,nhstepm,1,nlstate*2);
 /************ Variance of prevlim ******************/      free_matrix(gp,0,nhstepm,1,nlstate*2);
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
 {      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
   /* Variance of prevalence limit */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    }
   double **newm;    printf("\n");
   double **dnewm,**doldm;    fprintf(ficlog,"\n");
   int i, j, nhstepm, hstepm;  
   int k, cptcode;    free_vector(xp,1,npar);
   double *xp;    free_matrix(dnewm,1,nlstate*2,1,npar);
   double *gp, *gm;    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
   double **gradg, **trgradg;    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
   double age,agelim;  }
   int theta;  
      /************ Variance ******************/
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");  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)
   fprintf(ficresvpl,"# Age");  {
   for(i=1; i<=nlstate;i++)    /* Variance of health expectancies */
       fprintf(ficresvpl," %1d-%1d",i,i);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   fprintf(ficresvpl,"\n");    /* double **newm;*/
     double **dnewm,**doldm;
   xp=vector(1,npar);    double **dnewmp,**doldmp;
   dnewm=matrix(1,nlstate,1,npar);    int i, j, nhstepm, hstepm, h, nstepm ;
   doldm=matrix(1,nlstate,1,nlstate);    int k, cptcode;
      double *xp;
   hstepm=1*YEARM; /* Every year of age */    double **gp, **gm;  /* for var eij */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double ***gradg, ***trgradg; /*for var eij */
   agelim = AGESUP;    double **gradgp, **trgradgp; /* for var p point j */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double *gpp, *gmp; /* for var p point j */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     if (stepm >= YEARM) hstepm=1;    double ***p3mat;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double age,agelim, hf;
     gradg=matrix(1,npar,1,nlstate);    double ***mobaverage;
     gp=vector(1,nlstate);    int theta;
     gm=vector(1,nlstate);    char digit[4];
     char digitp[25];
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    char fileresprobmorprev[FILENAMELENGTH];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    if(popbased==1){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if(mobilav!=0)
       for(i=1;i<=nlstate;i++)        strcpy(digitp,"-populbased-mobilav-");
         gp[i] = prlim[i][i];      else strcpy(digitp,"-populbased-nomobil-");
        }
       for(i=1; i<=npar; i++) /* Computes gradient */    else 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      strcpy(digitp,"-stablbased-");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    if (mobilav!=0) {
         gm[i] = prlim[i][i];      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       for(i=1;i<=nlstate;i++)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     } /* End theta */      }
     }
     trgradg =matrix(1,nlstate,1,npar);  
     strcpy(fileresprobmorprev,"prmorprev"); 
     for(j=1; j<=nlstate;j++)    sprintf(digit,"%-d",ij);
       for(theta=1; theta <=npar; theta++)    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         trgradg[j][theta]=gradg[theta][j];    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     for(i=1;i<=nlstate;i++)    strcat(fileresprobmorprev,fileres);
       varpl[i][(int)age] =0.;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     for(i=1;i<=nlstate;i++)    }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    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(ficresvpl,"%.0f ",age );    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
     for(i=1; i<=nlstate;i++)    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fprintf(ficresvpl,"\n");      fprintf(ficresprobmorprev," p.%-d SE",j);
     free_vector(gp,1,nlstate);      for(i=1; i<=nlstate;i++)
     free_vector(gm,1,nlstate);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     free_matrix(gradg,1,npar,1,nlstate);    }  
     free_matrix(trgradg,1,nlstate,1,npar);    fprintf(ficresprobmorprev,"\n");
   } /* End age */    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   free_vector(xp,1,npar);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   free_matrix(doldm,1,nlstate,1,npar);      exit(0);
   free_matrix(dnewm,1,nlstate,1,nlstate);    }
     else{
 }      fprintf(ficgp,"\n# Routine varevsij");
     }
 /************ Variance of one-step probabilities  ******************/    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)      printf("Problem with html file: %s\n", optionfilehtm);
 {      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   int i, j=0,  i1, k1, l1, t, tj;      exit(0);
   int k2, l2, j1,  z1;    }
   int k=0,l, cptcode;    else{
   int first=1;      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");
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
   double **dnewm,**doldm;    }
   double *xp;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double *gp, *gm;  
   double **gradg, **trgradg;    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");
   double **mu;    fprintf(ficresvij,"# Age");
   double age,agelim, cov[NCOVMAX];    for(i=1; i<=nlstate;i++)
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */      for(j=1; j<=nlstate;j++)
   int theta;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   char fileresprob[FILENAMELENGTH];    fprintf(ficresvij,"\n");
   char fileresprobcov[FILENAMELENGTH];  
   char fileresprobcor[FILENAMELENGTH];    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   double ***varpij;    doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   strcpy(fileresprob,"prob");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcat(fileresprob,fileres);  
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     printf("Problem with resultfile: %s\n", fileresprob);    gpp=vector(nlstate+1,nlstate+ndeath);
   }    gmp=vector(nlstate+1,nlstate+ndeath);
   strcpy(fileresprobcov,"probcov");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   strcat(fileresprobcov,fileres);    
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    if(estepm < stepm){
     printf("Problem with resultfile: %s\n", fileresprobcov);      printf ("Problem %d lower than %d\n",estepm, stepm);
   }    }
   strcpy(fileresprobcor,"probcor");    else  hstepm=estepm;   
   strcat(fileresprobcor,fileres);    /* For example we decided to compute the life expectancy with the smallest unit */
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     printf("Problem with resultfile: %s\n", fileresprobcor);       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);       Look at hpijx to understand the reason of that which relies in memory size
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);       and note for a fixed period like k years */
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    /* 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
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");       means that if the survival funtion is printed only each two years of age and if
   fprintf(ficresprob,"# Age");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");       results. So we changed our mind and took the option of the best precision.
   fprintf(ficresprobcov,"# Age");    */
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fprintf(ficresprobcov,"# Age");    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   for(i=1; i<=nlstate;i++)      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for(j=1; j<=(nlstate+ndeath);j++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       fprintf(ficresprobcov," p%1d-%1d ",i,j);      gp=matrix(0,nhstepm,1,nlstate);
       fprintf(ficresprobcor," p%1d-%1d ",i,j);      gm=matrix(0,nhstepm,1,nlstate);
     }    
   fprintf(ficresprob,"\n");  
   fprintf(ficresprobcov,"\n");      for(theta=1; theta <=npar; theta++){
   fprintf(ficresprobcor,"\n");        for(i=1; i<=npar; i++){ /* Computes gradient */
   xp=vector(1,npar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);        }
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);  
   first=1;        if (popbased==1) {
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          if(mobilav ==0){
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);            for(i=1; i<=nlstate;i++)
     exit(0);              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
   else{            for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"\n# Routine varprob");              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {        }
     printf("Problem with html file: %s\n", optionfilehtm);    
     exit(0);        for(j=1; j<= nlstate; j++){
   }          for(h=0; h<=nhstepm; h++){
   else{            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");          }
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");        }
         /* This for computing forces of mortality (h=1)as a weighted average */
   }        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
           for(i=1; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   cov[1]=1;        }    
   tj=cptcoveff;        /* end force of mortality */
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}  
   j1=0;        for(i=1; i<=npar; i++) /* Computes gradient */
   for(t=1; t<=tj;t++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for(i1=1; i1<=ncodemax[t];i1++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       j1++;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         
       if  (cptcovn>0) {        if (popbased==1) {
         fprintf(ficresprob, "\n#********** Variable ");          if(mobilav ==0){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            for(i=1; i<=nlstate;i++)
         fprintf(ficresprob, "**********\n#");              prlim[i][i]=probs[(int)age][i][ij];
         fprintf(ficresprobcov, "\n#********** Variable ");          }else{ /* mobilav */ 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            for(i=1; i<=nlstate;i++)
         fprintf(ficresprobcov, "**********\n#");              prlim[i][i]=mobaverage[(int)age][i][ij];
                  }
         fprintf(ficgp, "\n#********** Variable ");        }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficgp, "**********\n#");        for(j=1; j<= nlstate; j++){
                  for(h=0; h<=nhstepm; h++){
                    for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         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\">");        }
                /* This for computing force of mortality (h=1)as a weighted average */
         fprintf(ficresprobcor, "\n#********** Variable ");            for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for(i=1; i<= nlstate; i++)
         fprintf(ficgp, "**********\n#");                gmp[j] += prlim[i][i]*p3mat[i][j][1];
       }        }    
              /* end force of mortality */
       for (age=bage; age<=fage; age ++){  
         cov[2]=age;        for(j=1; j<= nlstate; j++) /* vareij */
         for (k=1; k<=cptcovn;k++) {          for(h=0; h<=nhstepm; h++){
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         }          }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         for (k=1; k<=cptcovprod;k++)          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        }
          
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));      } /* End theta */
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
         gp=vector(1,(nlstate)*(nlstate+ndeath));      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
         gm=vector(1,(nlstate)*(nlstate+ndeath));  
          for(h=0; h<=nhstepm; h++) /* veij */
         for(theta=1; theta <=npar; theta++){        for(j=1; j<=nlstate;j++)
           for(i=1; i<=npar; i++)          for(theta=1; theta <=npar; theta++)
             xp[i] = x[i] + (i==theta ?delti[theta]:0);            trgradg[h][j][theta]=gradg[h][theta][j];
            
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                  for(theta=1; theta <=npar; theta++)
           k=0;          trgradgp[j][theta]=gradgp[theta][j];
           for(i=1; i<= (nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               k=k+1;      for(i=1;i<=nlstate;i++)
               gp[k]=pmmij[i][j];        for(j=1;j<=nlstate;j++)
             }          vareij[i][j][(int)age] =0.;
           }  
                for(h=0;h<=nhstepm;h++){
           for(i=1; i<=npar; i++)        for(k=0;k<=nhstepm;k++){
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
              matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          for(i=1;i<=nlstate;i++)
           k=0;            for(j=1;j<=nlstate;j++)
           for(i=1; i<=(nlstate); i++){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
             for(j=1; j<=(nlstate+ndeath);j++){        }
               k=k+1;      }
               gm[k]=pmmij[i][j];  
             }      /* pptj */
           }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
            matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)      for(j=nlstate+1;j<=nlstate+ndeath;j++)
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          for(i=nlstate+1;i<=nlstate+ndeath;i++)
         }          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           for(theta=1; theta <=npar; theta++)      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
             trgradg[j][theta]=gradg[theta][j];   
              if (popbased==1) {
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);        if(mobilav ==0){
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);          for(i=1; i<=nlstate;i++)
                    prlim[i][i]=probs[(int)age][i][ij];
         pmij(pmmij,cov,ncovmodel,x,nlstate);        }else{ /* mobilav */ 
                  for(i=1; i<=nlstate;i++)
         k=0;            prlim[i][i]=mobaverage[(int)age][i][ij];
         for(i=1; i<=(nlstate); i++){        }
           for(j=1; j<=(nlstate+ndeath);j++){      }
             k=k+1;      
             mu[k][(int) age]=pmmij[i][j];      /* This for computing force of mortality (h=1)as a weighted average */
           }      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
         }        for(i=1; i<= nlstate; i++)
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)      }    
             varpij[i][j][(int)age] = doldm[i][j];      /* end force of mortality */
   
         /*printf("\n%d ",(int)age);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
      for (i=1; i<=(nlstate)*(nlstate+ndeath);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," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
      }*/        for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         fprintf(ficresprob,"\n%d ",(int)age);        }
         fprintf(ficresprobcov,"\n%d ",(int)age);      } 
         fprintf(ficresprobcor,"\n%d ",(int)age);      fprintf(ficresprobmorprev,"\n");
   
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)      fprintf(ficresvij,"%.0f ",age );
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));      for(i=1; i<=nlstate;i++)
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){        for(j=1; j<=nlstate;j++){
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);        }
         }      fprintf(ficresvij,"\n");
         i=0;      free_matrix(gp,0,nhstepm,1,nlstate);
         for (k=1; k<=(nlstate);k++){      free_matrix(gm,0,nhstepm,1,nlstate);
           for (l=1; l<=(nlstate+ndeath);l++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
             i=i++;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
             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);    } /* End age */
             for (j=1; j<=i;j++){    free_vector(gpp,nlstate+1,nlstate+ndeath);
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    free_vector(gmp,nlstate+1,nlstate+ndeath);
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
             }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
         }/* end of loop for state */    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       } /* end of loop for age */    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
       for (k1=1; k1<=(nlstate);k1++){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
         for (l1=1; l1<=(nlstate+ndeath);l1++){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
           if(l1==k1) continue;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
           i=(k1-1)*(nlstate+ndeath)+l1;    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
           for (k2=1; k2<=(nlstate);k2++){    /*  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);
             for (l2=1; l2<=(nlstate+ndeath);l2++){  */
               if(l2==k2) continue;    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
               j=(k2-1)*(nlstate+ndeath)+l2;  
               if(j<=i) continue;    free_vector(xp,1,npar);
               for (age=bage; age<=fage; age ++){    free_matrix(doldm,1,nlstate,1,nlstate);
                 if ((int)age %5==0){    free_matrix(dnewm,1,nlstate,1,npar);
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   mu1=mu[i][(int) age]/stepm*YEARM ;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   mu2=mu[j][(int) age]/stepm*YEARM;    fclose(ficresprobmorprev);
                   /* Computing eigen value of matrix of covariance */    fclose(ficgp);
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    fclose(fichtm);
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));  }
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);  
                   /* Eigen vectors */  /************ Variance of prevlim ******************/
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));  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)
                   v21=sqrt(1.-v11*v11);  {
                   v12=-v21;    /* Variance of prevalence limit */
                   v22=v11;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
                   /*printf(fignu*/    double **newm;
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    double **dnewm,**doldm;
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */    int i, j, nhstepm, hstepm;
                   if(first==1){    int k, cptcode;
                     first=0;    double *xp;
                     fprintf(ficgp,"\nset parametric;set nolabel");    double *gp, *gm;
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);    double **gradg, **trgradg;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    double age,agelim;
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);    int theta;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);     
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    fprintf(ficresvpl,"# Age");
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    for(i=1; i<=nlstate;i++)
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\        fprintf(ficresvpl," %1d-%1d",i,i);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    fprintf(ficresvpl,"\n");
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  
                   }else{    xp=vector(1,npar);
                     first=0;    dnewm=matrix(1,nlstate,1,npar);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    doldm=matrix(1,nlstate,1,nlstate);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    hstepm=1*YEARM; /* Every year of age */
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    agelim = AGESUP;
                   }/* if first */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                 } /* age mod 5 */      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
               } /* end loop age */      if (stepm >= YEARM) hstepm=1;
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
               first=1;      gradg=matrix(1,npar,1,nlstate);
             } /*l12 */      gp=vector(1,nlstate);
           } /* k12 */      gm=vector(1,nlstate);
         } /*l1 */  
       }/* k1 */      for(theta=1; theta <=npar; theta++){
     } /* loop covariates */        for(i=1; i<=npar; i++){ /* Computes gradient */
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);        for(i=1;i<=nlstate;i++)
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          gp[i] = prlim[i][i];
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      
   }        for(i=1; i<=npar; i++) /* Computes gradient */
   free_vector(xp,1,npar);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   fclose(ficresprob);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   fclose(ficresprobcov);        for(i=1;i<=nlstate;i++)
   fclose(ficresprobcor);          gm[i] = prlim[i][i];
   fclose(ficgp);  
   fclose(fichtm);        for(i=1;i<=nlstate;i++)
 }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
 /******************* Printing html file ***********/      trgradg =matrix(1,nlstate,1,npar);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  
                   int lastpass, int stepm, int weightopt, char model[],\      for(j=1; j<=nlstate;j++)
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\        for(theta=1; theta <=npar; theta++)
                   int popforecast, int estepm ,\          trgradg[j][theta]=gradg[theta][j];
                   double jprev1, double mprev1,double anprev1, \  
                   double jprev2, double mprev2,double anprev2){      for(i=1;i<=nlstate;i++)
   int jj1, k1, i1, cpt;        varpl[i][(int)age] =0.;
   /*char optionfilehtm[FILENAMELENGTH];*/      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     printf("Problem with %s \n",optionfilehtm), exit(0);      for(i=1;i<=nlstate;i++)
   }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n      fprintf(ficresvpl,"%.0f ",age );
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n      for(i=1; i<=nlstate;i++)
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n      fprintf(ficresvpl,"\n");
  - Life expectancies by age and initial health status (estepm=%2d months):      free_vector(gp,1,nlstate);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \      free_vector(gm,1,nlstate);
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    } /* End age */
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    free_vector(xp,1,npar);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    free_matrix(doldm,1,nlstate,1,npar);
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    free_matrix(dnewm,1,nlstate,1,nlstate);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n  }
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  
   /************ Variance of one-step probabilities  ******************/
  if(popforecast==1) fprintf(fichtm,"\n  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
  - 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    int i, j=0,  i1, k1, l1, t, tj;
         <br>",fileres,fileres,fileres,fileres);    int k2, l2, j1,  z1;
  else    int k=0,l, cptcode;
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    int first=1, first1;
 fprintf(fichtm," <li><b>Graphs</b></li><p>");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
  m=cptcoveff;    double *xp;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double *gp, *gm;
     double **gradg, **trgradg;
  jj1=0;    double **mu;
  for(k1=1; k1<=m;k1++){    double age,agelim, cov[NCOVMAX];
    for(i1=1; i1<=ncodemax[k1];i1++){    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
      jj1++;    int theta;
      if (cptcovn > 0) {    char fileresprob[FILENAMELENGTH];
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    char fileresprobcov[FILENAMELENGTH];
        for (cpt=1; cpt<=cptcoveff;cpt++)    char fileresprobcor[FILENAMELENGTH];
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double ***varpij;
      }  
      /* Pij */    strcpy(fileresprob,"prob"); 
      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>    strcat(fileresprob,fileres);
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      /* Quasi-incidences */      printf("Problem with resultfile: %s\n", fileresprob);
      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>      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    }
        /* Stable prevalence in each health state */    strcpy(fileresprobcov,"probcov"); 
        for(cpt=1; cpt<nlstate;cpt++){    strcat(fileresprobcov,fileres);
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      printf("Problem with resultfile: %s\n", fileresprobcov);
        }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     for(cpt=1; cpt<=nlstate;cpt++) {    }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    strcpy(fileresprobcor,"probcor"); 
 interval) in state (%d): v%s%d%d.png <br>    strcat(fileresprobcor,fileres);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
      }      printf("Problem with resultfile: %s\n", fileresprobcor);
      for(cpt=1; cpt<=nlstate;cpt++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         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);    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);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
 health expectancies in states (1) and (2): e%s%d.png<br>    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    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);
  }    
 fclose(fichtm);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
 }    fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
 /******************* Gnuplot file **************/    fprintf(ficresprobcov,"# Age");
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  
   int ng;  
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    for(i=1; i<=nlstate;i++)
     printf("Problem with file %s",optionfilegnuplot);      for(j=1; j<=(nlstate+ndeath);j++){
   }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
 #ifdef windows        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     fprintf(ficgp,"cd \"%s\" \n",pathc);      }  
 #endif    fprintf(ficresprob,"\n");
 m=pow(2,cptcoveff);    fprintf(ficresprobcov,"\n");
      fprintf(ficresprobcor,"\n");
  /* 1eme*/    xp=vector(1,npar);
   for (cpt=1; cpt<= nlstate ; cpt ++) {    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    for (k1=1; k1<= m ; k1 ++) {    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
 #ifdef windows    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    first=1;
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 #endif      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
 #ifdef unix      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      exit(0);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    }
 #endif    else{
       fprintf(ficgp,"\n# Routine varprob");
 for (i=1; i<= nlstate ; i ++) {    }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");      printf("Problem with html file: %s\n", optionfilehtm);
 }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      exit(0);
     for (i=1; i<= nlstate ; i ++) {    }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    else{
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
 }      fprintf(fichtm,"\n");
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    }
 #ifdef unix  
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    cov[1]=1;
 #endif    tj=cptcoveff;
    }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   }    j1=0;
   /*2 eme*/    for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
   for (k1=1; k1<= m ; k1 ++) {        j1++;
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);        if  (cptcovn>0) {
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);          fprintf(ficresprob, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for (i=1; i<= nlstate+1 ; i ++) {          fprintf(ficresprob, "**********\n#");
       k=2*i;          fprintf(ficresprobcov, "\n#********** Variable "); 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for (j=1; j<= nlstate+1 ; j ++) {          fprintf(ficresprobcov, "**********\n#");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficgp, "\n#********** Variable "); 
 }            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          fprintf(ficgp, "**********\n#");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          
       for (j=1; j<= nlstate+1 ; j ++) {          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
 }            
       fprintf(ficgp,"\" t\"\" w l 0,");          fprintf(ficresprobcor, "\n#********** Variable ");    
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for (j=1; j<= nlstate+1 ; j ++) {          fprintf(ficgp, "**********\n#");    
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        
 }          for (age=bage; age<=fage; age ++){ 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          cov[2]=age;
       else fprintf(ficgp,"\" t\"\" w l 0,");          for (k=1; k<=cptcovn;k++) {
     }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   }          }
            for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /*3eme*/          for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for (k1=1; k1<= m ; k1 ++) {          
     for (cpt=1; cpt<= nlstate ; cpt ++) {          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       k=2+nlstate*(2*cpt-2);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          gp=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          gm=vector(1,(nlstate)*(nlstate+ndeath));
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for(theta=1; theta <=npar; theta++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            for(i=1; i<=npar; i++)
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);              xp[i] = x[i] + (i==theta ?delti[theta]:0);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
 */            k=0;
       for (i=1; i< nlstate ; i ++) {            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);              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
       }                gp[k]=pmmij[i][j];
     }              }
   }            }
              
   /* CV preval stat */            for(i=1; i<=npar; i++)
     for (k1=1; k1<= m ; k1 ++) {              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for (cpt=1; cpt<nlstate ; cpt ++) {      
       k=3;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            k=0;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);            for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
       for (i=1; i< nlstate ; i ++)                k=k+1;
         fprintf(ficgp,"+$%d",k+i+1);                gm[k]=pmmij[i][j];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              }
                  }
       l=3+(nlstate+ndeath)*cpt;       
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       for (i=1; i< nlstate ; i ++) {              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
         l=3+(nlstate+ndeath)*cpt;          }
         fprintf(ficgp,"+$%d",l+i+1);  
       }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              for(theta=1; theta <=npar; theta++)
     }              trgradg[j][theta]=gradg[theta][j];
   }            
            matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   /* proba elementaires */          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
    for(i=1,jk=1; i <=nlstate; i++){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     for(k=1; k <=(nlstate+ndeath); k++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       if (k != i) {          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         for(j=1; j <=ncovmodel; j++){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
          
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          pmij(pmmij,cov,ncovmodel,x,nlstate);
           jk++;          
           fprintf(ficgp,"\n");          k=0;
         }          for(i=1; i<=(nlstate); i++){
       }            for(j=1; j<=(nlstate+ndeath);j++){
     }              k=k+1;
    }              mu[k][(int) age]=pmmij[i][j];
             }
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/          }
      for(jk=1; jk <=m; jk++) {          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
        if (ng==2)              varpij[i][j][(int)age] = doldm[i][j];
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");  
        else          /*printf("\n%d ",(int)age);
          fprintf(ficgp,"\nset title \"Probability\"\n");            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        i=1;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        for(k2=1; k2<=nlstate; k2++) {            }*/
          k3=i;  
          for(k=1; k<=(nlstate+ndeath); k++) {          fprintf(ficresprob,"\n%d ",(int)age);
            if (k != k2){          fprintf(ficresprobcov,"\n%d ",(int)age);
              if(ng==2)          fprintf(ficresprobcor,"\n%d ",(int)age);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);  
              else          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
              ij=1;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
              for(j=3; j <=ncovmodel; j++) {            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          }
                  ij++;          i=0;
                }          for (k=1; k<=(nlstate);k++){
                else            for (l=1; l<=(nlstate+ndeath);l++){ 
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              i=i++;
              }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
              fprintf(ficgp,")/(1");              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                            for (j=1; j<=i;j++){
              for(k1=1; k1 <=nlstate; k1++){                  fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                ij=1;              }
                for(j=3; j <=ncovmodel; j++){            }
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          }/* end of loop for state */
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        } /* end of loop for age */
                    ij++;  
                  }        /* Confidence intervalle of pij  */
                  else        /*
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          fprintf(ficgp,"\nset noparametric;unset label");
                }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
                fprintf(ficgp,")");          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
              }          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
              i=i+ncovmodel;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
            }        */
          }  
        }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
      }        first1=1;
    }        for (k2=1; k2<=(nlstate);k2++){
    fclose(ficgp);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
 }  /* end gnuplot */            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
 /*************** Moving average **************/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){                if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
   int i, cpt, cptcod;                if(i<=j) continue;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)                for (age=bage; age<=fage; age ++){ 
       for (i=1; i<=nlstate;i++)                  if ((int)age %5==0){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
           mobaverage[(int)agedeb][i][cptcod]=0.;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                        cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){                    mu1=mu[i][(int) age]/stepm*YEARM ;
       for (i=1; i<=nlstate;i++){                    mu2=mu[j][(int) age]/stepm*YEARM;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                    c12=cv12/sqrt(v1*v2);
           for (cpt=0;cpt<=4;cpt++){                    /* Computing eigen value of matrix of covariance */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                    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.;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                    /* Eigen vectors */
         }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       }                    /*v21=sqrt(1.-v11*v11); *//* error */
     }                    v21=(lc1-v1)/cv12*v11;
                        v12=-v21;
 }                    v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
 /************** Forecasting ******************/                      first1=0;
 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){                      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 cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                    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);
   int *popage;                    /*printf(fignu*/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   double *popeffectif,*popcount;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   double ***p3mat;                    if(first==1){
   char fileresf[FILENAMELENGTH];                      first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
  agelim=AGESUP;                      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);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                        fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                        fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   strcpy(fileresf,"f");                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   strcat(fileresf,fileres);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   if((ficresf=fopen(fileresf,"w"))==NULL) {                      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",\
     printf("Problem with forecast resultfile: %s\n", fileresf);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   printf("Computing forecasting: result on file '%s' \n", fileresf);                    }else{
                       first=0;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   if (mobilav==1) {                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                      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",\
     movingaverage(agedeb, fage, ageminpar, mobaverage);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
   stepsize=(int) (stepm+YEARM-1)/YEARM;                  } /* age mod 5 */
   if (stepm<=12) stepsize=1;                } /* end loop age */
                  fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   agelim=AGESUP;                first=1;
                } /*l12 */
   hstepm=1;            } /* k12 */
   hstepm=hstepm/stepm;          } /*l1 */
   yp1=modf(dateintmean,&yp);        }/* k1 */
   anprojmean=yp;      } /* loop covariates */
   yp2=modf((yp1*12),&yp);    }
   mprojmean=yp;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   yp1=modf((yp2*30.5),&yp);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   jprojmean=yp;    free_vector(xp,1,npar);
   if(jprojmean==0) jprojmean=1;    fclose(ficresprob);
   if(mprojmean==0) jprojmean=1;    fclose(ficresprobcov);
      fclose(ficresprobcor);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    fclose(ficgp);
      fclose(fichtm);
   for(cptcov=1;cptcov<=i2;cptcov++){  }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;  
       fprintf(ficresf,"\n#******");  /******************* Printing html file ***********/
       for(j=1;j<=cptcoveff;j++) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    int lastpass, int stepm, int weightopt, char model[],\
       }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
       fprintf(ficresf,"******\n");                    int popforecast, int estepm ,\
       fprintf(ficresf,"# StartingAge FinalAge");                    double jprev1, double mprev1,double anprev1, \
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                    double jprev2, double mprev2,double anprev2){
          int jj1, k1, i1, cpt;
          /*char optionfilehtm[FILENAMELENGTH];*/
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
         fprintf(ficresf,"\n");      printf("Problem with %s \n",optionfilehtm), exit(0);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
           nhstepm = nhstepm/hstepm;   - 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
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
           oldm=oldms;savm=savms;   - Life expectancies by age and initial health status (estepm=%2d months): 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       <a href=\"e%s\">e%s</a> <br>\n</li>", \
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  
             }   m=cptcoveff;
             for(j=1; j<=nlstate+ndeath;j++) {   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                 jj1=0;
                 if (mobilav==1)   for(k1=1; k1<=m;k1++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];     for(i1=1; i1<=ncodemax[k1];i1++){
                 else {       jj1++;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];       if (cptcovn > 0) {
                 }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                         for (cpt=1; cpt<=cptcoveff;cpt++) 
               }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
               if (h==(int)(calagedate+12*cpt)){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                 fprintf(ficresf," %.3f", kk1);       }
                               /* Pij */
               }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
             }  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
           }       /* Quasi-incidences */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       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 */
     }         for(cpt=1; cpt<nlstate;cpt++){
   }           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
          <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         }
        for(cpt=1; cpt<=nlstate;cpt++) {
   fclose(ficresf);          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);
 /************** Forecasting ******************/       }
 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(fichtm,"\n<br>- Total life expectancy by age and
    health expectancies in states (1) and (2): e%s%d.png<br>
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   int *popage;     } /* end i1 */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;   }/* End k1 */
   double *popeffectif,*popcount;   fprintf(fichtm,"</ul>");
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];  
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
   agelim=AGESUP;   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
     - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
    
   strcpy(filerespop,"pop");   if(popforecast==1) fprintf(fichtm,"\n
   strcat(filerespop,fileres);   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
   if((ficrespop=fopen(filerespop,"w"))==NULL) {   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
     printf("Problem with forecast resultfile: %s\n", filerespop);          <br>",fileres,fileres,fileres,fileres);
   }   else 
   printf("Computing forecasting: result on file '%s' \n", filerespop);     fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
    m=cptcoveff;
   if (mobilav==1) {   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, ageminpar, mobaverage);   jj1=0;
   }   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;       jj1++;
   if (stepm<=12) stepsize=1;       if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   agelim=AGESUP;         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   hstepm=1;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   hstepm=hstepm/stepm;       }
         for(cpt=1; cpt<=nlstate;cpt++) {
   if (popforecast==1) {         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
     if((ficpop=fopen(popfile,"r"))==NULL) {  interval) in state (%d): v%s%d%d.png <br>
       printf("Problem with population file : %s\n",popfile);exit(0);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     }       }
     popage=ivector(0,AGESUP);     } /* end i1 */
     popeffectif=vector(0,AGESUP);   }/* End k1 */
     popcount=vector(0,AGESUP);   fprintf(fichtm,"</ul>");
      fclose(fichtm);
     i=1;    }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
      /******************* Gnuplot file **************/
     imx=i;  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   for(cptcov=1;cptcov<=i2;cptcov++){    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      printf("Problem with file %s",optionfilegnuplot);
       k=k+1;      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
       fprintf(ficrespop,"\n#******");    }
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*#ifdef windows */
       }      fprintf(ficgp,"cd \"%s\" \n",pathc);
       fprintf(ficrespop,"******\n");      /*#endif */
       fprintf(ficrespop,"# Age");  m=pow(2,cptcoveff);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    
       if (popforecast==1)  fprintf(ficrespop," [Population]");   /* 1eme*/
          for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (cpt=0; cpt<=0;cpt++) {     for (k1=1; k1<= m ; k1 ++) {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);         fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
               fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       for (i=1; i<= nlstate ; i ++) {
           nhstepm = nhstepm/hstepm;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                   else fprintf(ficgp," \%%*lf (\%%*lf)");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       }
           oldm=oldms;savm=savms;       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           for (h=0; h<=nhstepm; h++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
             if (h==(int) (calagedate+YEARM*cpt)) {       } 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
             }       for (i=1; i<= nlstate ; i ++) {
             for(j=1; j<=nlstate+ndeath;j++) {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
               kk1=0.;kk2=0;         else fprintf(ficgp," \%%*lf (\%%*lf)");
               for(i=1; i<=nlstate;i++) {                     }  
                 if (mobilav==1)       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];     }
                 else {    }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    /*2 eme*/
                 }    
               }    for (k1=1; k1<= m ; k1 ++) { 
               if (h==(int)(calagedate+12*cpt)){      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
                   /*fprintf(ficrespop," %.3f", kk1);      
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      for (i=1; i<= nlstate+1 ; i ++) {
               }        k=2*i;
             }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
             for(i=1; i<=nlstate;i++){        for (j=1; j<= nlstate+1 ; j ++) {
               kk1=0.;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                 for(j=1; j<=nlstate;j++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        }   
                 }        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
             }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          else fprintf(ficgp," \%%*lf (\%%*lf)");
           }        }   
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficgp,"\" t\"\" w l 0,");
         }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
       }        for (j=1; j<= nlstate+1 ; j ++) {
            if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   /******/          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          else fprintf(ficgp,"\" t\"\" w l 0,");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    }
           nhstepm = nhstepm/hstepm;    
              /*3eme*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           oldm=oldms;savm=savms;    for (k1=1; k1<= m ; k1 ++) { 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for (cpt=1; cpt<= nlstate ; cpt ++) {
           for (h=0; h<=nhstepm; h++){        k=2+nlstate*(2*cpt-2);
             if (h==(int) (calagedate+YEARM*cpt)) {        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
             }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
             for(j=1; j<=nlstate+ndeath;j++) {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
               kk1=0.;kk2=0;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
               for(i=1; i<=nlstate;i++) {                        fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
               }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          
             }        */
           }        for (i=1; i< nlstate ; i ++) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
         }          
       }        } 
    }      }
   }    }
      
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* CV preval stat */
     for (k1=1; k1<= m ; k1 ++) { 
   if (popforecast==1) {      for (cpt=1; cpt<nlstate ; cpt ++) {
     free_ivector(popage,0,AGESUP);        k=3;
     free_vector(popeffectif,0,AGESUP);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     free_vector(popcount,0,AGESUP);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
   }        
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (i=1; i< nlstate ; i ++)
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficgp,"+$%d",k+i+1);
   fclose(ficrespop);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
 }        
         l=3+(nlstate+ndeath)*cpt;
 /***********************************************/        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
 /**************** Main Program *****************/        for (i=1; i< nlstate ; i ++) {
 /***********************************************/          l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
 int main(int argc, char *argv[])        }
 {        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    }  
   double agedeb, agefin,hf;    
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
   double fret;      for(k=1; k <=(nlstate+ndeath); k++){
   double **xi,tmp,delta;        if (k != i) {
           for(j=1; j <=ncovmodel; j++){
   double dum; /* Dummy variable */            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   double ***p3mat;            jk++; 
   int *indx;            fprintf(ficgp,"\n");
   char line[MAXLINE], linepar[MAXLINE];          }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        }
   int firstobs=1, lastobs=10;      }
   int sdeb, sfin; /* Status at beginning and end */     }
   int c,  h , cpt,l;  
   int ju,jl, mi;     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;       for(jk=1; jk <=m; jk++) {
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
   int mobilav=0,popforecast=0;         if (ng==2)
   int hstepm, nhstepm;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;         else
            fprintf(ficgp,"\nset title \"Probability\"\n");
   double bage, fage, age, agelim, agebase;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   double ftolpl=FTOL;         i=1;
   double **prlim;         for(k2=1; k2<=nlstate; k2++) {
   double *severity;           k3=i;
   double ***param; /* Matrix of parameters */           for(k=1; k<=(nlstate+ndeath); k++) {
   double  *p;             if (k != k2){
   double **matcov; /* Matrix of covariance */               if(ng==2)
   double ***delti3; /* Scale */                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   double *delti; /* Scale */               else
   double ***eij, ***vareij;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   double **varpl; /* Variances of prevalence limits by age */               ij=1;
   double *epj, vepp;               for(j=3; j <=ncovmodel; j++) {
   double kk1, kk2;                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                     ij++;
                  }
   char *alph[]={"a","a","b","c","d","e"}, str[4];                 else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
   char z[1]="c", occ;               fprintf(ficgp,")/(1");
 #include <sys/time.h>               
 #include <time.h>               for(k1=1; k1 <=nlstate; k1++){   
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                   ij=1;
   /* long total_usecs;                 for(j=3; j <=ncovmodel; j++){
   struct timeval start_time, end_time;                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                       fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                     ij++;
   getcwd(pathcd, size);                   }
                    else
   printf("\n%s",version);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   if(argc <=1){                 }
     printf("\nEnter the parameter file name: ");                 fprintf(ficgp,")");
     scanf("%s",pathtot);               }
   }               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   else{               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     strcpy(pathtot,argv[1]);               i=i+ncovmodel;
   }             }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/           } /* end k */
   /*cygwin_split_path(pathtot,path,optionfile);         } /* end k2 */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/       } /* end jk */
   /* cutv(path,optionfile,pathtot,'\\');*/     } /* end ng */
      fclose(ficgp); 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  }  /* end gnuplot */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);  
   replace(pathc,path);  /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
 /*-------- arguments in the command line --------*/  
     int i, cpt, cptcod;
   strcpy(fileres,"r");    int modcovmax =1;
   strcat(fileres, optionfilefiname);    int mobilavrange, mob;
   strcat(fileres,".txt");    /* Other files have txt extension */    double age;
   
   /*---------arguments file --------*/    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   }      if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
   strcpy(filereso,"o");      for (age=bage; age<=fage; age++)
   strcat(filereso,fileres);        for (i=1; i<=nlstate;i++)
   if((ficparo=fopen(filereso,"w"))==NULL) {          for (cptcod=1;cptcod<=modcovmax;cptcod++)
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   }      /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   /* Reads comments: lines beginning with '#' */         we use a 5 terms etc. until the borders are no more concerned. 
   while((c=getc(ficpar))=='#' && c!= EOF){      */ 
     ungetc(c,ficpar);      for (mob=3;mob <=mobilavrange;mob=mob+2){
     fgets(line, MAXLINE, ficpar);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     puts(line);          for (i=1; i<=nlstate;i++){
     fputs(line,ficparo);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   ungetc(c,ficpar);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   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);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
 while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }/* end age */
     puts(line);      }/* end mob */
     fputs(line,ficparo);    }else return -1;
   }    return 0;
   ungetc(c,ficpar);  }/* End movingaverage */
    
      
   covar=matrix(0,NCOVMAX,1,n);  /************** Forecasting ******************/
   cptcovn=0;  prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   ncovmodel=2+cptcovn;    int *popage;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
      double *popeffectif,*popcount;
   /* Read guess parameters */    double ***p3mat;
   /* Reads comments: lines beginning with '#' */    double ***mobaverage;
   while((c=getc(ficpar))=='#' && c!= EOF){    char fileresf[FILENAMELENGTH];
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);   agelim=AGESUP;
     puts(line);   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
     fputs(line,ficparo);  
   }    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   ungetc(c,ficpar);   
     
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    strcpy(fileresf,"f"); 
     for(i=1; i <=nlstate; i++)    strcat(fileresf,fileres);
     for(j=1; j <=nlstate+ndeath-1; j++){    if((ficresf=fopen(fileresf,"w"))==NULL) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);      printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficparo,"%1d%1d",i1,j1);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
       printf("%1d%1d",i,j);    }
       for(k=1; k<=ncovmodel;k++){    printf("Computing forecasting: result on file '%s' \n", fileresf);
         fscanf(ficpar," %lf",&param[i][j][k]);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       }  
       fscanf(ficpar,"\n");    if (mobilav!=0) {
       printf("\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficparo,"\n");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          printf(" Error in movingaverage mobilav=%d\n",mobilav);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      }
     }
   p=param[1][1];  
      stepsize=(int) (stepm+YEARM-1)/YEARM;
   /* Reads comments: lines beginning with '#' */    if (stepm<=12) stepsize=1;
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    agelim=AGESUP;
     fgets(line, MAXLINE, ficpar);    
     puts(line);    hstepm=1;
     fputs(line,ficparo);    hstepm=hstepm/stepm; 
   }    yp1=modf(dateintmean,&yp);
   ungetc(c,ficpar);    anprojmean=yp;
     yp2=modf((yp1*12),&yp);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    mprojmean=yp;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    yp1=modf((yp2*30.5),&yp);
   for(i=1; i <=nlstate; i++){    jprojmean=yp;
     for(j=1; j <=nlstate+ndeath-1; j++){    if(jprojmean==0) jprojmean=1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    if(mprojmean==0) jprojmean=1;
       printf("%1d%1d",i,j);    
       fprintf(ficparo,"%1d%1d",i1,j1);    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
       for(k=1; k<=ncovmodel;k++){    
         fscanf(ficpar,"%le",&delti3[i][j][k]);    for(cptcov=1;cptcov<=i2;cptcov++){
         printf(" %le",delti3[i][j][k]);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         fprintf(ficparo," %le",delti3[i][j][k]);        k=k+1;
       }        fprintf(ficresf,"\n#******");
       fscanf(ficpar,"\n");        for(j=1;j<=cptcoveff;j++) {
       printf("\n");          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficparo,"\n");        }
     }        fprintf(ficresf,"******\n");
   }        fprintf(ficresf,"# StartingAge FinalAge");
   delti=delti3[1][1];        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
          
   /* Reads comments: lines beginning with '#' */        
   while((c=getc(ficpar))=='#' && c!= EOF){        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
     ungetc(c,ficpar);          fprintf(ficresf,"\n");
     fgets(line, MAXLINE, ficpar);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
     puts(line);  
     fputs(line,ficparo);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
   }            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   ungetc(c,ficpar);            nhstepm = nhstepm/hstepm; 
              
   matcov=matrix(1,npar,1,npar);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   for(i=1; i <=npar; i++){            oldm=oldms;savm=savms;
     fscanf(ficpar,"%s",&str);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     printf("%s",str);          
     fprintf(ficparo,"%s",str);            for (h=0; h<=nhstepm; h++){
     for(j=1; j <=i; j++){              if (h==(int) (calagedate+YEARM*cpt)) {
       fscanf(ficpar," %le",&matcov[i][j]);                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
       printf(" %.5le",matcov[i][j]);              } 
       fprintf(ficparo," %.5le",matcov[i][j]);              for(j=1; j<=nlstate+ndeath;j++) {
     }                kk1=0.;kk2=0;
     fscanf(ficpar,"\n");                for(i=1; i<=nlstate;i++) {              
     printf("\n");                  if (mobilav==1) 
     fprintf(ficparo,"\n");                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   }                  else {
   for(i=1; i <=npar; i++)                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     for(j=i+1;j<=npar;j++)                  }
       matcov[i][j]=matcov[j][i];                  
                    }
   printf("\n");                if (h==(int)(calagedate+12*cpt)){
                   fprintf(ficresf," %.3f", kk1);
                           
     /*-------- Rewriting paramater file ----------*/                }
      strcpy(rfileres,"r");    /* "Rparameterfile */              }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            }
      strcat(rfileres,".");    /* */            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          }
     if((ficres =fopen(rfileres,"w"))==NULL) {        }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      }
     }    }
     fprintf(ficres,"#%s\n",version);         
        if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     /*-------- data file ----------*/  
     if((fic=fopen(datafile,"r"))==NULL)    {    fclose(ficresf);
       printf("Problem with datafile: %s\n", datafile);goto end;  }
     }  /************** Forecasting ******************/
   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){
     n= lastobs;    
     severity = vector(1,maxwav);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     outcome=imatrix(1,maxwav+1,1,n);    int *popage;
     num=ivector(1,n);    double calagedate, agelim, kk1, kk2;
     moisnais=vector(1,n);    double *popeffectif,*popcount;
     annais=vector(1,n);    double ***p3mat,***tabpop,***tabpopprev;
     moisdc=vector(1,n);    double ***mobaverage;
     andc=vector(1,n);    char filerespop[FILENAMELENGTH];
     agedc=vector(1,n);  
     cod=ivector(1,n);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     weight=vector(1,n);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    agelim=AGESUP;
     mint=matrix(1,maxwav,1,n);    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     anint=matrix(1,maxwav,1,n);    
     s=imatrix(1,maxwav+1,1,n);    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     adl=imatrix(1,maxwav+1,1,n);        
     tab=ivector(1,NCOVMAX);    
     ncodemax=ivector(1,8);    strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     i=1;    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     while (fgets(line, MAXLINE, fic) != NULL)    {      printf("Problem with forecast resultfile: %s\n", filerespop);
       if ((i >= firstobs) && (i <=lastobs)) {      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
            }
         for (j=maxwav;j>=1;j--){    printf("Computing forecasting: result on file '%s' \n", filerespop);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    if (mobilav!=0) {
              mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
         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);    stepsize=(int) (stepm+YEARM-1)/YEARM;
         for (j=ncovcol;j>=1;j--){    if (stepm<=12) stepsize=1;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    
         }    agelim=AGESUP;
         num[i]=atol(stra);    
            hstepm=1;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    hstepm=hstepm/stepm; 
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    
     if (popforecast==1) {
         i=i+1;      if((ficpop=fopen(popfile,"r"))==NULL) {
       }        printf("Problem with population file : %s\n",popfile);exit(0);
     }        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
     /* printf("ii=%d", ij);      } 
        scanf("%d",i);*/      popage=ivector(0,AGESUP);
   imx=i-1; /* Number of individuals */      popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
   /* for (i=1; i<=imx; i++){      
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      i=1;   
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;     
     }*/      imx=i;
    /*  for (i=1; i<=imx; i++){      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
      if (s[4][i]==9)  s[4][i]=-1;    }
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/  
      for(cptcov=1;cptcov<=i2;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   /* Calculation of the number of parameter from char model*/        k=k+1;
   Tvar=ivector(1,15);        fprintf(ficrespop,"\n#******");
   Tprod=ivector(1,15);        for(j=1;j<=cptcoveff;j++) {
   Tvaraff=ivector(1,15);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   Tvard=imatrix(1,15,1,2);        }
   Tage=ivector(1,15);              fprintf(ficrespop,"******\n");
            fprintf(ficrespop,"# Age");
   if (strlen(model) >1){        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     j=0, j1=0, k1=1, k2=1;        if (popforecast==1)  fprintf(ficrespop," [Population]");
     j=nbocc(model,'+');        
     j1=nbocc(model,'*');        for (cpt=0; cpt<=0;cpt++) { 
     cptcovn=j+1;          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     cptcovprod=j1;          
              for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
     strcpy(modelsav,model);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            nhstepm = nhstepm/hstepm; 
       printf("Error. Non available option model=%s ",model);            
       goto end;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }            oldm=oldms;savm=savms;
                hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     for(i=(j+1); i>=1;i--){          
       cutv(stra,strb,modelsav,'+');            for (h=0; h<=nhstepm; h++){
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);              if (h==(int) (calagedate+YEARM*cpt)) {
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       /*scanf("%d",i);*/              } 
       if (strchr(strb,'*')) {              for(j=1; j<=nlstate+ndeath;j++) {
         cutv(strd,strc,strb,'*');                kk1=0.;kk2=0;
         if (strcmp(strc,"age")==0) {                for(i=1; i<=nlstate;i++) {              
           cptcovprod--;                  if (mobilav==1) 
           cutv(strb,stre,strd,'V');                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
           Tvar[i]=atoi(stre);                  else {
           cptcovage++;                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
             Tage[cptcovage]=i;                  }
             /*printf("stre=%s ", stre);*/                }
         }                if (h==(int)(calagedate+12*cpt)){
         else if (strcmp(strd,"age")==0) {                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
           cptcovprod--;                    /*fprintf(ficrespop," %.3f", kk1);
           cutv(strb,stre,strc,'V');                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
           Tvar[i]=atoi(stre);                }
           cptcovage++;              }
           Tage[cptcovage]=i;              for(i=1; i<=nlstate;i++){
         }                kk1=0.;
         else {                  for(j=1; j<=nlstate;j++){
           cutv(strb,stre,strc,'V');                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
           Tvar[i]=ncovcol+k1;                  }
           cutv(strb,strc,strd,'V');                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
           Tprod[k1]=i;              }
           Tvard[k1][1]=atoi(strc);  
           Tvard[k1][2]=atoi(stre);              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
           Tvar[cptcovn+k2]=Tvard[k1][1];                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];            }
           for (k=1; k<=lastobs;k++)            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          }
           k1++;        }
           k2=k2+2;   
         }    /******/
       }  
       else {        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
        /*  scanf("%d",i);*/          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
       cutv(strd,strc,strb,'V');            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       Tvar[i]=atoi(strc);            nhstepm = nhstepm/hstepm; 
       }            
       strcpy(modelsav,stra);              p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            oldm=oldms;savm=savms;
         scanf("%d",i);*/            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     }            for (h=0; h<=nhstepm; h++){
 }              if (h==(int) (calagedate+YEARM*cpt)) {
                  fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);              } 
   printf("cptcovprod=%d ", cptcovprod);              for(j=1; j<=nlstate+ndeath;j++) {
   scanf("%d ",i);*/                kk1=0.;kk2=0;
     fclose(fic);                for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
     /*  if(mle==1){*/                }
     if (weightopt != 1) { /* Maximisation without weights*/                if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
       for(i=1;i<=n;i++) weight[i]=1.0;              }
     }            }
     /*-calculation of age at interview from date of interview and age at death -*/            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     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;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
          s[m][i]=-1;  
        }    if (popforecast==1) {
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;      free_ivector(popage,0,AGESUP);
       }      free_vector(popeffectif,0,AGESUP);
     }      free_vector(popcount,0,AGESUP);
     }
     for (i=1; i<=imx; i++)  {    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(m=1; (m<= maxwav); m++){    fclose(ficrespop);
         if(s[m][i] >0){  }
           if (s[m][i] >= nlstate+1) {  
             if(agedc[i]>0)  /***********************************************/
               if(moisdc[i]!=99 && andc[i]!=9999)  /**************** Main Program *****************/
                 agev[m][i]=agedc[i];  /***********************************************/
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  
            else {  int main(int argc, char *argv[])
               if (andc[i]!=9999){  {
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
               agev[m][i]=-1;    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
               }    double agedeb, agefin,hf;
             }    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
           }  
           else if(s[m][i] !=9){ /* Should no more exist */    double fret;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    double **xi,tmp,delta;
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;    double dum; /* Dummy variable */
             else if(agev[m][i] <agemin){    double ***p3mat;
               agemin=agev[m][i];    double ***mobaverage;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    int *indx;
             }    char line[MAXLINE], linepar[MAXLINE];
             else if(agev[m][i] >agemax){    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
               agemax=agev[m][i];    int firstobs=1, lastobs=10;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    int sdeb, sfin; /* Status at beginning and end */
             }    int c,  h , cpt,l;
             /*agev[m][i]=anint[m][i]-annais[i];*/    int ju,jl, mi;
             /*   agev[m][i] = age[i]+2*m;*/    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
           }    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
           else { /* =9 */    int mobilav=0,popforecast=0;
             agev[m][i]=1;    int hstepm, nhstepm;
             s[m][i]=-1;    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
           }  
         }    double bage, fage, age, agelim, agebase;
         else /*= 0 Unknown */    double ftolpl=FTOL;
           agev[m][i]=1;    double **prlim;
       }    double *severity;
        double ***param; /* Matrix of parameters */
     }    double  *p;
     for (i=1; i<=imx; i++)  {    double **matcov; /* Matrix of covariance */
       for(m=1; (m<= maxwav); m++){    double ***delti3; /* Scale */
         if (s[m][i] > (nlstate+ndeath)) {    double *delti; /* Scale */
           printf("Error: Wrong value in nlstate or ndeath\n");      double ***eij, ***vareij;
           goto end;    double **varpl; /* Variances of prevalence limits by age */
         }    double *epj, vepp;
       }    double kk1, kk2;
     }    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);    char z[1]="c", occ;
     free_vector(moisnais,1,n);  #include <sys/time.h>
     free_vector(annais,1,n);  #include <time.h>
     /* free_matrix(mint,1,maxwav,1,n);    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
        free_matrix(anint,1,maxwav,1,n);*/   
     free_vector(moisdc,1,n);    /* long total_usecs;
     free_vector(andc,1,n);       struct timeval start_time, end_time;
     
           gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     wav=ivector(1,imx);    getcwd(pathcd, size);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    printf("\n%s",version);
        if(argc <=1){
     /* Concatenates waves */      printf("\nEnter the parameter file name: ");
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      scanf("%s",pathtot);
     }
     else{
       Tcode=ivector(1,100);      strcpy(pathtot,argv[1]);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    }
       ncodemax[1]=1;    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    /*cygwin_split_path(pathtot,path,optionfile);
            printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
    codtab=imatrix(1,100,1,10);    /* cutv(path,optionfile,pathtot,'\\');*/
    h=0;  
    m=pow(2,cptcoveff);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
      printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
    for(k=1;k<=cptcoveff; k++){    chdir(path);
      for(i=1; i <=(m/pow(2,k));i++){    replace(pathc,path);
        for(j=1; j <= ncodemax[k]; j++){  
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    /*-------- arguments in the command line --------*/
            h++;  
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    /* Log file */
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    strcat(filelog, optionfilefiname);
          }    strcat(filelog,".log");    /* */
        }    if((ficlog=fopen(filelog,"w"))==NULL)    {
      }      printf("Problem with logfile %s\n",filelog);
    }      goto end;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    }
       codtab[1][2]=1;codtab[2][2]=2; */    fprintf(ficlog,"Log filename:%s\n",filelog);
    /* for(i=1; i <=m ;i++){    fprintf(ficlog,"\n%s",version);
       for(k=1; k <=cptcovn; k++){    fprintf(ficlog,"\nEnter the parameter file name: ");
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
       }    fflush(ficlog);
       printf("\n");  
       }    /* */
       scanf("%d",i);*/    strcpy(fileres,"r");
        strcat(fileres, optionfilefiname);
    /* Calculates basic frequencies. Computes observed prevalence at single age    strcat(fileres,".txt");    /* Other files have txt extension */
        and prints on file fileres'p'. */  
     /*---------arguments file --------*/
      
        if((ficpar=fopen(optionfile,"r"))==NULL)    {
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf("Problem with optionfile %s\n",optionfile);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      goto end;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
          strcpy(filereso,"o");
     /* For Powell, parameters are in a vector p[] starting at p[1]    strcat(filereso,fileres);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    if((ficparo=fopen(filereso,"w"))==NULL) {
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
     if(mle==1){      goto end;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    }
     }  
        /* Reads comments: lines beginning with '#' */
     /*--------- results files --------------*/    while((c=getc(ficpar))=='#' && c!= EOF){
     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);      ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
       puts(line);
    jk=1;      fputs(line,ficparo);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    }
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    ungetc(c,ficpar);
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){    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);
        if (k != i)    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);
            printf("%d%d ",i,k);    while((c=getc(ficpar))=='#' && c!= EOF){
            fprintf(ficres,"%1d%1d ",i,k);      ungetc(c,ficpar);
            for(j=1; j <=ncovmodel; j++){      fgets(line, MAXLINE, ficpar);
              printf("%f ",p[jk]);      puts(line);
              fprintf(ficres,"%f ",p[jk]);      fputs(line,ficparo);
              jk++;    }
            }    ungetc(c,ficpar);
            printf("\n");    
            fprintf(ficres,"\n");     
          }    covar=matrix(0,NCOVMAX,1,n); 
      }    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
    }    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
  if(mle==1){  
     /* Computing hessian and covariance matrix */    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     ftolhess=ftol; /* Usually correct */    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     hesscov(matcov, p, npar, delti, ftolhess, func);    
  }    /* Read guess parameters */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    /* Reads comments: lines beginning with '#' */
     printf("# Scales (for hessian or gradient estimation)\n");    while((c=getc(ficpar))=='#' && c!= EOF){
      for(i=1,jk=1; i <=nlstate; i++){      ungetc(c,ficpar);
       for(j=1; j <=nlstate+ndeath; j++){      fgets(line, MAXLINE, ficpar);
         if (j!=i) {      puts(line);
           fprintf(ficres,"%1d%1d",i,j);      fputs(line,ficparo);
           printf("%1d%1d",i,j);    }
           for(k=1; k<=ncovmodel;k++){    ungetc(c,ficpar);
             printf(" %.5e",delti[jk]);    
             fprintf(ficres," %.5e",delti[jk]);    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
             jk++;    for(i=1; i <=nlstate; i++)
           }      for(j=1; j <=nlstate+ndeath-1; j++){
           printf("\n");        fscanf(ficpar,"%1d%1d",&i1,&j1);
           fprintf(ficres,"\n");        fprintf(ficparo,"%1d%1d",i1,j1);
         }        if(mle==1)
       }          printf("%1d%1d",i,j);
      }        fprintf(ficlog,"%1d%1d",i,j);
            for(k=1; k<=ncovmodel;k++){
     k=1;          fscanf(ficpar," %lf",&param[i][j][k]);
     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");            printf(" %lf",param[i][j][k]);
     for(i=1;i<=npar;i++){            fprintf(ficlog," %lf",param[i][j][k]);
       /*  if (k>nlstate) k=1;          }
       i1=(i-1)/(ncovmodel*nlstate)+1;          else
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            fprintf(ficlog," %lf",param[i][j][k]);
       printf("%s%d%d",alph[k],i1,tab[i]);*/          fprintf(ficparo," %lf",param[i][j][k]);
       fprintf(ficres,"%3d",i);        }
       printf("%3d",i);        fscanf(ficpar,"\n");
       for(j=1; j<=i;j++){        if(mle==1)
         fprintf(ficres," %.5e",matcov[i][j]);          printf("\n");
         printf(" %.5e",matcov[i][j]);        fprintf(ficlog,"\n");
       }        fprintf(ficparo,"\n");
       fprintf(ficres,"\n");      }
       printf("\n");    
       k++;    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
     }  
        p=param[1][1];
     while((c=getc(ficpar))=='#' && c!= EOF){    
       ungetc(c,ficpar);    /* Reads comments: lines beginning with '#' */
       fgets(line, MAXLINE, ficpar);    while((c=getc(ficpar))=='#' && c!= EOF){
       puts(line);      ungetc(c,ficpar);
       fputs(line,ficparo);      fgets(line, MAXLINE, ficpar);
     }      puts(line);
     ungetc(c,ficpar);      fputs(line,ficparo);
     estepm=0;    }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    ungetc(c,ficpar);
     if (estepm==0 || estepm < stepm) estepm=stepm;  
     if (fage <= 2) {    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       bage = ageminpar;    delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
       fage = agemaxpar;    for(i=1; i <=nlstate; i++){
     }      for(j=1; j <=nlstate+ndeath-1; j++){
            fscanf(ficpar,"%1d%1d",&i1,&j1);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        printf("%1d%1d",i,j);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        fprintf(ficparo,"%1d%1d",i1,j1);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        for(k=1; k<=ncovmodel;k++){
            fscanf(ficpar,"%le",&delti3[i][j][k]);
     while((c=getc(ficpar))=='#' && c!= EOF){          printf(" %le",delti3[i][j][k]);
     ungetc(c,ficpar);          fprintf(ficparo," %le",delti3[i][j][k]);
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        fscanf(ficpar,"\n");
     fputs(line,ficparo);        printf("\n");
   }        fprintf(ficparo,"\n");
   ungetc(c,ficpar);      }
      }
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    delti=delti3[1][1];
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    /* Reads comments: lines beginning with '#' */
          while((c=getc(ficpar))=='#' && c!= EOF){
   while((c=getc(ficpar))=='#' && c!= EOF){      ungetc(c,ficpar);
     ungetc(c,ficpar);      fgets(line, MAXLINE, ficpar);
     fgets(line, MAXLINE, ficpar);      puts(line);
     puts(line);      fputs(line,ficparo);
     fputs(line,ficparo);    }
   }    ungetc(c,ficpar);
   ungetc(c,ficpar);    
      matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      fscanf(ficpar,"%s",&str);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      if(mle==1)
         printf("%s",str);
   fscanf(ficpar,"pop_based=%d\n",&popbased);      fprintf(ficlog,"%s",str);
   fprintf(ficparo,"pop_based=%d\n",popbased);        fprintf(ficparo,"%s",str);
   fprintf(ficres,"pop_based=%d\n",popbased);        for(j=1; j <=i; j++){
          fscanf(ficpar," %le",&matcov[i][j]);
   while((c=getc(ficpar))=='#' && c!= EOF){        if(mle==1){
     ungetc(c,ficpar);          printf(" %.5le",matcov[i][j]);
     fgets(line, MAXLINE, ficpar);          fprintf(ficlog," %.5le",matcov[i][j]);
     puts(line);        }
     fputs(line,ficparo);        else
   }          fprintf(ficlog," %.5le",matcov[i][j]);
   ungetc(c,ficpar);        fprintf(ficparo," %.5le",matcov[i][j]);
       }
   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);      fscanf(ficpar,"\n");
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      if(mle==1)
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
 while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    for(i=1; i <=npar; i++)
     fgets(line, MAXLINE, ficpar);      for(j=i+1;j<=npar;j++)
     puts(line);        matcov[i][j]=matcov[j][i];
     fputs(line,ficparo);     
   }    if(mle==1)
   ungetc(c,ficpar);      printf("\n");
     fprintf(ficlog,"\n");
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  
   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);    /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
 /*------------ gnuplot -------------*/    strcat(rfileres,optionfilext);    /* Other files have txt extension */
   strcpy(optionfilegnuplot,optionfilefiname);    if((ficres =fopen(rfileres,"w"))==NULL) {
   strcat(optionfilegnuplot,".gp");      printf("Problem writing new parameter file: %s\n", fileres);goto end;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     printf("Problem with file %s",optionfilegnuplot);    }
   }    fprintf(ficres,"#%s\n",version);
   fclose(ficgp);      
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    /*-------- data file ----------*/
 /*--------- index.htm --------*/    if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
   strcpy(optionfilehtm,optionfile);      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
   strcat(optionfilehtm,".htm");    }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);    n= lastobs;
   }    severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    num=ivector(1,n);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    moisnais=vector(1,n);
 \n    annais=vector(1,n);
 Total number of observations=%d <br>\n    moisdc=vector(1,n);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    andc=vector(1,n);
 <hr  size=\"2\" color=\"#EC5E5E\">    agedc=vector(1,n);
  <ul><li><h4>Parameter files</h4>\n    cod=ivector(1,n);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    weight=vector(1,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,optionfilegnuplot,optionfilegnuplot);    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
   fclose(fichtm);    mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    s=imatrix(1,maxwav+1,1,n);
      tab=ivector(1,NCOVMAX);
 /*------------ free_vector  -------------*/    ncodemax=ivector(1,8);
  chdir(path);  
      i=1;
  free_ivector(wav,1,imx);    while (fgets(line, MAXLINE, fic) != NULL)    {
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      if ((i >= firstobs) && (i <=lastobs)) {
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            
  free_ivector(num,1,n);        for (j=maxwav;j>=1;j--){
  free_vector(agedc,1,n);          cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          strcpy(line,stra);
  fclose(ficparo);          cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
  fclose(ficres);          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
   /*--------------- Prevalence limit --------------*/        cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
          cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        for (j=ncovcol;j>=1;j--){
   fprintf(ficrespl,"#Prevalence limit\n");          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
   fprintf(ficrespl,"#Age ");        } 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        num[i]=atol(stra);
   fprintf(ficrespl,"\n");          
          /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
   prlim=matrix(1,nlstate,1,nlstate);          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;}*/
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        i=i+1;
   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 */    /* printf("ii=%d", ij);
   k=0;       scanf("%d",i);*/
   agebase=ageminpar;    imx=i-1; /* Number of individuals */
   agelim=agemaxpar;  
   ftolpl=1.e-10;    /* for (i=1; i<=imx; i++){
   i1=cptcoveff;      if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
   if (cptcovn < 1){i1=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;
   for(cptcov=1;cptcov<=i1;cptcov++){      }*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     /*  for (i=1; i<=imx; i++){
         k=k+1;       if (s[4][i]==9)  s[4][i]=-1; 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/       printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
         fprintf(ficrespl,"\n#******");    
         for(j=1;j<=cptcoveff;j++)   
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* Calculation of the number of parameter from char model*/
         fprintf(ficrespl,"******\n");    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
            Tprod=ivector(1,15); 
         for (age=agebase; age<=agelim; age++){    Tvaraff=ivector(1,15); 
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    Tvard=imatrix(1,15,1,2);
           fprintf(ficrespl,"%.0f",age );    Tage=ivector(1,15);      
           for(i=1; i<=nlstate;i++)     
           fprintf(ficrespl," %.5f", prlim[i][i]);    if (strlen(model) >1){ /* If there is at least 1 covariate */
           fprintf(ficrespl,"\n");      j=0, j1=0, k1=1, k2=1;
         }      j=nbocc(model,'+'); /* j=Number of '+' */
       }      j1=nbocc(model,'*'); /* j1=Number of '*' */
     }      cptcovn=j+1; 
   fclose(ficrespl);      cptcovprod=j1; /*Number of products */
       
   /*------------- h Pij x at various ages ------------*/      strcpy(modelsav,model); 
        if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        printf("Error. Non available option model=%s ",model);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        fprintf(ficlog,"Error. Non available option model=%s ",model);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        goto end;
   }      }
   printf("Computing pij: result on file '%s' \n", filerespij);      
        /* This loop fills the array Tvar from the string 'model'.*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/      for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
   agelim=AGESUP;        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
   hstepm=stepsize*YEARM; /* Every year of age */        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
   /* hstepm=1;   aff par mois*/          cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
   k=0;            cptcovprod--;
   for(cptcov=1;cptcov<=i1;cptcov++){            cutv(strb,stre,strd,'V');
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
       k=k+1;            cptcovage++;
         fprintf(ficrespij,"\n#****** ");              Tage[cptcovage]=i;
         for(j=1;j<=cptcoveff;j++)              /*printf("stre=%s ", stre);*/
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
         fprintf(ficrespij,"******\n");          else if (strcmp(strd,"age")==0) { /* or age*Vn */
                    cptcovprod--;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            cutv(strb,stre,strc,'V');
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            Tvar[i]=atoi(stre);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            cptcovage++;
             Tage[cptcovage]=i;
           /*      nhstepm=nhstepm*YEARM; aff par mois*/          }
           else {  /* Age is not in the model */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
           oldm=oldms;savm=savms;            Tvar[i]=ncovcol+k1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
           fprintf(ficrespij,"# Age");            Tprod[k1]=i;
           for(i=1; i<=nlstate;i++)            Tvard[k1][1]=atoi(strc); /* m*/
             for(j=1; j<=nlstate+ndeath;j++)            Tvard[k1][2]=atoi(stre); /* n */
               fprintf(ficrespij," %1d-%1d",i,j);            Tvar[cptcovn+k2]=Tvard[k1][1];
           fprintf(ficrespij,"\n");            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
            for (h=0; h<=nhstepm; h++){            for (k=1; k<=lastobs;k++) 
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );              covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             for(i=1; i<=nlstate;i++)            k1++;
               for(j=1; j<=nlstate+ndeath;j++)            k2=k2+2;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          }
             fprintf(ficrespij,"\n");        }
              }        else { /* no more sum */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
           fprintf(ficrespij,"\n");         /*  scanf("%d",i);*/
         }        cutv(strd,strc,strb,'V');
     }        Tvar[i]=atoi(strc);
   }        }
         strcpy(modelsav,stra);  
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
   fclose(ficrespij);      } /* end of loop + */
     } /* end model */
     
   /*---------- Forecasting ------------------*/    /*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((stepm == 1) && (strcmp(model,".")==0)){      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=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);    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
   }    printf("cptcovprod=%d ", cptcovprod);
   else{    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
     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);    scanf("%d ",i);
   }    fclose(fic);*/
    
       /*  if(mle==1){*/
   /*---------- Health expectancies and variances ------------*/    if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
   strcpy(filerest,"t");    }
   strcat(filerest,fileres);      /*-calculation of age at interview from date of interview and age at death -*/
   if((ficrest=fopen(filerest,"w"))==NULL) {    agev=matrix(1,maxwav,1,imx);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }    for (i=1; i<=imx; i++) {
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
   strcpy(filerese,"e");          s[m][i]=-1;
   strcat(filerese,fileres);        }
   if((ficreseij=fopen(filerese,"w"))==NULL) {        if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      }
   }    }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
     for (i=1; i<=imx; i++)  {
  strcpy(fileresv,"v");      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
   strcat(fileresv,fileres);      for(m=1; (m<= maxwav); m++){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        if(s[m][i] >0){
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          if (s[m][i] >= nlstate+1) {
   }            if(agedc[i]>0)
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);              if(moisdc[i]!=99 && andc[i]!=9999)
   calagedate=-1;                agev[m][i]=agedc[i];
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
   k=0;                if (andc[i]!=9999){
   for(cptcov=1;cptcov<=i1;cptcov++){                  printf("Warning negative age at death: %d line:%d\n",num[i],i);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                  fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
       k=k+1;                  agev[m][i]=-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");          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]);
       fprintf(ficreseij,"\n#****** ");            if(mint[m][i]==99 || anint[m][i]==9999)
       for(j=1;j<=cptcoveff;j++)              agev[m][i]=1;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            else if(agev[m][i] <agemin){ 
       fprintf(ficreseij,"******\n");              agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
       fprintf(ficresvij,"\n#****** ");            }
       for(j=1;j<=cptcoveff;j++)            else if(agev[m][i] >agemax){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              agemax=agev[m][i];
       fprintf(ficresvij,"******\n");              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            /*agev[m][i]=anint[m][i]-annais[i];*/
       oldm=oldms;savm=savms;            /*     agev[m][i] = age[i]+2*m;*/
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);            }
            else { /* =9 */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            agev[m][i]=1;
       oldm=oldms;savm=savms;            s[m][i]=-1;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);          }
            }
         else /*= 0 Unknown */
            agev[m][i]=1;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      
       fprintf(ficrest,"\n");    }
     for (i=1; i<=imx; i++)  {
       epj=vector(1,nlstate+1);      for(m=1; (m<= maxwav); m++){
       for(age=bage; age <=fage ;age++){        if (s[m][i] > (nlstate+ndeath)) {
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          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);     
         if (popbased==1) {          fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           for(i=1; i<=nlstate;i++)          goto end;
             prlim[i][i]=probs[(int)age][i][k];        }
         }      }
            }
         fprintf(ficrest," %4.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    free_vector(severity,1,maxwav);
           }    free_imatrix(outcome,1,maxwav+1,1,n);
           epj[nlstate+1] +=epj[j];    free_vector(moisnais,1,n);
         }    free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
         for(i=1, vepp=0.;i <=nlstate;i++)       free_matrix(anint,1,maxwav,1,n);*/
           for(j=1;j <=nlstate;j++)    free_vector(moisdc,1,n);
             vepp += vareij[i][j][(int)age];    free_vector(andc,1,n);
         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]));    wav=ivector(1,imx);
         }    dh=imatrix(1,lastpass-firstpass+1,1,imx);
         fprintf(ficrest,"\n");    bh=imatrix(1,lastpass-firstpass+1,1,imx);
       }    mw=imatrix(1,lastpass-firstpass+1,1,imx);
     }     
   }    /* Concatenates waves */
 free_matrix(mint,1,maxwav,1,n);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   fclose(ficreseij);  
   fclose(ficresvij);    Tcode=ivector(1,100);
   fclose(ficrest);    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
   fclose(ficpar);    ncodemax[1]=1;
   free_vector(epj,1,nlstate+1);    if (cptcovn > 0) tricode(Tvar,nbcode,imx);
          
   /*------- Variance limit prevalence------*/      codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
   strcpy(fileresvpl,"vpl");    h=0;
   strcat(fileresvpl,fileres);    m=pow(2,cptcoveff);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {   
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    for(k=1;k<=cptcoveff; k++){
     exit(0);      for(i=1; i <=(m/pow(2,k));i++){
   }        for(j=1; j <= ncodemax[k]; j++){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
   k=0;            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
   for(cptcov=1;cptcov<=i1;cptcov++){            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
     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]]);    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
       fprintf(ficresvpl,"******\n");       codtab[1][2]=1;codtab[2][2]=2; */
          /* for(i=1; i <=m ;i++){ 
       varpl=matrix(1,nlstate,(int) bage, (int) fage);       for(k=1; k <=cptcovn; k++){
       oldm=oldms;savm=savms;       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       }
     }       printf("\n");
  }       }
        scanf("%d",i);*/
   fclose(ficresvpl);      
     /* Calculates basic frequencies. Computes observed prevalence at single age
   /*---------- End : free ----------------*/       and prints on file fileres'p'. */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
        pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      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 */
   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);    /* For Powell, parameters are in a vector p[] starting at p[1]
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       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) */
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    if(mle>=1){ /* Could be 1 or 2 */
   free_matrix(agev,1,maxwav,1,imx);      mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    }
       
   fprintf(fichtm,"\n</body>");    /*--------- results files --------------*/
   fclose(fichtm);    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(ficgp);    
    
     jk=1;
   if(erreur >0)    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("End of Imach with error or warning %d\n",erreur);    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   else   printf("End of Imach\n");    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    for(i=1,jk=1; i <=nlstate; i++){
        for(k=1; k <=(nlstate+ndeath); k++){
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        if (k != i) 
   /*printf("Total time was %d uSec.\n", total_usecs);*/          {
   /*------ End -----------*/            printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
  end:            for(j=1; j <=ncovmodel; j++){
 #ifdef windows              printf("%f ",p[jk]);
   /* chdir(pathcd);*/              fprintf(ficlog,"%f ",p[jk]);
 #endif              fprintf(ficres,"%f ",p[jk]);
  /*system("wgnuplot graph.plt");*/              jk++; 
  /*system("../gp37mgw/wgnuplot graph.plt");*/            }
  /*system("cd ../gp37mgw");*/            printf("\n");
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            fprintf(ficlog,"\n");
  strcpy(plotcmd,GNUPLOTPROGRAM);            fprintf(ficres,"\n");
  strcat(plotcmd," ");          }
  strcat(plotcmd,optionfilegnuplot);      }
  system(plotcmd);    }
     if(mle==1){
 #ifdef windows      /* Computing hessian and covariance matrix */
   while (z[0] != 'q') {      ftolhess=ftol; /* Usually correct */
     /* chdir(path); */      hesscov(matcov, p, npar, delti, ftolhess, func);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    }
     scanf("%s",z);    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     if (z[0] == 'c') system("./imach");    printf("# Scales (for hessian or gradient estimation)\n");
     else if (z[0] == 'e') system(optionfilehtm);    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     else if (z[0] == 'g') system(plotcmd);    for(i=1,jk=1; i <=nlstate; i++){
     else if (z[0] == 'q') exit(0);      for(j=1; j <=nlstate+ndeath; j++){
   }        if (j!=i) {
 #endif          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.1.49  
changed lines
  Added in v.1.62


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