Diff for /imach/src/imach.c between versions 1.40 and 1.79

version 1.40, 2002/04/19 13:46:19 version 1.79, 2003/06/05 15:17:23
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "wgnuplot"    read datafile
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    concatwav
 #define FILENAMELENGTH 80    if (mle >= 1)
 /*#define DEBUG*/      mlikeli
 #define windows    print results files
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    if mle==1 
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */        begin-prev-date,...
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open gnuplot file
     open html file
 #define NINTERVMAX 8    stable prevalence
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */     for age prevalim()
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    h Pij x
 #define NCOVMAX 8 /* Maximum number of covariates */    variance of p varprob
 #define MAXN 20000    forecasting if prevfcast==1 prevforecast call prevalence()
 #define YEARM 12. /* Number of months per year */    health expectancies
 #define AGESUP 130    Variance-covariance of DFLE
 #define AGEBASE 40    prevalence()
      movingaverage()
     varevsij() 
 int erreur; /* Error number */    if popbased==1 varevsij(,popbased)
 int nvar;    total life expectancies
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Variance of stable prevalence
 int npar=NPARMAX;   end
 int nlstate=2; /* Number of live states */  */
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;  
    
 int *wav; /* Number of waves for this individuual 0 is possible */  #include <math.h>
 int maxwav; /* Maxim number of waves */  #include <stdio.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <stdlib.h>
 int mle, weightopt;  #include <unistd.h>
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define MAXLINE 256
 double jmean; /* Mean space between 2 waves */  #define GNUPLOTPROGRAM "gnuplot"
 double **oldm, **newm, **savm; /* Working pointers to matrices */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #define FILENAMELENGTH 80
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  /*#define DEBUG*/
 FILE *ficgp,*ficresprob,*ficpop;  #define windows
 FILE *ficreseij;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   char filerese[FILENAMELENGTH];  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
  FILE  *ficresvpl;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   char fileresvpl[FILENAMELENGTH];  
   #define NINTERVMAX 8
 #define NR_END 1  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define FREE_ARG char*  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define FTOL 1.0e-10  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
 #define NRANSI  #define YEARM 12. /* Number of months per year */
 #define ITMAX 200  #define AGESUP 130
   #define AGEBASE 40
 #define TOL 2.0e-4  #ifdef windows
   #define DIRSEPARATOR '\\'
 #define CGOLD 0.3819660  #define ODIRSEPARATOR '/'
 #define ZEPS 1.0e-10  #else
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 #define GOLD 1.618034  #endif
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  /* $Id$ */
   /* $Log$
 static double maxarg1,maxarg2;   * Revision 1.79  2003/06/05 15:17:23  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))   * *** empty log message ***
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))   * */
    char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int erreur; /* Error number */
 #define rint(a) floor(a+0.5)  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 static double sqrarg;  int npar=NPARMAX;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  int nlstate=2; /* Number of live states */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int imx;  int popbased=0;
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 int estepm;  int jmin, jmax; /* min, max spacing between 2 waves */
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int m,nb;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 double **pmmij, ***probs, ***mobaverage;  double jmean; /* Mean space between 2 waves */
 double dateintmean=0;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 double *weight;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 int **s; /* Status */  FILE *ficlog, *ficrespow;
 double *agedc, **covar, idx;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  FILE *ficreseij;
 double ftolhess; /* Tolerance for computing hessian */  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 /**************** split *************************/  char fileresv[FILENAMELENGTH];
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  FILE  *ficresvpl;
 {  char fileresvpl[FILENAMELENGTH];
    char *s;                             /* pointer */  char title[MAXLINE];
    int  l1, l2;                         /* length counters */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #ifdef windows  char filelog[FILENAMELENGTH]; /* Log file */
    s = strrchr( path, '\\' );           /* find last / */  char filerest[FILENAMELENGTH];
 #else  char fileregp[FILENAMELENGTH];
    s = strrchr( path, '/' );            /* find last / */  char popfile[FILENAMELENGTH];
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  #define NR_END 1
   #define FREE_ARG char*
       if ( getwd( dirc ) == NULL ) {  #define FTOL 1.0e-10
 #else  
       extern char       *getcwd( );  #define NRANSI 
   #define ITMAX 200 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  #define TOL 2.0e-4 
          return( GLOCK_ERROR_GETCWD );  
       }  #define CGOLD 0.3819660 
       strcpy( name, path );             /* we've got it */  #define ZEPS 1.0e-10 
    } else {                             /* strip direcotry from path */  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  #define GOLD 1.618034 
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define GLIMIT 100.0 
       strcpy( name, s );                /* save file name */  #define TINY 1.0e-20 
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  static double maxarg1,maxarg2;
    }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    l1 = strlen( dirc );                 /* length of directory */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 #ifdef windows    
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #else  #define rint(a) floor(a+0.5)
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif  static double sqrarg;
    s = strrchr( name, '.' );            /* find last / */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    s++;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);  int imx; 
    l2= strlen( s)+1;  int stepm;
    strncpy( finame, name, l1-l2);  /* Stepm, step in month: minimum step interpolation*/
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */  int estepm;
 }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
   int m,nb;
 /******************************************/  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 void replace(char *s, char*t)  double **pmmij, ***probs;
 {  double dateintmean=0;
   int i;  
   int lg=20;  double *weight;
   i=0;  int **s; /* Status */
   lg=strlen(t);  double *agedc, **covar, idx;
   for(i=0; i<= lg; i++) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   }  double ftolhess; /* Tolerance for computing hessian */
 }  
   /**************** split *************************/
 int nbocc(char *s, char occ)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
   int i,j=0;    char  *ss;                            /* pointer */
   int lg=20;    int   l1, l2;                         /* length counters */
   i=0;  
   lg=strlen(s);    l1 = strlen(path );                   /* length of path */
   for(i=0; i<= lg; i++) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   if  (s[i] == occ ) j++;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   }    if ( ss == NULL ) {                   /* no directory, so use current */
   return j;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* get current working directory */
 void cutv(char *u,char *v, char*t, char occ)      /*    extern  char* getcwd ( char *buf , int len);*/
 {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   int i,lg,j,p=0;        return( GLOCK_ERROR_GETCWD );
   i=0;      }
   for(j=0; j<=strlen(t)-1; j++) {      strcpy( name, path );               /* we've got it */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    } else {                              /* strip direcotry from path */
   }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
   lg=strlen(t);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(j=0; j<p; j++) {      strcpy( name, ss );         /* save file name */
     (u[j] = t[j]);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   }      dirc[l1-l2] = 0;                    /* add zero */
      u[p]='\0';    }
     l1 = strlen( dirc );                  /* length of directory */
    for(j=0; j<= lg; j++) {  #ifdef windows
     if (j>=(p+1))(v[j-p-1] = t[j]);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   }  #else
 }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
 /********************** nrerror ********************/    ss = strrchr( name, '.' );            /* find last / */
     ss++;
 void nrerror(char error_text[])    strcpy(ext,ss);                       /* save extension */
 {    l1= strlen( name);
   fprintf(stderr,"ERREUR ...\n");    l2= strlen(ss)+1;
   fprintf(stderr,"%s\n",error_text);    strncpy( finame, name, l1-l2);
   exit(1);    finame[l1-l2]= 0;
 }    return( 0 );                          /* we're done */
 /*********************** vector *******************/  }
 double *vector(int nl, int nh)  
 {  
   double *v;  /******************************************/
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  void replace(char *s, char*t)
   return v-nl+NR_END;  {
 }    int i;
     int lg=20;
 /************************ free vector ******************/    i=0;
 void free_vector(double*v, int nl, int nh)    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   free((FREE_ARG)(v+nl-NR_END));      (s[i] = t[i]);
 }      if (t[i]== '\\') s[i]='/';
     }
 /************************ivector *******************************/  }
 int *ivector(long nl,long nh)  
 {  int nbocc(char *s, char occ)
   int *v;  {
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    int i,j=0;
   if (!v) nrerror("allocation failure in ivector");    int lg=20;
   return v-nl+NR_END;    i=0;
 }    lg=strlen(s);
     for(i=0; i<= lg; i++) {
 /******************free ivector **************************/    if  (s[i] == occ ) j++;
 void free_ivector(int *v, long nl, long nh)    }
 {    return j;
   free((FREE_ARG)(v+nl-NR_END));  }
 }  
   void cutv(char *u,char *v, char*t, char occ)
 /******************* imatrix *******************************/  {
 int **imatrix(long nrl, long nrh, long ncl, long nch)    /* cuts string t into u and v where u is ended by char occ excluding it
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 {       gives u="abcedf" and v="ghi2j" */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    int i,lg,j,p=0;
   int **m;    i=0;
      for(j=0; j<=strlen(t)-1; j++) {
   /* allocate pointers to rows */      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    lg=strlen(t);
   m -= nrl;    for(j=0; j<p; j++) {
        (u[j] = t[j]);
      }
   /* allocate rows and set pointers to them */       u[p]='\0';
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");     for(j=0; j<= lg; j++) {
   m[nrl] += NR_END;      if (j>=(p+1))(v[j-p-1] = t[j]);
   m[nrl] -= ncl;    }
    }
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    /********************** nrerror ********************/
   /* return pointer to array of pointers to rows */  
   return m;  void nrerror(char error_text[])
 }  {
     fprintf(stderr,"ERREUR ...\n");
 /****************** free_imatrix *************************/    fprintf(stderr,"%s\n",error_text);
 void free_imatrix(m,nrl,nrh,ncl,nch)    exit(EXIT_FAILURE);
       int **m;  }
       long nch,ncl,nrh,nrl;  /*********************** vector *******************/
      /* free an int matrix allocated by imatrix() */  double *vector(int nl, int nh)
 {  {
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    double *v;
   free((FREE_ARG) (m+nrl-NR_END));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /******************* matrix *******************************/  }
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  /************************ free vector ******************/
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  void free_vector(double*v, int nl, int nh)
   double **m;  {
     free((FREE_ARG)(v+nl-NR_END));
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /************************ivector *******************************/
   m -= nrl;  char *cvector(long nl,long nh)
   {
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    char *v;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   m[nrl] += NR_END;    if (!v) nrerror("allocation failure in cvector");
   m[nrl] -= ncl;    return v-nl+NR_END;
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  /******************free ivector **************************/
 }  void free_cvector(char *v, long nl, long nh)
   {
 /*************************free matrix ************************/    free((FREE_ARG)(v+nl-NR_END));
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  }
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /************************ivector *******************************/
   free((FREE_ARG)(m+nrl-NR_END));  int *ivector(long nl,long nh)
 }  {
     int *v;
 /******************* ma3x *******************************/    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    if (!v) nrerror("allocation failure in ivector");
 {    return v-nl+NR_END;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  }
   double ***m;  
   /******************free ivector **************************/
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  void free_ivector(int *v, long nl, long nh)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    free((FREE_ARG)(v+nl-NR_END));
   m -= nrl;  }
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /******************* imatrix *******************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   m[nrl] += NR_END;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   m[nrl] -= ncl;  { 
     long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    int **m; 
     
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    /* allocate pointers to rows */ 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   m[nrl][ncl] += NR_END;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   m[nrl][ncl] -= nll;    m += NR_END; 
   for (j=ncl+1; j<=nch; j++)    m -= nrl; 
     m[nrl][j]=m[nrl][j-1]+nlay;    
      
   for (i=nrl+1; i<=nrh; i++) {    /* allocate rows and set pointers to them */ 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     for (j=ncl+1; j<=nch; j++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       m[i][j]=m[i][j-1]+nlay;    m[nrl] += NR_END; 
   }    m[nrl] -= ncl; 
   return m;    
 }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
 /*************************free ma3x ************************/    /* return pointer to array of pointers to rows */ 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    return m; 
 {  } 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /****************** free_imatrix *************************/
   free((FREE_ARG)(m+nrl-NR_END));  void free_imatrix(m,nrl,nrh,ncl,nch)
 }        int **m;
         long nch,ncl,nrh,nrl; 
 /***************** f1dim *************************/       /* free an int matrix allocated by imatrix() */ 
 extern int ncom;  { 
 extern double *pcom,*xicom;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 extern double (*nrfunc)(double []);    free((FREE_ARG) (m+nrl-NR_END)); 
    } 
 double f1dim(double x)  
 {  /******************* matrix *******************************/
   int j;  double **matrix(long nrl, long nrh, long ncl, long nch)
   double f;  {
   double *xt;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
      double **m;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   f=(*nrfunc)(xt);    if (!m) nrerror("allocation failure 1 in matrix()");
   free_vector(xt,1,ncom);    m += NR_END;
   return f;    m -= nrl;
 }  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /*****************brent *************************/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    m[nrl] += NR_END;
 {    m[nrl] -= ncl;
   int iter;  
   double a,b,d,etemp;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double fu,fv,fw,fx;    return m;
   double ftemp;    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
   double p,q,r,tol1,tol2,u,v,w,x,xm;     */
   double e=0.0;  }
    
   a=(ax < cx ? ax : cx);  /*************************free matrix ************************/
   b=(ax > cx ? ax : cx);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   x=w=v=bx;  {
   fw=fv=fx=(*f)(x);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (iter=1;iter<=ITMAX;iter++) {    free((FREE_ARG)(m+nrl-NR_END));
     xm=0.5*(a+b);  }
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  /******************* ma3x *******************************/
     printf(".");fflush(stdout);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 #ifdef DEBUG  {
     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);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    double ***m;
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       *xmin=x;    if (!m) nrerror("allocation failure 1 in matrix()");
       return fx;    m += NR_END;
     }    m -= nrl;
     ftemp=fu;  
     if (fabs(e) > tol1) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       r=(x-w)*(fx-fv);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       q=(x-v)*(fx-fw);    m[nrl] += NR_END;
       p=(x-v)*q-(x-w)*r;    m[nrl] -= ncl;
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       q=fabs(q);  
       etemp=e;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       e=d;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m[nrl][ncl] += NR_END;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl][ncl] -= nll;
       else {    for (j=ncl+1; j<=nch; j++) 
         d=p/q;      m[nrl][j]=m[nrl][j-1]+nlay;
         u=x+d;    
         if (u-a < tol2 || b-u < tol2)    for (i=nrl+1; i<=nrh; i++) {
           d=SIGN(tol1,xm-x);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       }      for (j=ncl+1; j<=nch; j++) 
     } else {        m[i][j]=m[i][j-1]+nlay;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    }
     }    return m; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     fu=(*f)(u);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     if (fu <= fx) {    */
       if (u >= x) a=x; else b=x;  }
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  /*************************free ma3x ************************/
         } else {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
           if (u < x) a=u; else b=u;  {
           if (fu <= fw || w == x) {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
             v=w;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
             w=u;    free((FREE_ARG)(m+nrl-NR_END));
             fv=fw;  }
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  /***************** f1dim *************************/
             v=u;  extern int ncom; 
             fv=fu;  extern double *pcom,*xicom;
           }  extern double (*nrfunc)(double []); 
         }   
   }  double f1dim(double x) 
   nrerror("Too many iterations in brent");  { 
   *xmin=x;    int j; 
   return fx;    double f;
 }    double *xt; 
    
 /****************** mnbrak ***********************/    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    f=(*nrfunc)(xt); 
             double (*func)(double))    free_vector(xt,1,ncom); 
 {    return f; 
   double ulim,u,r,q, dum;  } 
   double fu;  
    /*****************brent *************************/
   *fa=(*func)(*ax);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   *fb=(*func)(*bx);  { 
   if (*fb > *fa) {    int iter; 
     SHFT(dum,*ax,*bx,dum)    double a,b,d,etemp;
       SHFT(dum,*fb,*fa,dum)    double fu,fv,fw,fx;
       }    double ftemp;
   *cx=(*bx)+GOLD*(*bx-*ax);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   *fc=(*func)(*cx);    double e=0.0; 
   while (*fb > *fc) {   
     r=(*bx-*ax)*(*fb-*fc);    a=(ax < cx ? ax : cx); 
     q=(*bx-*cx)*(*fb-*fa);    b=(ax > cx ? ax : cx); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    x=w=v=bx; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    fw=fv=fx=(*f)(x); 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    for (iter=1;iter<=ITMAX;iter++) { 
     if ((*bx-u)*(u-*cx) > 0.0) {      xm=0.5*(a+b); 
       fu=(*func)(u);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       fu=(*func)(u);      printf(".");fflush(stdout);
       if (fu < *fc) {      fprintf(ficlog,".");fflush(ficlog);
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #ifdef DEBUG
           SHFT(*fb,*fc,fu,(*func)(u))      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);
           }      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);
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       u=ulim;  #endif
       fu=(*func)(u);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     } else {        *xmin=x; 
       u=(*cx)+GOLD*(*cx-*bx);        return fx; 
       fu=(*func)(u);      } 
     }      ftemp=fu;
     SHFT(*ax,*bx,*cx,u)      if (fabs(e) > tol1) { 
       SHFT(*fa,*fb,*fc,fu)        r=(x-w)*(fx-fv); 
       }        q=(x-v)*(fx-fw); 
 }        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
 /*************** linmin ************************/        if (q > 0.0) p = -p; 
         q=fabs(q); 
 int ncom;        etemp=e; 
 double *pcom,*xicom;        e=d; 
 double (*nrfunc)(double []);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
            d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        else { 
 {          d=p/q; 
   double brent(double ax, double bx, double cx,          u=x+d; 
                double (*f)(double), double tol, double *xmin);          if (u-a < tol2 || b-u < tol2) 
   double f1dim(double x);            d=SIGN(tol1,xm-x); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        } 
               double *fc, double (*func)(double));      } else { 
   int j;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double xx,xmin,bx,ax;      } 
   double fx,fb,fa;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
        fu=(*f)(u); 
   ncom=n;      if (fu <= fx) { 
   pcom=vector(1,n);        if (u >= x) a=x; else b=x; 
   xicom=vector(1,n);        SHFT(v,w,x,u) 
   nrfunc=func;          SHFT(fv,fw,fx,fu) 
   for (j=1;j<=n;j++) {          } else { 
     pcom[j]=p[j];            if (u < x) a=u; else b=u; 
     xicom[j]=xi[j];            if (fu <= fw || w == x) { 
   }              v=w; 
   ax=0.0;              w=u; 
   xx=1.0;              fv=fw; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);              fw=fu; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);            } else if (fu <= fv || v == x || v == w) { 
 #ifdef DEBUG              v=u; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);              fv=fu; 
 #endif            } 
   for (j=1;j<=n;j++) {          } 
     xi[j] *= xmin;    } 
     p[j] += xi[j];    nrerror("Too many iterations in brent"); 
   }    *xmin=x; 
   free_vector(xicom,1,n);    return fx; 
   free_vector(pcom,1,n);  } 
 }  
   /****************** mnbrak ***********************/
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
             double (*func)(double []))              double (*func)(double)) 
 {  { 
   void linmin(double p[], double xi[], int n, double *fret,    double ulim,u,r,q, dum;
               double (*func)(double []));    double fu; 
   int i,ibig,j;   
   double del,t,*pt,*ptt,*xit;    *fa=(*func)(*ax); 
   double fp,fptt;    *fb=(*func)(*bx); 
   double *xits;    if (*fb > *fa) { 
   pt=vector(1,n);      SHFT(dum,*ax,*bx,dum) 
   ptt=vector(1,n);        SHFT(dum,*fb,*fa,dum) 
   xit=vector(1,n);        } 
   xits=vector(1,n);    *cx=(*bx)+GOLD*(*bx-*ax); 
   *fret=(*func)(p);    *fc=(*func)(*cx); 
   for (j=1;j<=n;j++) pt[j]=p[j];    while (*fb > *fc) { 
   for (*iter=1;;++(*iter)) {      r=(*bx-*ax)*(*fb-*fc); 
     fp=(*fret);      q=(*bx-*cx)*(*fb-*fa); 
     ibig=0;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     del=0.0;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     for (i=1;i<=n;i++)      if ((*bx-u)*(u-*cx) > 0.0) { 
       printf(" %d %.12f",i, p[i]);        fu=(*func)(u); 
     printf("\n");      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     for (i=1;i<=n;i++) {        fu=(*func)(u); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        if (fu < *fc) { 
       fptt=(*fret);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 #ifdef DEBUG            SHFT(*fb,*fc,fu,(*func)(u)) 
       printf("fret=%lf \n",*fret);            } 
 #endif      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       printf("%d",i);fflush(stdout);        u=ulim; 
       linmin(p,xit,n,fret,func);        fu=(*func)(u); 
       if (fabs(fptt-(*fret)) > del) {      } else { 
         del=fabs(fptt-(*fret));        u=(*cx)+GOLD*(*cx-*bx); 
         ibig=i;        fu=(*func)(u); 
       }      } 
 #ifdef DEBUG      SHFT(*ax,*bx,*cx,u) 
       printf("%d %.12e",i,(*fret));        SHFT(*fa,*fb,*fc,fu) 
       for (j=1;j<=n;j++) {        } 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  } 
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  /*************** linmin ************************/
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  int ncom; 
       printf("\n");  double *pcom,*xicom;
 #endif  double (*nrfunc)(double []); 
     }   
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 #ifdef DEBUG  { 
       int k[2],l;    double brent(double ax, double bx, double cx, 
       k[0]=1;                 double (*f)(double), double tol, double *xmin); 
       k[1]=-1;    double f1dim(double x); 
       printf("Max: %.12e",(*func)(p));    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       for (j=1;j<=n;j++)                double *fc, double (*func)(double)); 
         printf(" %.12e",p[j]);    int j; 
       printf("\n");    double xx,xmin,bx,ax; 
       for(l=0;l<=1;l++) {    double fx,fb,fa;
         for (j=1;j<=n;j++) {   
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    ncom=n; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    pcom=vector(1,n); 
         }    xicom=vector(1,n); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    nrfunc=func; 
       }    for (j=1;j<=n;j++) { 
 #endif      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
     } 
       free_vector(xit,1,n);    ax=0.0; 
       free_vector(xits,1,n);    xx=1.0; 
       free_vector(ptt,1,n);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       free_vector(pt,1,n);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       return;  #ifdef DEBUG
     }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for (j=1;j<=n;j++) {  #endif
       ptt[j]=2.0*p[j]-pt[j];    for (j=1;j<=n;j++) { 
       xit[j]=p[j]-pt[j];      xi[j] *= xmin; 
       pt[j]=p[j];      p[j] += xi[j]; 
     }    } 
     fptt=(*func)(ptt);    free_vector(xicom,1,n); 
     if (fptt < fp) {    free_vector(pcom,1,n); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  } 
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  /*************** powell ************************/
         for (j=1;j<=n;j++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
           xi[j][ibig]=xi[j][n];              double (*func)(double [])) 
           xi[j][n]=xit[j];  { 
         }    void linmin(double p[], double xi[], int n, double *fret, 
 #ifdef DEBUG                double (*func)(double [])); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    int i,ibig,j; 
         for(j=1;j<=n;j++)    double del,t,*pt,*ptt,*xit;
           printf(" %.12e",xit[j]);    double fp,fptt;
         printf("\n");    double *xits;
 #endif    pt=vector(1,n); 
       }    ptt=vector(1,n); 
     }    xit=vector(1,n); 
   }    xits=vector(1,n); 
 }    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
 /**** Prevalence limit ****************/    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      ibig=0; 
 {      del=0.0; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
      matrix by transitions matrix until convergence is reached */      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       fprintf(ficrespow,"%d %.12f",*iter,*fret);
   int i, ii,j,k;      for (i=1;i<=n;i++) {
   double min, max, maxmin, maxmax,sumnew=0.;        printf(" %d %.12f",i, p[i]);
   double **matprod2();        fprintf(ficlog," %d %.12lf",i, p[i]);
   double **out, cov[NCOVMAX], **pmij();        fprintf(ficrespow," %.12lf", p[i]);
   double **newm;      }
   double agefin, delaymax=50 ; /* Max number of years to converge */      printf("\n");
       fprintf(ficlog,"\n");
   for (ii=1;ii<=nlstate+ndeath;ii++)      fprintf(ficrespow,"\n");
     for (j=1;j<=nlstate+ndeath;j++){      for (i=1;i<=n;i++) { 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     }        fptt=(*fret); 
   #ifdef DEBUG
    cov[1]=1.;        printf("fret=%lf \n",*fret);
          fprintf(ficlog,"fret=%lf \n",*fret);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #endif
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        printf("%d",i);fflush(stdout);
     newm=savm;        fprintf(ficlog,"%d",i);fflush(ficlog);
     /* Covariates have to be included here again */        linmin(p,xit,n,fret,func); 
      cov[2]=agefin;        if (fabs(fptt-(*fret)) > del) { 
            del=fabs(fptt-(*fret)); 
       for (k=1; k<=cptcovn;k++) {          ibig=i; 
         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]]);*/  #ifdef DEBUG
       }        printf("%d %.12e",i,(*fret));
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        fprintf(ficlog,"%d %.12e",i,(*fret));
       for (k=1; k<=cptcovprod;k++)        for (j=1;j<=n;j++) {
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        }
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        for(j=1;j<=n;j++) {
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
     savm=oldm;        }
     oldm=newm;        printf("\n");
     maxmax=0.;        fprintf(ficlog,"\n");
     for(j=1;j<=nlstate;j++){  #endif
       min=1.;      } 
       max=0.;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       for(i=1; i<=nlstate; i++) {  #ifdef DEBUG
         sumnew=0;        int k[2],l;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        k[0]=1;
         prlim[i][j]= newm[i][j]/(1-sumnew);        k[1]=-1;
         max=FMAX(max,prlim[i][j]);        printf("Max: %.12e",(*func)(p));
         min=FMIN(min,prlim[i][j]);        fprintf(ficlog,"Max: %.12e",(*func)(p));
       }        for (j=1;j<=n;j++) {
       maxmin=max-min;          printf(" %.12e",p[j]);
       maxmax=FMAX(maxmax,maxmin);          fprintf(ficlog," %.12e",p[j]);
     }        }
     if(maxmax < ftolpl){        printf("\n");
       return prlim;        fprintf(ficlog,"\n");
     }        for(l=0;l<=1;l++) {
   }          for (j=1;j<=n;j++) {
 }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 /*************** transition probabilities ***************/            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double s1, s2;        }
   /*double t34;*/  #endif
   int i,j,j1, nc, ii, jj;  
   
     for(i=1; i<= nlstate; i++){        free_vector(xit,1,n); 
     for(j=1; j<i;j++){        free_vector(xits,1,n); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        free_vector(ptt,1,n); 
         /*s2 += param[i][j][nc]*cov[nc];*/        free_vector(pt,1,n); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        return; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      } 
       }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       ps[i][j]=s2;      for (j=1;j<=n;j++) { 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        ptt[j]=2.0*p[j]-pt[j]; 
     }        xit[j]=p[j]-pt[j]; 
     for(j=i+1; j<=nlstate+ndeath;j++){        pt[j]=p[j]; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      fptt=(*func)(ptt); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      if (fptt < fp) { 
       }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       ps[i][j]=s2;        if (t < 0.0) { 
     }          linmin(p,xit,n,fret,func); 
   }          for (j=1;j<=n;j++) { 
     /*ps[3][2]=1;*/            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
   for(i=1; i<= nlstate; i++){          }
      s1=0;  #ifdef DEBUG
     for(j=1; j<i; j++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       s1+=exp(ps[i][j]);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(j=i+1; j<=nlstate+ndeath; j++)          for(j=1;j<=n;j++){
       s1+=exp(ps[i][j]);            printf(" %.12e",xit[j]);
     ps[i][i]=1./(s1+1.);            fprintf(ficlog," %.12e",xit[j]);
     for(j=1; j<i; j++)          }
       ps[i][j]= exp(ps[i][j])*ps[i][i];          printf("\n");
     for(j=i+1; j<=nlstate+ndeath; j++)          fprintf(ficlog,"\n");
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #endif
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        }
   } /* end i */      } 
     } 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  } 
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  /**** Prevalence limit (stable prevalence)  ****************/
       ps[ii][ii]=1;  
     }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   }  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){    int i, ii,j,k;
      printf("%lf ",ps[ii][jj]);    double min, max, maxmin, maxmax,sumnew=0.;
    }    double **matprod2();
     printf("\n ");    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
     printf("\n ");printf("%lf ",cov[2]);*/    double agefin, delaymax=50 ; /* Max number of years to converge */
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    for (ii=1;ii<=nlstate+ndeath;ii++)
   goto end;*/      for (j=1;j<=nlstate+ndeath;j++){
     return ps;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }      }
   
 /**************** Product of 2 matrices ******************/     cov[1]=1.;
    
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      newm=savm;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      /* Covariates have to be included here again */
   /* in, b, out are matrice of pointers which should have been initialized       cov[2]=agefin;
      before: only the contents of out is modified. The function returns    
      a pointer to pointers identical to out */        for (k=1; k<=cptcovn;k++) {
   long i, j, k;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for(i=nrl; i<= nrh; i++)          /*      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=ncolol; k<=ncoloh; k++)        }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         out[i][k] +=in[i][j]*b[j][k];        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]]];
   return out;  
 }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 /************* Higher Matrix Product ***************/      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      savm=oldm;
 {      oldm=newm;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      maxmax=0.;
      duration (i.e. until      for(j=1;j<=nlstate;j++){
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        min=1.;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        max=0.;
      (typically every 2 years instead of every month which is too big).        for(i=1; i<=nlstate; i++) {
      Model is determined by parameters x and covariates have to be          sumnew=0;
      included manually here.          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
      */          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
   int i, j, d, h, k;        }
   double **out, cov[NCOVMAX];        maxmin=max-min;
   double **newm;        maxmax=FMAX(maxmax,maxmin);
       }
   /* Hstepm could be zero and should return the unit matrix */      if(maxmax < ftolpl){
   for (i=1;i<=nlstate+ndeath;i++)        return prlim;
     for (j=1;j<=nlstate+ndeath;j++){      }
       oldm[i][j]=(i==j ? 1.0 : 0.0);    }
       po[i][j][0]=(i==j ? 1.0 : 0.0);  }
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*************** transition probabilities ***************/ 
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       newm=savm;  {
       /* Covariates have to be included here again */    double s1, s2;
       cov[1]=1.;    /*double t34;*/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    int i,j,j1, nc, ii, jj;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)      for(i=1; i<= nlstate; i++){
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      for(j=1; j<i;j++){
       for (k=1; k<=cptcovprod;k++)        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          /*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);*/
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        ps[i][j]=s2;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      }
       savm=oldm;      for(j=i+1; j<=nlstate+ndeath;j++){
       oldm=newm;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     }          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     for(i=1; i<=nlstate+ndeath; i++)          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       for(j=1;j<=nlstate+ndeath;j++) {        }
         po[i][j][h]=newm[i][j];        ps[i][j]=s2;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      }
          */    }
       }      /*ps[3][2]=1;*/
   } /* end h */  
   return po;    for(i=1; i<= nlstate; i++){
 }       s1=0;
       for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
 /*************** log-likelihood *************/      for(j=i+1; j<=nlstate+ndeath; j++)
 double func( double *x)        s1+=exp(ps[i][j]);
 {      ps[i][i]=1./(s1+1.);
   int i, ii, j, k, mi, d, kk;      for(j=1; j<i; j++)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        ps[i][j]= exp(ps[i][j])*ps[i][i];
   double **out;      for(j=i+1; j<=nlstate+ndeath; j++)
   double sw; /* Sum of weights */        ps[i][j]= exp(ps[i][j])*ps[i][i];
   double lli; /* Individual log likelihood */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   long ipmx;    } /* end i */
   /*extern weight */  
   /* We are differentiating ll according to initial status */    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      for(jj=1; jj<= nlstate+ndeath; jj++){
   /*for(i=1;i<imx;i++)        ps[ii][jj]=0;
     printf(" %d\n",s[4][i]);        ps[ii][ii]=1;
   */      }
   cov[1]=1.;    }
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      for(jj=1; jj<= nlstate+ndeath; jj++){
     for(mi=1; mi<= wav[i]-1; mi++){       printf("%lf ",ps[ii][jj]);
       for (ii=1;ii<=nlstate+ndeath;ii++)     }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf("\n ");
       for(d=0; d<dh[mi][i]; d++){      }
         newm=savm;      printf("\n ");printf("%lf ",cov[2]);*/
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /*
         for (kk=1; kk<=cptcovage;kk++) {    for(i=1; i<= npar; i++) printf("%f ",x[i]);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    goto end;*/
         }      return ps;
          }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /**************** Product of 2 matrices ******************/
         savm=oldm;  
         oldm=newm;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
          {
            /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       } /* end mult */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
          /* in, b, out are matrice of pointers which should have been initialized 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);       before: only the contents of out is modified. The function returns
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/       a pointer to pointers identical to out */
       ipmx +=1;    long i, j, k;
       sw += weight[i];    for(i=nrl; i<= nrh; i++)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      for(k=ncolol; k<=ncoloh; k++)
     } /* end of wave */        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   } /* end of individual */          out[i][k] +=in[i][j]*b[j][k];
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    return out;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  }
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;  
 }  /************* 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 )
 /*********** Maximum Likelihood Estimation ***************/  {
     /* Computes the transition matrix starting at age 'age' over 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))       'nhstepm*hstepm*stepm' months (i.e. until
 {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   int i,j, iter;       nhstepm*hstepm matrices. 
   double **xi,*delti;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   double fret;       (typically every 2 years instead of every month which is too big 
   xi=matrix(1,npar,1,npar);       for the memory).
   for (i=1;i<=npar;i++)       Model is determined by parameters x and covariates have to be 
     for (j=1;j<=npar;j++)       included manually here. 
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");       */
   powell(p,xi,npar,ftol,&iter,&fret,func);  
     int i, j, d, h, k;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    double **out, cov[NCOVMAX];
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    double **newm;
   
 }    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
 /**** Computes Hessian and covariance matrix ***/      for (j=1;j<=nlstate+ndeath;j++){
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        oldm[i][j]=(i==j ? 1.0 : 0.0);
 {        po[i][j][0]=(i==j ? 1.0 : 0.0);
   double  **a,**y,*x,pd;      }
   double **hess;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int i, j,jk;    for(h=1; h <=nhstepm; h++){
   int *indx;      for(d=1; d <=hstepm; d++){
         newm=savm;
   double hessii(double p[], double delta, int theta, double delti[]);        /* Covariates have to be included here again */
   double hessij(double p[], double delti[], int i, int j);        cov[1]=1.;
   void lubksb(double **a, int npar, int *indx, double b[]) ;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   void ludcmp(double **a, int npar, int *indx, double *d) ;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
   hess=matrix(1,npar,1,npar);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   printf("\nCalculation of the hessian matrix. Wait...\n");          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     /*printf(" %f ",p[i]);*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     /*printf(" %lf ",hess[i][i]);*/        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
          savm=oldm;
   for (i=1;i<=npar;i++) {        oldm=newm;
     for (j=1;j<=npar;j++)  {      }
       if (j>i) {      for(i=1; i<=nlstate+ndeath; i++)
         printf(".%d%d",i,j);fflush(stdout);        for(j=1;j<=nlstate+ndeath;j++) {
         hess[i][j]=hessij(p,delti,i,j);          po[i][j][h]=newm[i][j];
         hess[j][i]=hess[i][j];              /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         /*printf(" %lf ",hess[i][j]);*/           */
       }        }
     }    } /* end h */
   }    return po;
   printf("\n");  }
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
    /*************** log-likelihood *************/
   a=matrix(1,npar,1,npar);  double func( double *x)
   y=matrix(1,npar,1,npar);  {
   x=vector(1,npar);    int i, ii, j, k, mi, d, kk;
   indx=ivector(1,npar);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   for (i=1;i<=npar;i++)    double **out;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    double sw; /* Sum of weights */
   ludcmp(a,npar,indx,&pd);    double lli; /* Individual log likelihood */
     int s1, s2;
   for (j=1;j<=npar;j++) {    double bbh, survp;
     for (i=1;i<=npar;i++) x[i]=0;    long ipmx;
     x[j]=1;    /*extern weight */
     lubksb(a,npar,indx,x);    /* We are differentiating ll according to initial status */
     for (i=1;i<=npar;i++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       matcov[i][j]=x[i];    /*for(i=1;i<imx;i++) 
     }      printf(" %d\n",s[4][i]);
   }    */
     cov[1]=1.;
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);    if(mle==1){
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     printf("\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   /* Recompute Inverse */            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++) a[i][j]=matcov[i][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   ludcmp(a,npar,indx,&pd);            }
           for(d=0; d<dh[mi][i]; d++){
   /*  printf("\n#Hessian matrix recomputed#\n");            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);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=1;i<=npar;i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       y[i][j]=x[i];            savm=oldm;
       printf("%.3e ",y[i][j]);            oldm=newm;
     }          } /* end mult */
     printf("\n");        
   }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   */          /* But now since version 0.9 we anticipate for bias and large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
   free_matrix(a,1,npar,1,npar);           * (in months) between two waves is not a multiple of stepm, we rounded to 
   free_matrix(y,1,npar,1,npar);           * the nearest (and in case of equal distance, to the lowest) interval but now
   free_vector(x,1,npar);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   free_ivector(indx,1,npar);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   free_matrix(hess,1,npar,1,npar);           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
 }           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
 /*************** hessian matrix ****************/           */
 double hessii( double x[], double delta, int theta, double delti[])          s1=s[mw[mi][i]][i];
 {          s2=s[mw[mi+1][i]][i];
   int i;          bbh=(double)bh[mi][i]/(double)stepm; 
   int l=1, lmax=20;          /* bias is positive if real duration
   double k1,k2;           * is higher than the multiple of stepm and negative otherwise.
   double p2[NPARMAX+1];           */
   double res;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          if( s2 > nlstate){ 
   double fx;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   int k=0,kmax=10;               to the likelihood is the probability to die between last step unit time and current 
   double l1;               step unit time, which is also the differences between probability to die before dh 
                and probability to die before dh-stepm . 
   fx=func(x);               In version up to 0.92 likelihood was computed
   for (i=1;i<=npar;i++) p2[i]=x[i];          as if date of death was unknown. Death was treated as any other
   for(l=0 ; l <=lmax; l++){          health state: the date of the interview describes the actual state
     l1=pow(10,l);          and not the date of a change in health state. The former idea was
     delts=delt;          to consider that at each interview the state was recorded
     for(k=1 ; k <kmax; k=k+1){          (healthy, disable or death) and IMaCh was corrected; but when we
       delt = delta*(l1*k);          introduced the exact date of death then we should have modified
       p2[theta]=x[theta] +delt;          the contribution of an exact death to the likelihood. This new
       k1=func(p2)-fx;          contribution is smaller and very dependent of the step unit
       p2[theta]=x[theta]-delt;          stepm. It is no more the probability to die between last interview
       k2=func(p2)-fx;          and month of death but the probability to survive from last
       /*res= (k1-2.0*fx+k2)/delt/delt; */          interview up to one month before death multiplied by the
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          probability to die within a month. Thanks to Chris
                Jackson for correcting this bug.  Former versions increased
 #ifdef DEBUG          mortality artificially. The bad side is that we add another loop
       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);          which slows down the processing. The difference can be up to 10%
 #endif          lower mortality.
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            lli=log(out[s1][s2] - savm[s1][s2]);
         k=kmax;          }else{
       }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         k=kmax; l=lmax*10.;          } 
       }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          /*if(lli ==000.0)*/
         delts=delt;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       }          ipmx +=1;
     }          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   delti[theta]=delts;        } /* end of wave */
   return res;      } /* end of individual */
      }  else if(mle==2){
 }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 double hessij( double x[], double delti[], int thetai,int thetaj)        for(mi=1; mi<= wav[i]-1; mi++){
 {          for (ii=1;ii<=nlstate+ndeath;ii++)
   int i;            for (j=1;j<=nlstate+ndeath;j++){
   int l=1, l1, lmax=20;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double k1,k2,k3,k4,res,fx;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double p2[NPARMAX+1];            }
   int k;          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
   fx=func(x);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (k=1; k<=2; k++) {            for (kk=1; kk<=cptcovage;kk++) {
     for (i=1;i<=npar;i++) p2[i]=x[i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     p2[thetai]=x[thetai]+delti[thetai]/k;            }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     k1=func(p2)-fx;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
     p2[thetai]=x[thetai]+delti[thetai]/k;            oldm=newm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          } /* end mult */
     k2=func(p2)-fx;        
            /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     p2[thetai]=x[thetai]-delti[thetai]/k;          /* But now since version 0.9 we anticipate for bias and large stepm.
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     k3=func(p2)-fx;           * (in months) between two waves is not a multiple of stepm, we rounded to 
             * the nearest (and in case of equal distance, to the lowest) interval but now
     p2[thetai]=x[thetai]-delti[thetai]/k;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     k4=func(p2)-fx;           * probability in order to take into account the bias as a fraction of the way
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 #ifdef DEBUG           * -stepm/2 to stepm/2 .
     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);           * For stepm=1 the results are the same as for previous versions of Imach.
 #endif           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
   return res;          s1=s[mw[mi][i]][i];
 }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
 /************** Inverse of matrix **************/          /* bias is positive if real duration
 void ludcmp(double **a, int n, int *indx, double *d)           * is higher than the multiple of stepm and negative otherwise.
 {           */
   int i,imax,j,k;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   double big,dum,sum,temp;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double *vv;          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
            /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   vv=vector(1,n);          /*if(lli ==000.0)*/
   *d=1.0;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   for (i=1;i<=n;i++) {          ipmx +=1;
     big=0.0;          sw += weight[i];
     for (j=1;j<=n;j++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       if ((temp=fabs(a[i][j])) > big) big=temp;        } /* end of wave */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      } /* end of individual */
     vv[i]=1.0/big;    }  else if(mle==3){  /* exponential inter-extrapolation */
   }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (j=1;j<=n;j++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (i=1;i<j;i++) {        for(mi=1; mi<= wav[i]-1; mi++){
       sum=a[i][j];          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            for (j=1;j<=nlstate+ndeath;j++){
       a[i][j]=sum;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     big=0.0;            }
     for (i=j;i<=n;i++) {          for(d=0; d<dh[mi][i]; d++){
       sum=a[i][j];            newm=savm;
       for (k=1;k<j;k++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         sum -= a[i][k]*a[k][j];            for (kk=1; kk<=cptcovage;kk++) {
       a[i][j]=sum;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if ( (dum=vv[i]*fabs(sum)) >= big) {            }
         big=dum;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         imax=i;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
     }            oldm=newm;
     if (j != imax) {          } /* end mult */
       for (k=1;k<=n;k++) {        
         dum=a[imax][k];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         a[imax][k]=a[j][k];          /* But now since version 0.9 we anticipate for bias and large stepm.
         a[j][k]=dum;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       }           * (in months) between two waves is not a multiple of stepm, we rounded to 
       *d = -(*d);           * the nearest (and in case of equal distance, to the lowest) interval but now
       vv[imax]=vv[j];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     }           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     indx[j]=imax;           * probability in order to take into account the bias as a fraction of the way
     if (a[j][j] == 0.0) a[j][j]=TINY;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     if (j != n) {           * -stepm/2 to stepm/2 .
       dum=1.0/(a[j][j]);           * For stepm=1 the results are the same as for previous versions of Imach.
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * For stepm > 1 the results are less biased than in previous versions. 
     }           */
   }          s1=s[mw[mi][i]][i];
   free_vector(vv,1,n);  /* Doesn't work */          s2=s[mw[mi+1][i]][i];
 ;          bbh=(double)bh[mi][i]/(double)stepm; 
 }          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
 void lubksb(double **a, int n, int *indx, double b[])           */
 {          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
   int i,ii=0,ip,j;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   double sum;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            /*if(lli ==000.0)*/
   for (i=1;i<=n;i++) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     ip=indx[i];          ipmx +=1;
     sum=b[ip];          sw += weight[i];
     b[ip]=b[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     if (ii)        } /* end of wave */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      } /* end of individual */
     else if (sum) ii=i;    }else{  /* ml=4 no inter-extrapolation */
     b[i]=sum;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (i=n;i>=1;i--) {        for(mi=1; mi<= wav[i]-1; mi++){
     sum=b[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            for (j=1;j<=nlstate+ndeath;j++){
     b[i]=sum/a[i][i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<dh[mi][i]; d++){
 /************ Frequencies ********************/            newm=savm;
 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)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {  /* Some frequencies */            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            }
   double ***freq; /* Frequencies */          
   double *pp;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double pos, k2, dateintsum=0,k2cpt=0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   FILE *ficresp;            savm=oldm;
   char fileresp[FILENAMELENGTH];            oldm=newm;
            } /* end mult */
   pp=vector(1,nlstate);        
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   strcpy(fileresp,"p");          ipmx +=1;
   strcat(fileresp,fileres);          sw += weight[i];
   if((ficresp=fopen(fileresp,"w"))==NULL) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     printf("Problem with prevalence resultfile: %s\n", fileresp);        } /* end of wave */
     exit(0);      } /* end of individual */
   }    } /* End of if */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   j1=0;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   j=cptcoveff;    return -l;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  }
    
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){  /*********** Maximum Likelihood Estimation ***************/
       j1++;  
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         scanf("%d", i);*/  {
       for (i=-1; i<=nlstate+ndeath; i++)      int i,j, iter;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double **xi;
           for(m=agemin; m <= agemax+3; m++)    double fret;
             freq[i][jk][m]=0;    char filerespow[FILENAMELENGTH];
          xi=matrix(1,npar,1,npar);
       dateintsum=0;    for (i=1;i<=npar;i++)
       k2cpt=0;      for (j=1;j<=npar;j++)
       for (i=1; i<=imx; i++) {        xi[i][j]=(i==j ? 1.0 : 0.0);
         bool=1;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         if  (cptcovn>0) {    strcpy(filerespow,"pow"); 
           for (z1=1; z1<=cptcoveff; z1++)    strcat(filerespow,fileres);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    if((ficrespow=fopen(filerespow,"w"))==NULL) {
               bool=0;      printf("Problem with resultfile: %s\n", filerespow);
         }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         if (bool==1) {    }
           for(m=firstpass; m<=lastpass; m++){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
             k2=anint[m][i]+(mint[m][i]/12.);    for (i=1;i<=nlstate;i++)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      for(j=1;j<=nlstate+ndeath;j++)
               if(agev[m][i]==0) agev[m][i]=agemax+1;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
               if(agev[m][i]==1) agev[m][i]=agemax+2;    fprintf(ficrespow,"\n");
               if (m<lastpass) {    powell(p,xi,npar,ftol,&iter,&fret,func);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    fclose(ficrespow);
               }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
                  fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
                 dateintsum=dateintsum+k2;  
                 k2cpt++;  }
               }  
             }  /**** Computes Hessian and covariance matrix ***/
           }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         }  {
       }    double  **a,**y,*x,pd;
            double **hess;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int i, j,jk;
     int *indx;
       if  (cptcovn>0) {  
         fprintf(ficresp, "\n#********** Variable ");    double hessii(double p[], double delta, int theta, double delti[]);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double hessij(double p[], double delti[], int i, int j);
         fprintf(ficresp, "**********\n#");    void lubksb(double **a, int npar, int *indx, double b[]) ;
       }    void ludcmp(double **a, int npar, int *indx, double *d) ;
       for(i=1; i<=nlstate;i++)  
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    hess=matrix(1,npar,1,npar);
       fprintf(ficresp, "\n");  
          printf("\nCalculation of the hessian matrix. Wait...\n");
       for(i=(int)agemin; i <= (int)agemax+3; i++){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         if(i==(int)agemax+3)    for (i=1;i<=npar;i++){
           printf("Total");      printf("%d",i);fflush(stdout);
         else      fprintf(ficlog,"%d",i);fflush(ficlog);
           printf("Age %d", i);      hess[i][i]=hessii(p,ftolhess,i,delti);
         for(jk=1; jk <=nlstate ; jk++){      /*printf(" %f ",p[i]);*/
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      /*printf(" %lf ",hess[i][i]);*/
             pp[jk] += freq[jk][m][i];    }
         }    
         for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=npar;i++) {
           for(m=-1, pos=0; m <=0 ; m++)      for (j=1;j<=npar;j++)  {
             pos += freq[jk][m][i];        if (j>i) { 
           if(pp[jk]>=1.e-10)          printf(".%d%d",i,j);fflush(stdout);
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           else          hess[i][j]=hessij(p,delti,i,j);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          hess[j][i]=hess[i][j];    
         }          /*printf(" %lf ",hess[i][j]);*/
         }
         for(jk=1; jk <=nlstate ; jk++){      }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    }
             pp[jk] += freq[jk][m][i];    printf("\n");
         }    fprintf(ficlog,"\n");
   
         for(jk=1,pos=0; jk <=nlstate ; jk++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           pos += pp[jk];    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         for(jk=1; jk <=nlstate ; jk++){    
           if(pos>=1.e-5)    a=matrix(1,npar,1,npar);
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    y=matrix(1,npar,1,npar);
           else    x=vector(1,npar);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    indx=ivector(1,npar);
           if( i <= (int) agemax){    for (i=1;i<=npar;i++)
             if(pos>=1.e-5){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    ludcmp(a,npar,indx,&pd);
               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]);*/    for (j=1;j<=npar;j++) {
             }      for (i=1;i<=npar;i++) x[i]=0;
             else      x[j]=1;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      lubksb(a,npar,indx,x);
           }      for (i=1;i<=npar;i++){ 
         }        matcov[i][j]=x[i];
              }
         for(jk=-1; jk <=nlstate+ndeath; jk++)    }
           for(m=-1; m <=nlstate+ndeath; m++)  
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    printf("\n#Hessian matrix#\n");
         if(i <= (int) agemax)    fprintf(ficlog,"\n#Hessian matrix#\n");
           fprintf(ficresp,"\n");    for (i=1;i<=npar;i++) { 
         printf("\n");      for (j=1;j<=npar;j++) { 
       }        printf("%.3e ",hess[i][j]);
     }        fprintf(ficlog,"%.3e ",hess[i][j]);
   }      }
   dateintmean=dateintsum/k2cpt;      printf("\n");
        fprintf(ficlog,"\n");
   fclose(ficresp);    }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);    /* Recompute Inverse */
      for (i=1;i<=npar;i++)
   /* End of Freq */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 }    ludcmp(a,npar,indx,&pd);
   
 /************ Prevalence ********************/    /*  printf("\n#Hessian matrix recomputed#\n");
 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)  
 {  /* Some frequencies */    for (j=1;j<=npar;j++) {
        for (i=1;i<=npar;i++) x[i]=0;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      x[j]=1;
   double ***freq; /* Frequencies */      lubksb(a,npar,indx,x);
   double *pp;      for (i=1;i<=npar;i++){ 
   double pos, k2;        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
   pp=vector(1,nlstate);        fprintf(ficlog,"%.3e ",y[i][j]);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      }
        printf("\n");
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      fprintf(ficlog,"\n");
   j1=0;    }
      */
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    free_matrix(a,1,npar,1,npar);
      free_matrix(y,1,npar,1,npar);
  for(k1=1; k1<=j;k1++){    free_vector(x,1,npar);
     for(i1=1; i1<=ncodemax[k1];i1++){    free_ivector(indx,1,npar);
       j1++;    free_matrix(hess,1,npar,1,npar);
    
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)    }
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  /*************** hessian matrix ****************/
        double hessii( double x[], double delta, int theta, double delti[])
       for (i=1; i<=imx; i++) {  {
         bool=1;    int i;
         if  (cptcovn>0) {    int l=1, lmax=20;
           for (z1=1; z1<=cptcoveff; z1++)    double k1,k2;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double p2[NPARMAX+1];
               bool=0;    double res;
         }    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         if (bool==1) {    double fx;
           for(m=firstpass; m<=lastpass; m++){    int k=0,kmax=10;
             k2=anint[m][i]+(mint[m][i]/12.);    double l1;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;    fx=func(x);
               if(agev[m][i]==1) agev[m][i]=agemax+2;    for (i=1;i<=npar;i++) p2[i]=x[i];
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    for(l=0 ; l <=lmax; l++){
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */      l1=pow(10,l);
             }      delts=delt;
           }      for(k=1 ; k <kmax; k=k+1){
         }        delt = delta*(l1*k);
       }        p2[theta]=x[theta] +delt;
         for(i=(int)agemin; i <= (int)agemax+3; i++){        k1=func(p2)-fx;
           for(jk=1; jk <=nlstate ; jk++){        p2[theta]=x[theta]-delt;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        k2=func(p2)-fx;
               pp[jk] += freq[jk][m][i];        /*res= (k1-2.0*fx+k2)/delt/delt; */
           }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           for(jk=1; jk <=nlstate ; jk++){        
             for(m=-1, pos=0; m <=0 ; m++)  #ifdef DEBUG
             pos += freq[jk][m][i];        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
          for(jk=1; jk <=nlstate ; jk++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
              pp[jk] += freq[jk][m][i];          k=kmax;
          }        }
                  else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          k=kmax; l=lmax*10.;
         }
          for(jk=1; jk <=nlstate ; jk++){                  else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
            if( i <= (int) agemax){          delts=delt;
              if(pos>=1.e-5){        }
                probs[i][jk][j1]= pp[jk]/pos;      }
              }    }
            }    delti[theta]=delts;
          }    return res; 
              
         }  }
     }  
   }  double hessij( double x[], double delti[], int thetai,int thetaj)
    {
      int i;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    int l=1, l1, lmax=20;
   free_vector(pp,1,nlstate);    double k1,k2,k3,k4,res,fx;
      double p2[NPARMAX+1];
 }  /* End of Freq */    int k;
   
 /************* Waves Concatenation ***************/    fx=func(x);
     for (k=1; k<=2; k++) {
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      for (i=1;i<=npar;i++) p2[i]=x[i];
 {      p2[thetai]=x[thetai]+delti[thetai]/k;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      Death is a valid wave (if date is known).      k1=func(p2)-fx;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      p2[thetai]=x[thetai]+delti[thetai]/k;
      and mw[mi+1][i]. dh depends on stepm.      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      */      k2=func(p2)-fx;
     
   int i, mi, m;      p2[thetai]=x[thetai]-delti[thetai]/k;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      double sum=0., jmean=0.;*/      k3=func(p2)-fx;
     
   int j, k=0,jk, ju, jl;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double sum=0.;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   jmin=1e+5;      k4=func(p2)-fx;
   jmax=-1;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   jmean=0.;  #ifdef DEBUG
   for(i=1; i<=imx; i++){      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     mi=0;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     m=firstpass;  #endif
     while(s[m][i] <= nlstate){    }
       if(s[m][i]>=1)    return res;
         mw[++mi][i]=m;  }
       if(m >=lastpass)  
         break;  /************** Inverse of matrix **************/
       else  void ludcmp(double **a, int n, int *indx, double *d) 
         m++;  { 
     }/* end while */    int i,imax,j,k; 
     if (s[m][i] > nlstate){    double big,dum,sum,temp; 
       mi++;     /* Death is another wave */    double *vv; 
       /* if(mi==0)  never been interviewed correctly before death */   
          /* Only death is a correct wave */    vv=vector(1,n); 
       mw[mi][i]=m;    *d=1.0; 
     }    for (i=1;i<=n;i++) { 
       big=0.0; 
     wav[i]=mi;      for (j=1;j<=n;j++) 
     if(mi==0)        if ((temp=fabs(a[i][j])) > big) big=temp; 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   }      vv[i]=1.0/big; 
     } 
   for(i=1; i<=imx; i++){    for (j=1;j<=n;j++) { 
     for(mi=1; mi<wav[i];mi++){      for (i=1;i<j;i++) { 
       if (stepm <=0)        sum=a[i][j]; 
         dh[mi][i]=1;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       else{        a[i][j]=sum; 
         if (s[mw[mi+1][i]][i] > nlstate) {      } 
           if (agedc[i] < 2*AGESUP) {      big=0.0; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      for (i=j;i<=n;i++) { 
           if(j==0) j=1;  /* Survives at least one month after exam */        sum=a[i][j]; 
           k=k+1;        for (k=1;k<j;k++) 
           if (j >= jmax) jmax=j;          sum -= a[i][k]*a[k][j]; 
           if (j <= jmin) jmin=j;        a[i][j]=sum; 
           sum=sum+j;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          big=dum; 
           }          imax=i; 
         }        } 
         else{      } 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      if (j != imax) { 
           k=k+1;        for (k=1;k<=n;k++) { 
           if (j >= jmax) jmax=j;          dum=a[imax][k]; 
           else if (j <= jmin)jmin=j;          a[imax][k]=a[j][k]; 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          a[j][k]=dum; 
           sum=sum+j;        } 
         }        *d = -(*d); 
         jk= j/stepm;        vv[imax]=vv[j]; 
         jl= j -jk*stepm;      } 
         ju= j -(jk+1)*stepm;      indx[j]=imax; 
         if(jl <= -ju)      if (a[j][j] == 0.0) a[j][j]=TINY; 
           dh[mi][i]=jk;      if (j != n) { 
         else        dum=1.0/(a[j][j]); 
           dh[mi][i]=jk+1;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         if(dh[mi][i]==0)      } 
           dh[mi][i]=1; /* At least one step */    } 
       }    free_vector(vv,1,n);  /* Doesn't work */
     }  ;
   }  } 
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  void lubksb(double **a, int n, int *indx, double b[]) 
  }  { 
 /*********** Tricode ****************************/    int i,ii=0,ip,j; 
 void tricode(int *Tvar, int **nbcode, int imx)    double sum; 
 {   
   int Ndum[20],ij=1, k, j, i;    for (i=1;i<=n;i++) { 
   int cptcode=0;      ip=indx[i]; 
   cptcoveff=0;      sum=b[ip]; 
        b[ip]=b[i]; 
   for (k=0; k<19; k++) Ndum[k]=0;      if (ii) 
   for (k=1; k<=7; k++) ncodemax[k]=0;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      b[i]=sum; 
     for (i=1; i<=imx; i++) {    } 
       ij=(int)(covar[Tvar[j]][i]);    for (i=n;i>=1;i--) { 
       Ndum[ij]++;      sum=b[i]; 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       if (ij > cptcode) cptcode=ij;      b[i]=sum/a[i][i]; 
     }    } 
   } 
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;  /************ Frequencies ********************/
     }  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
     ij=1;  {  /* Some frequencies */
     
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     for (i=1; i<=ncodemax[j]; i++) {    int first;
       for (k=0; k<=19; k++) {    double ***freq; /* Frequencies */
         if (Ndum[k] != 0) {    double *pp, **prop;
           nbcode[Tvar[j]][ij]=k;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
              FILE *ficresp;
           ij++;    char fileresp[FILENAMELENGTH];
         }    
         if (ij > ncodemax[j]) break;    pp=vector(1,nlstate);
       }      prop=matrix(1,nlstate,iagemin,iagemax+3);
     }    strcpy(fileresp,"p");
   }      strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
  for (k=0; k<19; k++) Ndum[k]=0;      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
  for (i=1; i<=ncovmodel-2; i++) {      exit(0);
       ij=Tvar[i];    }
       Ndum[ij]++;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     }    j1=0;
     
  ij=1;    j=cptcoveff;
  for (i=1; i<=10; i++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    if((Ndum[i]!=0) && (i<=ncovcol)){  
      Tvaraff[ij]=i;    first=1;
      ij++;  
    }    for(k1=1; k1<=j;k1++){
  }      for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;
     cptcoveff=ij-1;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 }          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
 /*********** Health Expectancies ****************/          for (jk=-1; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)              freq[i][jk][m]=0;
 {  
   /* Health expectancies */      for (i=1; i<=nlstate; i++)  
   int i, j, nhstepm, hstepm, h, nstepm;        for(m=iagemin; m <= iagemax+3; m++)
   double age, agelim, hf;          prop[i][m]=0;
   double ***p3mat;        
          dateintsum=0;
   fprintf(ficreseij,"# Health expectancies\n");        k2cpt=0;
   fprintf(ficreseij,"# Age");        for (i=1; i<=imx; i++) {
   for(i=1; i<=nlstate;i++)          bool=1;
     for(j=1; j<=nlstate;j++)          if  (cptcovn>0) {
       fprintf(ficreseij," %1d-%1d",i,j);            for (z1=1; z1<=cptcoveff; z1++) 
   fprintf(ficreseij,"\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
   if(estepm < stepm){          }
     printf ("Problem %d lower than %d\n",estepm, stepm);          if (bool==1){
   }            for(m=firstpass; m<=lastpass; m++){
   else  hstepm=estepm;                k2=anint[m][i]+(mint[m][i]/12.);
   /* We compute the life expectancy from trapezoids spaced every estepm months              if ((k2>=dateprev1) && (k2<=dateprev2)) {
    * This is mainly to measure the difference between two models: for example                if(agev[m][i]==0) agev[m][i]=iagemax+1;
    * if stepm=24 months pijx are given only every 2 years and by summing them                if(agev[m][i]==1) agev[m][i]=iagemax+2;
    * we are calculating an estimate of the Life Expectancy assuming a linear                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
    * progression inbetween and thus overestimating or underestimating according                if (m<lastpass) {
    * to the curvature of the survival function. If, for the same date, we                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    * estimate the model with stepm=1 month, we can keep estepm to 24 months                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    * 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. */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
   /* For example we decided to compute the life expectancy with the smallest unit */                  k2cpt++;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.                }
      nhstepm is the number of hstepm from age to agelim              }
      nstepm is the number of stepm from age to agelin.            }
      Look at hpijx to understand the reason of that which relies in memory size          }
      and note for a fixed period like estepm months */        }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the         
      survival function given by stepm (the optimization length). Unfortunately it        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
      means that if the survival funtion is printed only each two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        if  (cptcovn>0) {
      results. So we changed our mind and took the option of the best precision.          fprintf(ficresp, "\n#********** Variable "); 
   */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          fprintf(ficresp, "**********\n#");
         }
   agelim=AGESUP;        for(i=1; i<=nlstate;i++) 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     /* nhstepm age range expressed in number of stepm */        fprintf(ficresp, "\n");
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        for(i=iagemin; i <= iagemax+3; i++){
     /* if (stepm >= YEARM) hstepm=1;*/          if(i==iagemax+3){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            fprintf(ficlog,"Total");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }else{
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            if(first==1){
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */              first=0;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                printf("See log file for details...\n");
              }
     /*for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++) printf("%f %.5f\n", age*12+h, p3mat[1][1][h]);*/            fprintf(ficlog,"Age %d", i);
           }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          for(jk=1; jk <=nlstate ; jk++){
     for(i=1; i<=nlstate;i++)            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       for(j=1; j<=nlstate;j++)              pp[jk] += freq[jk][m][i]; 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          }
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          for(jk=1; jk <=nlstate ; jk++){
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/            for(m=-1, pos=0; m <=0 ; m++)
         }              pos += freq[jk][m][i];
     fprintf(ficreseij,"%3.0f",age );            if(pp[jk]>=1.e-10){
     for(i=1; i<=nlstate;i++)              if(first==1){
       for(j=1; j<=nlstate;j++){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);              }
       }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     fprintf(ficreseij,"\n");            }else{
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if(first==1)
   }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 /************ Variance ******************/          }
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)  
 {          for(jk=1; jk <=nlstate ; jk++){
   /* Variance of health expectancies */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/              pp[jk] += freq[jk][m][i];
   double **newm;          }       
   double **dnewm,**doldm;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   int i, j, nhstepm, hstepm, h, nstepm ;            pos += pp[jk];
   int k, cptcode;            posprop += prop[jk][i];
   double *xp;          }
   double **gp, **gm;          for(jk=1; jk <=nlstate ; jk++){
   double ***gradg, ***trgradg;            if(pos>=1.e-5){
   double ***p3mat;              if(first==1)
   double age,agelim, hf;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   int theta;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
    fprintf(ficresvij,"# Covariances of life expectancies\n");              if(first==1)
   fprintf(ficresvij,"# Age");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     for(j=1; j<=nlstate;j++)            }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            if( i <= iagemax){
   fprintf(ficresvij,"\n");              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   xp=vector(1,npar);                probs[i][jk][j1]= pp[jk]/pos;
   dnewm=matrix(1,nlstate,1,npar);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   doldm=matrix(1,nlstate,1,nlstate);              }
                else
   if(estepm < stepm){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     printf ("Problem %d lower than %d\n",estepm, stepm);            }
   }          }
   else  hstepm=estepm;            
   /* For example we decided to compute the life expectancy with the smallest unit */          for(jk=-1; jk <=nlstate+ndeath; jk++)
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            for(m=-1; m <=nlstate+ndeath; m++)
      nhstepm is the number of hstepm from age to agelim              if(freq[jk][m][i] !=0 ) {
      nstepm is the number of stepm from age to agelin.              if(first==1)
      Look at hpijx to understand the reason of that which relies in memory size                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
      and note for a fixed period like k years */                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   /* 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          if(i <= iagemax)
      means that if the survival funtion is printed only each two years of age and if            fprintf(ficresp,"\n");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          if(first==1)
      results. So we changed our mind and took the option of the best precision.            printf("Others in log...\n");
   */          fprintf(ficlog,"\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        }
   agelim = AGESUP;      }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    dateintmean=dateintsum/k2cpt; 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */   
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fclose(ficresp);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     gp=matrix(0,nhstepm,1,nlstate);    free_vector(pp,1,nlstate);
     gm=matrix(0,nhstepm,1,nlstate);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
     for(theta=1; theta <=npar; theta++){  }
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /************ Prevalence ********************/
       }  void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    {  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
       if (popbased==1) {       We still use firstpass and lastpass as another selection.
         for(i=1; i<=nlstate;i++)    */
           prlim[i][i]=probs[(int)age][i][ij];   
       }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
      double ***freq; /* Frequencies */
       for(j=1; j<= nlstate; j++){    double *pp, **prop;
         for(h=0; h<=nhstepm; h++){    double pos,posprop; 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    double  y2; /* in fractional years */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    int iagemin, iagemax;
         }  
       }    iagemin= (int) agemin;
        iagemax= (int) agemax;
       for(i=1; i<=npar; i++) /* Computes gradient */    /*pp=vector(1,nlstate);*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    j1=0;
      
       if (popbased==1) {    j=cptcoveff;
         for(i=1; i<=nlstate;i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           prlim[i][i]=probs[(int)age][i][ij];    
       }    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
       for(j=1; j<= nlstate; j++){        j1++;
         for(h=0; h<=nhstepm; h++){        
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        for (i=1; i<=nlstate; i++)  
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          for(m=iagemin; m <= iagemax+3; m++)
         }            prop[i][m]=0.0;
       }       
         for (i=1; i<=imx; i++) { /* Each individual */
       for(j=1; j<= nlstate; j++)          bool=1;
         for(h=0; h<=nhstepm; h++){          if  (cptcovn>0) {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            for (z1=1; z1<=cptcoveff; z1++) 
         }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     } /* End theta */                bool=0;
           } 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     for(h=0; h<=nhstepm; h++)              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       for(j=1; j<=nlstate;j++)              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         for(theta=1; theta <=npar; theta++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           trgradg[h][j][theta]=gradg[h][theta][j];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     for(i=1;i<=nlstate;i++)                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       for(j=1;j<=nlstate;j++)                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         vareij[i][j][(int)age] =0.;                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
     for(h=0;h<=nhstepm;h++){              }
       for(k=0;k<=nhstepm;k++){            } /* end selection of waves */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        }
         for(i=1;i<=nlstate;i++)        for(i=iagemin; i <= iagemax+3; i++){  
           for(j=1;j<=nlstate;j++)          
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       }            posprop += prop[jk][i]; 
     }          } 
   
     fprintf(ficresvij,"%.0f ",age );          for(jk=1; jk <=nlstate ; jk++){     
     for(i=1; i<=nlstate;i++)            if( i <=  iagemax){ 
       for(j=1; j<=nlstate;j++){              if(posprop>=1.e-5){ 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);                probs[i][jk][j1]= prop[jk][i]/posprop;
       }              } 
     fprintf(ficresvij,"\n");            } 
     free_matrix(gp,0,nhstepm,1,nlstate);          }/* end jk */ 
     free_matrix(gm,0,nhstepm,1,nlstate);        }/* end i */ 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      } /* end i1 */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    } /* end k1 */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
   } /* End age */    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      /*free_vector(pp,1,nlstate);*/
   free_vector(xp,1,npar);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   free_matrix(doldm,1,nlstate,1,npar);  }  /* End of prevalence */
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   /************* Waves Concatenation ***************/
 }  
   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)
 /************ Variance of prevlim ******************/  {
 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)    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 {       Death is a valid wave (if date is known).
   /* Variance of prevalence limit */       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   double **newm;       and mw[mi+1][i]. dh depends on stepm.
   double **dnewm,**doldm;       */
   int i, j, nhstepm, hstepm;  
   int k, cptcode;    int i, mi, m;
   double *xp;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   double *gp, *gm;       double sum=0., jmean=0.;*/
   double **gradg, **trgradg;    int first;
   double age,agelim;    int j, k=0,jk, ju, jl;
   int theta;    double sum=0.;
        first=0;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    jmin=1e+5;
   fprintf(ficresvpl,"# Age");    jmax=-1;
   for(i=1; i<=nlstate;i++)    jmean=0.;
       fprintf(ficresvpl," %1d-%1d",i,i);    for(i=1; i<=imx; i++){
   fprintf(ficresvpl,"\n");      mi=0;
       m=firstpass;
   xp=vector(1,npar);      while(s[m][i] <= nlstate){
   dnewm=matrix(1,nlstate,1,npar);        if(s[m][i]>=1)
   doldm=matrix(1,nlstate,1,nlstate);          mw[++mi][i]=m;
          if(m >=lastpass)
   hstepm=1*YEARM; /* Every year of age */          break;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        else
   agelim = AGESUP;          m++;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }/* end while */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      if (s[m][i] > nlstate){
     if (stepm >= YEARM) hstepm=1;        mi++;     /* Death is another wave */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        /* if(mi==0)  never been interviewed correctly before death */
     gradg=matrix(1,npar,1,nlstate);           /* Only death is a correct wave */
     gp=vector(1,nlstate);        mw[mi][i]=m;
     gm=vector(1,nlstate);      }
   
     for(theta=1; theta <=npar; theta++){      wav[i]=mi;
       for(i=1; i<=npar; i++){ /* Computes gradient */      if(mi==0){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        if(first==0){
       }          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          first=1;
       for(i=1;i<=nlstate;i++)        }
         gp[i] = prlim[i][i];        if(first==1){
              fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
       for(i=1; i<=npar; i++) /* Computes gradient */        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      } /* end mi==0 */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    } /* End individuals */
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
       for(i=1;i<=nlstate;i++)        if (stepm <=0)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          dh[mi][i]=1;
     } /* End theta */        else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     trgradg =matrix(1,nlstate,1,npar);            if (agedc[i] < 2*AGESUP) {
             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     for(j=1; j<=nlstate;j++)            if(j==0) j=1;  /* Survives at least one month after exam */
       for(theta=1; theta <=npar; theta++)            k=k+1;
         trgradg[j][theta]=gradg[theta][j];            if (j >= jmax) jmax=j;
             if (j <= jmin) jmin=j;
     for(i=1;i<=nlstate;i++)            sum=sum+j;
       varpl[i][(int)age] =0.;            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     for(i=1;i<=nlstate;i++)            }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          }
           else{
     fprintf(ficresvpl,"%.0f ",age );            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     for(i=1; i<=nlstate;i++)            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            k=k+1;
     fprintf(ficresvpl,"\n");            if (j >= jmax) jmax=j;
     free_vector(gp,1,nlstate);            else if (j <= jmin)jmin=j;
     free_vector(gm,1,nlstate);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     free_matrix(gradg,1,npar,1,nlstate);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
     free_matrix(trgradg,1,nlstate,1,npar);            if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   } /* End age */            sum=sum+j;
           }
   free_vector(xp,1,npar);          jk= j/stepm;
   free_matrix(doldm,1,nlstate,1,npar);          jl= j -jk*stepm;
   free_matrix(dnewm,1,nlstate,1,nlstate);          ju= j -(jk+1)*stepm;
           if(mle <=1){ 
 }            if(jl==0){
               dh[mi][i]=jk;
 /************ Variance of one-step probabilities  ******************/              bh[mi][i]=0;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)            }else{ /* We want a negative bias in order to only have interpolation ie
 {                    * at the price of an extra matrix product in likelihood */
   int i, j, i1, k1, j1, z1;              dh[mi][i]=jk+1;
   int k=0, cptcode;              bh[mi][i]=ju;
   double **dnewm,**doldm;            }
   double *xp;          }else{
   double *gp, *gm;            if(jl <= -ju){
   double **gradg, **trgradg;              dh[mi][i]=jk;
   double age,agelim, cov[NCOVMAX];              bh[mi][i]=jl;       /* bias is positive if real duration
   int theta;                                   * is higher than the multiple of stepm and negative otherwise.
   char fileresprob[FILENAMELENGTH];                                   */
             }
   strcpy(fileresprob,"prob");            else{
   strcat(fileresprob,fileres);              dh[mi][i]=jk+1;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {              bh[mi][i]=ju;
     printf("Problem with resultfile: %s\n", fileresprob);            }
   }            if(dh[mi][i]==0){
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);              dh[mi][i]=1; /* At least one step */
                bh[mi][i]=ju; /* At least one step */
               /*  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=vector(1,npar);            }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          }
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        } /* end if mle */
        } /* end wave */
   cov[1]=1;    }
   j=cptcoveff;    jmean=sum/k;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   j1=0;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   for(k1=1; k1<=1;k1++){   }
     for(i1=1; i1<=ncodemax[k1];i1++){  
     j1++;  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
     if  (cptcovn>0) {  {
       fprintf(ficresprob, "\n#********** Variable ");    
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    int Ndum[20],ij=1, k, j, i, maxncov=19;
       fprintf(ficresprob, "**********\n#");    int cptcode=0;
     }    cptcoveff=0; 
       
       for (age=bage; age<=fage; age ++){    for (k=0; k<maxncov; k++) Ndum[k]=0;
         cov[2]=age;    for (k=1; k<=7; k++) ncodemax[k]=0;
         for (k=1; k<=cptcovn;k++) {  
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
                for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         }                                 modality*/ 
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         for (k=1; k<=cptcovprod;k++)        Ndum[ij]++; /*store the modality */
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        /*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 
         gradg=matrix(1,npar,1,9);                                         Tvar[j]. If V=sex and male is 0 and 
         trgradg=matrix(1,9,1,npar);                                         female is 1, then  cptcode=1.*/
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      }
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
          for (i=0; i<=cptcode; i++) {
         for(theta=1; theta <=npar; theta++){        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
           for(i=1; i<=npar; i++)      }
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  
                ij=1; 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (i=1; i<=ncodemax[j]; i++) {
                  for (k=0; k<= maxncov; k++) {
           k=0;          if (Ndum[k] != 0) {
           for(i=1; i<= (nlstate+ndeath); i++){            nbcode[Tvar[j]][ij]=k; 
             for(j=1; j<=(nlstate+ndeath);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; */
               k=k+1;            
               gp[k]=pmmij[i][j];            ij++;
             }          }
           }          if (ij > ncodemax[j]) break; 
                  }  
           for(i=1; i<=npar; i++)      } 
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    }  
      
           pmij(pmmij,cov,ncovmodel,xp,nlstate);   for (k=0; k< maxncov; k++) Ndum[k]=0;
           k=0;  
           for(i=1; i<=(nlstate+ndeath); i++){   for (i=1; i<=ncovmodel-2; i++) { 
             for(j=1; j<=(nlstate+ndeath);j++){     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
               k=k+1;     ij=Tvar[i];
               gm[k]=pmmij[i][j];     Ndum[ij]++;
             }   }
           }  
         ij=1;
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)   for (i=1; i<= maxncov; i++) {
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];       if((Ndum[i]!=0) && (i<=ncovcol)){
         }       Tvaraff[ij]=i; /*For printing */
        ij++;
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)     }
           for(theta=1; theta <=npar; theta++)   }
             trgradg[j][theta]=gradg[theta][j];   
           cptcoveff=ij-1; /*Number of simple covariates*/
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  }
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  
          /*********** Health Expectancies ****************/
         pmij(pmmij,cov,ncovmodel,x,nlstate);  
          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 )
         k=0;  
         for(i=1; i<=(nlstate+ndeath); i++){  {
           for(j=1; j<=(nlstate+ndeath);j++){    /* Health expectancies */
             k=k+1;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
             gm[k]=pmmij[i][j];    double age, agelim, hf;
           }    double ***p3mat,***varhe;
         }    double **dnewm,**doldm;
          double *xp;
      /*printf("\n%d ",(int)age);    double **gp, **gm;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double ***gradg, ***trgradg;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    int theta;
      }*/  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         fprintf(ficresprob,"\n%d ",(int)age);    xp=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],doldm[i][i]);    
      fprintf(ficreseij,"# Health expectancies\n");
       }    fprintf(ficreseij,"# Age");
     }    for(i=1; i<=nlstate;i++)
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      for(j=1; j<=nlstate;j++)
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fprintf(ficreseij,"\n");
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   }    if(estepm < stepm){
   free_vector(xp,1,npar);      printf ("Problem %d lower than %d\n",estepm, stepm);
   fclose(ficresprob);    }
      else  hstepm=estepm;   
 }    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
 /******************* Printing html file ***********/     * if stepm=24 months pijx are given only every 2 years and by summing them
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \     * we are calculating an estimate of the Life Expectancy assuming a linear 
  int lastpass, int stepm, int weightopt, char model[],\     * progression in between and thus overestimating or underestimating according
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \     * to the curvature of the survival function. If, for the same date, we 
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\     * estimate the model with stepm=1 month, we can keep estepm to 24 months
  char version[], int popforecast, int estepm ){     * to compare the new estimate of Life expectancy with the same linear 
   int jj1, k1, i1, cpt;     * hypothesis. A more precise result, taking into account a more precise
   FILE *fichtm;     * curvature will be obtained if estepm is as small as stepm. */
   /*char optionfilehtm[FILENAMELENGTH];*/  
     /* For example we decided to compute the life expectancy with the smallest unit */
   strcpy(optionfilehtm,optionfile);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   strcat(optionfilehtm,".htm");       nhstepm is the number of hstepm from age to agelim 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {       nstepm is the number of stepm from age to agelin. 
     printf("Problem with %s \n",optionfilehtm), exit(0);       Look at hpijx to understand the reason of that which relies in memory size
   }       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n       survival function given by stepm (the optimization length). Unfortunately it
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n       means that if the survival funtion is printed only each two years of age and if
 \n       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 Total number of observations=%d <br>\n       results. So we changed our mind and took the option of the best precision.
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    */
 <hr  size=\"2\" color=\"#EC5E5E\">    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  <ul><li>Outputs files<br>\n  
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    agelim=AGESUP;
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      /* nhstepm age range expressed in number of stepm */
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  fprintf(fichtm,"\n      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      gp=matrix(0,nhstepm,1,nlstate*nlstate);
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      gm=matrix(0,nhstepm,1,nlstate*nlstate);
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
  if(popforecast==1) fprintf(fichtm,"\n         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n   
         <br>",fileres,fileres,fileres,fileres);  
  else      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    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," <li>Graphs</li><p>");      /* Computing Variances of health expectancies */
   
  m=cptcoveff;       for(theta=1; theta <=npar; theta++){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
  jj1=0;        }
  for(k1=1; k1<=m;k1++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
    for(i1=1; i1<=ncodemax[k1];i1++){    
        jj1++;        cptj=0;
        if (cptcovn > 0) {        for(j=1; j<= nlstate; j++){
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          for(i=1; i<=nlstate; i++){
          for (cpt=1; cpt<=cptcoveff;cpt++)            cptj=cptj+1;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
        }            }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            }
        for(cpt=1; cpt<nlstate;cpt++){       
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>       
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for(i=1; i<=npar; i++) 
        }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for(cpt=1; cpt<=nlstate;cpt++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        
 interval) in state (%d): v%s%d%d.gif <br>        cptj=0;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(j=1; j<= nlstate; j++){
      }          for(i=1;i<=nlstate;i++){
      for(cpt=1; cpt<=nlstate;cpt++) {            cptj=cptj+1;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
      }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            }
 health expectancies in states (1) and (2): e%s%d.gif<br>          }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        }
 fprintf(fichtm,"\n</body>");        for(j=1; j<= nlstate*nlstate; j++)
    }          for(h=0; h<=nhstepm-1; h++){
    }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 fclose(fichtm);          }
 }       } 
      
 /******************* Gnuplot file **************/  /* End theta */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
        trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  
        for(h=0; h<=nhstepm-1; h++)
   strcpy(optionfilegnuplot,optionfilefiname);        for(j=1; j<=nlstate*nlstate;j++)
   strcat(optionfilegnuplot,".gp.txt");          for(theta=1; theta <=npar; theta++)
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            trgradg[h][j][theta]=gradg[h][theta][j];
     printf("Problem with file %s",optionfilegnuplot);       
   }  
        for(i=1;i<=nlstate*nlstate;i++)
 #ifdef windows        for(j=1;j<=nlstate*nlstate;j++)
     fprintf(ficgp,"cd \"%s\" \n",pathc);          varhe[i][j][(int)age] =0.;
 #endif  
 m=pow(2,cptcoveff);       printf("%d|",(int)age);fflush(stdout);
         fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  /* 1eme*/       for(h=0;h<=nhstepm-1;h++){
   for (cpt=1; cpt<= nlstate ; cpt ++) {        for(k=0;k<=nhstepm-1;k++){
    for (k1=1; k1<= m ; k1 ++) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
 #ifdef windows          for(i=1;i<=nlstate*nlstate;i++)
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);            for(j=1;j<=nlstate*nlstate;j++)
 #endif              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
 #ifdef unix        }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      }
 #endif      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
 for (i=1; i<= nlstate ; i ++) {        for(j=1; j<=nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 }            
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      fprintf(ficreseij,"%3.0f",age );
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      cptj=0;
      for (i=1; i<= nlstate ; i ++) {      for(i=1; i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<=nlstate;j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          cptj++;
 }            fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        }
 #ifdef unix      fprintf(ficreseij,"\n");
 fprintf(ficgp,"\nset ter gif small size 400,300");     
 #endif      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
    }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   /*2 eme*/      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }
   for (k1=1; k1<= m ; k1 ++) {    printf("\n");
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    fprintf(ficlog,"\n");
      
     for (i=1; i<= nlstate+1 ; i ++) {    free_vector(xp,1,npar);
       k=2*i;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    /************ Variance ******************/
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  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)
       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);    /* Variance of health expectancies */
       for (j=1; j<= nlstate+1 ; j ++) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* double **newm;*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double **dnewm,**doldm;
 }      double **dnewmp,**doldmp;
       fprintf(ficgp,"\" t\"\" w l 0,");    int i, j, nhstepm, hstepm, h, nstepm ;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    int k, cptcode;
       for (j=1; j<= nlstate+1 ; j ++) {    double *xp;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double **gp, **gm;  /* for var eij */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double ***gradg, ***trgradg; /*for var eij */
 }      double **gradgp, **trgradgp; /* for var p point j */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    double *gpp, *gmp; /* for var p point j */
       else fprintf(ficgp,"\" t\"\" w l 0,");    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     }    double ***p3mat;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    double age,agelim, hf;
   }    double ***mobaverage;
      int theta;
   /*3eme*/    char digit[4];
     char digitp[25];
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {    char fileresprobmorprev[FILENAMELENGTH];
       k=2+nlstate*(cpt-1);  
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    if(popbased==1){
       for (i=1; i< nlstate ; i ++) {      if(mobilav!=0)
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);        strcpy(digitp,"-populbased-mobilav-");
       }      else strcpy(digitp,"-populbased-nomobil-");
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
     }    else 
     }      strcpy(digitp,"-stablbased-");
    
   /* CV preval stat */    if (mobilav!=0) {
     for (k1=1; k1<= m ; k1 ++) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for (cpt=1; cpt<nlstate ; cpt ++) {      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       k=3;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
       for (i=1; i< nlstate ; i ++)    }
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    strcpy(fileresprobmorprev,"prmorprev"); 
          sprintf(digit,"%-d",ij);
       l=3+(nlstate+ndeath)*cpt;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       for (i=1; i< nlstate ; i ++) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         l=3+(nlstate+ndeath)*cpt;    strcat(fileresprobmorprev,fileres);
         fprintf(ficgp,"+$%d",l+i+1);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
     }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   }      fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   /* proba elementaires */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
    for(i=1,jk=1; i <=nlstate; i++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     for(k=1; k <=(nlstate+ndeath); k++){      fprintf(ficresprobmorprev," p.%-d SE",j);
       if (k != i) {      for(i=1; i<=nlstate;i++)
         for(j=1; j <=ncovmodel; j++){        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
            }  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(ficresprobmorprev,"\n");
           jk++;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           fprintf(ficgp,"\n");      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
         }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       }      exit(0);
     }    }
     }    else{
       fprintf(ficgp,"\n# Routine varevsij");
     for(jk=1; jk <=m; jk++) {    }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
    i=1;      printf("Problem with html file: %s\n", optionfilehtm);
    for(k2=1; k2<=nlstate; k2++) {      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
      k3=i;      exit(0);
      for(k=1; k<=(nlstate+ndeath); k++) {    }
        if (k != k2){    else{
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
 ij=1;      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
         for(j=3; j <=ncovmodel; j++) {    }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
           }    fprintf(ficresvij,"# Age");
           else    for(i=1; i<=nlstate;i++)
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for(j=1; j<=nlstate;j++)
         }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
           fprintf(ficgp,")/(1");    fprintf(ficresvij,"\n");
          
         for(k1=1; k1 <=nlstate; k1++){      xp=vector(1,npar);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    dnewm=matrix(1,nlstate,1,npar);
 ij=1;    doldm=matrix(1,nlstate,1,nlstate);
           for(j=3; j <=ncovmodel; j++){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           }    gpp=vector(nlstate+1,nlstate+ndeath);
           else    gmp=vector(nlstate+1,nlstate+ndeath);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           }    
           fprintf(ficgp,")");    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    else  hstepm=estepm;   
         i=i+ncovmodel;    /* 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. 
      }       nhstepm is the number of hstepm from age to agelim 
    }       nstepm is the number of stepm from age to agelin. 
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);       Look at hpijx to understand the reason of that which relies in memory size
    }       and note for a fixed period like k years */
        /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   fclose(ficgp);       survival function given by stepm (the optimization length). Unfortunately it
 }  /* end gnuplot */       means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
 /*************** Moving average **************/    */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   int i, cpt, cptcod;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)      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 (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           mobaverage[(int)agedeb][i][cptcod]=0.;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
          gp=matrix(0,nhstepm,1,nlstate);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      gm=matrix(0,nhstepm,1,nlstate);
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){      for(theta=1; theta <=npar; theta++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        }
         }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }  
            if (popbased==1) {
 }          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
 /************** Forecasting ******************/          }else{ /* mobilav */ 
 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){            for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          }
   int *popage;        }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    
   double *popeffectif,*popcount;        for(j=1; j<= nlstate; j++){
   double ***p3mat;          for(h=0; h<=nhstepm; h++){
   char fileresf[FILENAMELENGTH];            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
  agelim=AGESUP;          }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        }
         /* This for computing probability of death (h=1 means
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
          */
   strcpy(fileresf,"f");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   strcat(fileresf,fileres);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   if((ficresf=fopen(fileresf,"w"))==NULL) {            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     printf("Problem with forecast resultfile: %s\n", fileresf);        }    
   }        /* end probability of death */
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (mobilav==1) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
     movingaverage(agedeb, fage, ageminpar, mobaverage);        if (popbased==1) {
   }          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;              prlim[i][i]=probs[(int)age][i][ij];
   if (stepm<=12) stepsize=1;          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
   agelim=AGESUP;              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
   hstepm=1;        }
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);        for(j=1; j<= nlstate; j++){
   anprojmean=yp;          for(h=0; h<=nhstepm; h++){
   yp2=modf((yp1*12),&yp);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   mprojmean=yp;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   yp1=modf((yp2*30.5),&yp);          }
   jprojmean=yp;        }
   if(jprojmean==0) jprojmean=1;        /* This for computing probability of death (h=1 means
   if(mprojmean==0) jprojmean=1;           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   for(cptcov=1;cptcov<=i2;cptcov++){          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       k=k+1;        }    
       fprintf(ficresf,"\n#******");        /* end probability of death */
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<= nlstate; j++) /* vareij */
       }          for(h=0; h<=nhstepm; h++){
       fprintf(ficresf,"******\n");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       fprintf(ficresf,"# StartingAge FinalAge");          }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
              for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        }
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        } /* End theta */
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;      for(h=0; h<=nhstepm; h++) /* veij */
                  for(j=1; j<=nlstate;j++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(theta=1; theta <=npar; theta++)
           oldm=oldms;savm=savms;            trgradg[h][j][theta]=gradg[h][theta][j];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
              for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
           for (h=0; h<=nhstepm; h++){        for(theta=1; theta <=npar; theta++)
             if (h==(int) (calagedate+YEARM*cpt)) {          trgradgp[j][theta]=gradgp[theta][j];
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    
             }  
             for(j=1; j<=nlstate+ndeath;j++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               kk1=0.;kk2=0;      for(i=1;i<=nlstate;i++)
               for(i=1; i<=nlstate;i++) {                      for(j=1;j<=nlstate;j++)
                 if (mobilav==1)          vareij[i][j][(int)age] =0.;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {      for(h=0;h<=nhstepm;h++){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        for(k=0;k<=nhstepm;k++){
                 }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
               }          for(i=1;i<=nlstate;i++)
               if (h==(int)(calagedate+12*cpt)){            for(j=1;j<=nlstate;j++)
                 fprintf(ficresf," %.3f", kk1);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                                }
               }      }
             }    
           }      /* pptj */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      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(j=nlstate+1;j<=nlstate+ndeath;j++)
     }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   }          varppt[j][i]=doldmp[j][i];
              /* end ppptj */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   fclose(ficresf);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
 }   
 /************** Forecasting ******************/      if (popbased==1) {
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){        if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            prlim[i][i]=probs[(int)age][i][ij];
   int *popage;        }else{ /* mobilav */ 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          for(i=1; i<=nlstate;i++)
   double *popeffectif,*popcount;            prlim[i][i]=mobaverage[(int)age][i][ij];
   double ***p3mat,***tabpop,***tabpopprev;        }
   char filerespop[FILENAMELENGTH];      }
                
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /* This for computing probability of death (h=1 means
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   agelim=AGESUP;         as a weighted average of prlim.
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        }    
   strcpy(filerespop,"pop");      /* end probability of death */
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     printf("Problem with forecast resultfile: %s\n", filerespop);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   printf("Computing forecasting: result on file '%s' \n", filerespop);        for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        }
       } 
   if (mobilav==1) {      fprintf(ficresprobmorprev,"\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, ageminpar, mobaverage);      fprintf(ficresvij,"%.0f ",age );
   }      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   if (stepm<=12) stepsize=1;        }
        fprintf(ficresvij,"\n");
   agelim=AGESUP;      free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
   hstepm=1;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   hstepm=hstepm/stepm;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (popforecast==1) {    } /* End age */
     if((ficpop=fopen(popfile,"r"))==NULL) {    free_vector(gpp,nlstate+1,nlstate+ndeath);
       printf("Problem with population file : %s\n",popfile);exit(0);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     popage=ivector(0,AGESUP);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     popeffectif=vector(0,AGESUP);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     popcount=vector(0,AGESUP);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
        fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     i=1;    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
      /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     imx=i;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
   }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /*  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);
       k=k+1;  */
       fprintf(ficrespop,"\n#******");    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_vector(xp,1,npar);
       }    free_matrix(doldm,1,nlstate,1,nlstate);
       fprintf(ficrespop,"******\n");    free_matrix(dnewm,1,nlstate,1,npar);
       fprintf(ficrespop,"# Age");    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       if (popforecast==1)  fprintf(ficrespop," [Population]");    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
          if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for (cpt=0; cpt<=0;cpt++) {    fclose(ficresprobmorprev);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fclose(ficgp);
            fclose(fichtm);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  }  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;  /************ Variance of prevlim ******************/
            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)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
           oldm=oldms;savm=savms;    /* Variance of prevalence limit */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
            double **newm;
           for (h=0; h<=nhstepm; h++){    double **dnewm,**doldm;
             if (h==(int) (calagedate+YEARM*cpt)) {    int i, j, nhstepm, hstepm;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    int k, cptcode;
             }    double *xp;
             for(j=1; j<=nlstate+ndeath;j++) {    double *gp, *gm;
               kk1=0.;kk2=0;    double **gradg, **trgradg;
               for(i=1; i<=nlstate;i++) {                  double age,agelim;
                 if (mobilav==1)    int theta;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];     
                 else {    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    fprintf(ficresvpl,"# Age");
                 }    for(i=1; i<=nlstate;i++)
               }        fprintf(ficresvpl," %1d-%1d",i,i);
               if (h==(int)(calagedate+12*cpt)){    fprintf(ficresvpl,"\n");
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  
                   /*fprintf(ficrespop," %.3f", kk1);    xp=vector(1,npar);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    dnewm=matrix(1,nlstate,1,npar);
               }    doldm=matrix(1,nlstate,1,nlstate);
             }    
             for(i=1; i<=nlstate;i++){    hstepm=1*YEARM; /* Every year of age */
               kk1=0.;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                 for(j=1; j<=nlstate;j++){    agelim = AGESUP;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                 }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      if (stepm >= YEARM) hstepm=1;
             }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      gp=vector(1,nlstate);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      gm=vector(1,nlstate);
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(theta=1; theta <=npar; theta++){
         }        for(i=1; i<=npar; i++){ /* Computes gradient */
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
   /******/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          gp[i] = prlim[i][i];
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(i=1; i<=npar; i++) /* Computes gradient */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           nhstepm = nhstepm/hstepm;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                  for(i=1;i<=nlstate;i++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          gm[i] = prlim[i][i];
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(i=1;i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
             if (h==(int) (calagedate+YEARM*cpt)) {      } /* End theta */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }      trgradg =matrix(1,nlstate,1,npar);
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;      for(j=1; j<=nlstate;j++)
               for(i=1; i<=nlstate;i++) {                      for(theta=1; theta <=npar; theta++)
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              trgradg[j][theta]=gradg[theta][j];
               }  
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      for(i=1;i<=nlstate;i++)
             }        varpl[i][(int)age] =0.;
           }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
         }      for(i=1;i<=nlstate;i++)
       }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    }  
   }      fprintf(ficresvpl,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
   if (popforecast==1) {      free_vector(gp,1,nlstate);
     free_ivector(popage,0,AGESUP);      free_vector(gm,1,nlstate);
     free_vector(popeffectif,0,AGESUP);      free_matrix(gradg,1,npar,1,nlstate);
     free_vector(popcount,0,AGESUP);      free_matrix(trgradg,1,nlstate,1,npar);
   }    } /* End age */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_vector(xp,1,npar);
   fclose(ficrespop);    free_matrix(doldm,1,nlstate,1,npar);
 }    free_matrix(dnewm,1,nlstate,1,nlstate);
   
 /***********************************************/  }
 /**************** Main Program *****************/  
 /***********************************************/  /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
 int main(int argc, char *argv[])  {
 {    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    int k=0,l, cptcode;
   double agedeb, agefin,hf;    int first=1, first1;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
   double fret;    double *xp;
   double **xi,tmp,delta;    double *gp, *gm;
     double **gradg, **trgradg;
   double dum; /* Dummy variable */    double **mu;
   double ***p3mat;    double age,agelim, cov[NCOVMAX];
   int *indx;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   char line[MAXLINE], linepar[MAXLINE];    int theta;
   char title[MAXLINE];    char fileresprob[FILENAMELENGTH];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    char fileresprobcov[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    char fileresprobcor[FILENAMELENGTH];
    
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    double ***varpij;
   
   char filerest[FILENAMELENGTH];    strcpy(fileresprob,"prob"); 
   char fileregp[FILENAMELENGTH];    strcat(fileresprob,fileres);
   char popfile[FILENAMELENGTH];    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      printf("Problem with resultfile: %s\n", fileresprob);
   int firstobs=1, lastobs=10;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   int sdeb, sfin; /* Status at beginning and end */    }
   int c,  h , cpt,l;    strcpy(fileresprobcov,"probcov"); 
   int ju,jl, mi;    strcat(fileresprobcov,fileres);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      printf("Problem with resultfile: %s\n", fileresprobcov);
   int mobilav=0,popforecast=0;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   int hstepm, nhstepm;    }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
   double bage, fage, age, agelim, agebase;    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   double ftolpl=FTOL;      printf("Problem with resultfile: %s\n", fileresprobcor);
   double **prlim;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   double *severity;    }
   double ***param; /* Matrix of parameters */    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   double  *p;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   double **matcov; /* Matrix of covariance */    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   double ***delti3; /* Scale */    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   double *delti; /* Scale */    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   double ***eij, ***vareij;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   double **varpl; /* Variances of prevalence limits by age */    
   double *epj, vepp;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   double kk1, kk2;    fprintf(ficresprob,"# Age");
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";    fprintf(ficresprobcov,"# Age");
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
   
     for(i=1; i<=nlstate;i++)
   char z[1]="c", occ;      for(j=1; j<=(nlstate+ndeath);j++){
 #include <sys/time.h>        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
 #include <time.h>        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
   /* long total_usecs;   /* fprintf(ficresprob,"\n");
   struct timeval start_time, end_time;    fprintf(ficresprobcov,"\n");
      fprintf(ficresprobcor,"\n");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */   */
   getcwd(pathcd, size);   xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   printf("\n%s",version);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   if(argc <=1){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     printf("\nEnter the parameter file name: ");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     scanf("%s",pathtot);    first=1;
   }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   else{      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     strcpy(pathtot,argv[1]);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   }      exit(0);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    }
   /*cygwin_split_path(pathtot,path,optionfile);    else{
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      fprintf(ficgp,"\n# Routine varprob");
   /* cutv(path,optionfile,pathtot,'\\');*/    }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      printf("Problem with html file: %s\n", optionfilehtm);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   chdir(path);      exit(0);
   replace(pathc,path);    }
     else{
 /*-------- arguments in the command line --------*/      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(fichtm,"\n");
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   strcat(fileres,".txt");    /* Other files have txt extension */      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");
   /*---------arguments file --------*/  
     }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);    cov[1]=1;
     goto end;    tj=cptcoveff;
   }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
   strcpy(filereso,"o");    for(t=1; t<=tj;t++){
   strcat(filereso,fileres);      for(i1=1; i1<=ncodemax[t];i1++){ 
   if((ficparo=fopen(filereso,"w"))==NULL) {        j1++;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        if  (cptcovn>0) {
   }          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* Reads comments: lines beginning with '#' */          fprintf(ficresprob, "**********\n#\n");
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobcov, "\n#********** Variable "); 
     ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcov, "**********\n#\n");
     puts(line);          
     fputs(line,ficparo);          fprintf(ficgp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   ungetc(c,ficpar);          fprintf(ficgp, "**********\n#\n");
           
   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);          
   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(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   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);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcor, "\n#********** Variable ");    
     puts(line);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fputs(line,ficparo);          fprintf(ficresprobcor, "**********\n#");    
   }        }
   ungetc(c,ficpar);        
          for (age=bage; age<=fage; age ++){ 
              cov[2]=age;
   covar=matrix(0,NCOVMAX,1,n);          for (k=1; k<=cptcovn;k++) {
   cptcovn=0;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   ncovmodel=2+cptcovn;          for (k=1; k<=cptcovprod;k++)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
            
   /* Read guess parameters */          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   /* Reads comments: lines beginning with '#' */          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){          gp=vector(1,(nlstate)*(nlstate+ndeath));
     ungetc(c,ficpar);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     fgets(line, MAXLINE, ficpar);      
     puts(line);          for(theta=1; theta <=npar; theta++){
     fputs(line,ficparo);            for(i=1; i<=npar; i++)
   }              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   ungetc(c,ficpar);            
              pmij(pmmij,cov,ncovmodel,xp,nlstate);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            
     for(i=1; i <=nlstate; i++)            k=0;
     for(j=1; j <=nlstate+ndeath-1; j++){            for(i=1; i<= (nlstate); i++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);              for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficparo,"%1d%1d",i1,j1);                k=k+1;
       printf("%1d%1d",i,j);                gp[k]=pmmij[i][j];
       for(k=1; k<=ncovmodel;k++){              }
         fscanf(ficpar," %lf",&param[i][j][k]);            }
         printf(" %lf",param[i][j][k]);            
         fprintf(ficparo," %lf",param[i][j][k]);            for(i=1; i<=npar; i++)
       }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       fscanf(ficpar,"\n");      
       printf("\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fprintf(ficparo,"\n");            k=0;
     }            for(i=1; i<=(nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                k=k+1;
                 gm[k]=pmmij[i][j];
   p=param[1][1];              }
              }
   /* Reads comments: lines beginning with '#' */       
   while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     ungetc(c,ficpar);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     fgets(line, MAXLINE, ficpar);          }
     puts(line);  
     fputs(line,ficparo);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   }            for(theta=1; theta <=npar; theta++)
   ungetc(c,ficpar);              trgradg[j][theta]=gradg[theta][j];
           
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   for(i=1; i <=nlstate; i++){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     for(j=1; j <=nlstate+ndeath-1; j++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       fscanf(ficpar,"%1d%1d",&i1,&j1);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       printf("%1d%1d",i,j);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){          pmij(pmmij,cov,ncovmodel,x,nlstate);
         fscanf(ficpar,"%le",&delti3[i][j][k]);          
         printf(" %le",delti3[i][j][k]);          k=0;
         fprintf(ficparo," %le",delti3[i][j][k]);          for(i=1; i<=(nlstate); i++){
       }            for(j=1; j<=(nlstate+ndeath);j++){
       fscanf(ficpar,"\n");              k=k+1;
       printf("\n");              mu[k][(int) age]=pmmij[i][j];
       fprintf(ficparo,"\n");            }
     }          }
   }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   delti=delti3[1][1];            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                varpij[i][j][(int)age] = doldm[i][j];
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){          /*printf("\n%d ",(int)age);
     ungetc(c,ficpar);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     fgets(line, MAXLINE, ficpar);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     puts(line);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     fputs(line,ficparo);            }*/
   }  
   ungetc(c,ficpar);          fprintf(ficresprob,"\n%d ",(int)age);
            fprintf(ficresprobcov,"\n%d ",(int)age);
   matcov=matrix(1,npar,1,npar);          fprintf(ficresprobcor,"\n%d ",(int)age);
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     printf("%s",str);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     fprintf(ficparo,"%s",str);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     for(j=1; j <=i; j++){            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       fscanf(ficpar," %le",&matcov[i][j]);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       printf(" %.5le",matcov[i][j]);          }
       fprintf(ficparo," %.5le",matcov[i][j]);          i=0;
     }          for (k=1; k<=(nlstate);k++){
     fscanf(ficpar,"\n");            for (l=1; l<=(nlstate+ndeath);l++){ 
     printf("\n");              i=i++;
     fprintf(ficparo,"\n");              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   for(i=1; i <=npar; i++)              for (j=1; j<=i;j++){
     for(j=i+1;j<=npar;j++)                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       matcov[i][j]=matcov[j][i];                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                  }
   printf("\n");            }
           }/* end of loop for state */
         } /* end of loop for age */
     /*-------- Rewriting paramater file ----------*/  
      strcpy(rfileres,"r");    /* "Rparameterfile */        /* Confidence intervalle of pij  */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        /*
      strcat(rfileres,".");    /* */          fprintf(ficgp,"\nset noparametric;unset label");
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     if((ficres =fopen(rfileres,"w"))==NULL) {          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
     }          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     fprintf(ficres,"#%s\n",version);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
              fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     /*-------- data file ----------*/        */
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     }        first1=1;
         for (k2=1; k2<=(nlstate);k2++){
     n= lastobs;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     severity = vector(1,maxwav);            if(l2==k2) continue;
     outcome=imatrix(1,maxwav+1,1,n);            j=(k2-1)*(nlstate+ndeath)+l2;
     num=ivector(1,n);            for (k1=1; k1<=(nlstate);k1++){
     moisnais=vector(1,n);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     annais=vector(1,n);                if(l1==k1) continue;
     moisdc=vector(1,n);                i=(k1-1)*(nlstate+ndeath)+l1;
     andc=vector(1,n);                if(i<=j) continue;
     agedc=vector(1,n);                for (age=bage; age<=fage; age ++){ 
     cod=ivector(1,n);                  if ((int)age %5==0){
     weight=vector(1,n);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     mint=matrix(1,maxwav,1,n);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     anint=matrix(1,maxwav,1,n);                    mu1=mu[i][(int) age]/stepm*YEARM ;
     s=imatrix(1,maxwav+1,1,n);                    mu2=mu[j][(int) age]/stepm*YEARM;
     adl=imatrix(1,maxwav+1,1,n);                        c12=cv12/sqrt(v1*v2);
     tab=ivector(1,NCOVMAX);                    /* Computing eigen value of matrix of covariance */
     ncodemax=ivector(1,8);                    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.;
     i=1;                    /* Eigen vectors */
     while (fgets(line, MAXLINE, fic) != NULL)    {                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       if ((i >= firstobs) && (i <=lastobs)) {                    /*v21=sqrt(1.-v11*v11); *//* error */
                            v21=(lc1-v1)/cv12*v11;
         for (j=maxwav;j>=1;j--){                    v12=-v21;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                    v22=v11;
           strcpy(line,stra);                    tnalp=v21/v11;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    if(first1==1){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                      first1=0;
         }                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                            }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                    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);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                    /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                    if(first==1){
                       first=0;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                      fprintf(ficgp,"\nset parametric;unset label");
         for (j=ncovcol;j>=1;j--){                      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);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                      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);
         num[i]=atol(stra);                      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);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         i=i+1;                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
       }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     /* printf("ii=%d", ij);                    }else{
        scanf("%d",i);*/                      first=0;
   imx=i-1; /* Number of individuals */                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   /* for (i=1; i<=imx; i++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                      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",\
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     }*/                    }/* if first */
    /*  for (i=1; i<=imx; i++){                  } /* age mod 5 */
      if (s[4][i]==9)  s[4][i]=-1;                } /* end loop age */
      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(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                  first=1;
                } /*l12 */
   /* Calculation of the number of parameter from char model*/            } /* k12 */
   Tvar=ivector(1,15);          } /*l1 */
   Tprod=ivector(1,15);        }/* k1 */
   Tvaraff=ivector(1,15);      } /* loop covariates */
   Tvard=imatrix(1,15,1,2);    }
   Tage=ivector(1,15);          free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
        free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   if (strlen(model) >1){    free_vector(xp,1,npar);
     j=0, j1=0, k1=1, k2=1;    fclose(ficresprob);
     j=nbocc(model,'+');    fclose(ficresprobcov);
     j1=nbocc(model,'*');    fclose(ficresprobcor);
     cptcovn=j+1;    fclose(ficgp);
     cptcovprod=j1;    fclose(fichtm);
      }
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);  /******************* Printing html file ***********/
       goto end;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     }                    int lastpass, int stepm, int weightopt, char model[],\
                        int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     for(i=(j+1); i>=1;i--){                    int popforecast, int estepm ,\
       cutv(stra,strb,modelsav,'+');                    double jprev1, double mprev1,double anprev1, \
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                    double jprev2, double mprev2,double anprev2){
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    int jj1, k1, i1, cpt;
       /*scanf("%d",i);*/    /*char optionfilehtm[FILENAMELENGTH];*/
       if (strchr(strb,'*')) {    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
         cutv(strd,strc,strb,'*');      printf("Problem with %s \n",optionfilehtm), exit(0);
         if (strcmp(strc,"age")==0) {      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
           cptcovprod--;    }
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
           cptcovage++;   - 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
             Tage[cptcovage]=i;   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
             /*printf("stre=%s ", stre);*/   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
         }   - Life expectancies by age and initial health status (estepm=%2d months): 
         else if (strcmp(strd,"age")==0) {     <a href=\"e%s\">e%s</a> <br>\n</li>", \
           cptcovprod--;    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           cptcovage++;  
           Tage[cptcovage]=i;   m=cptcoveff;
         }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         else {  
           cutv(strb,stre,strc,'V');   jj1=0;
           Tvar[i]=ncovcol+k1;   for(k1=1; k1<=m;k1++){
           cutv(strb,strc,strd,'V');     for(i1=1; i1<=ncodemax[k1];i1++){
           Tprod[k1]=i;       jj1++;
           Tvard[k1][1]=atoi(strc);       if (cptcovn > 0) {
           Tvard[k1][2]=atoi(stre);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           Tvar[cptcovn+k2]=Tvard[k1][1];         for (cpt=1; cpt<=cptcoveff;cpt++) 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           for (k=1; k<=lastobs;k++)         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];       }
           k1++;       /* Pij */
           k2=k2+2;       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 */
       else {       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>
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
        /*  scanf("%d",i);*/         /* Stable prevalence in each health state */
       cutv(strd,strc,strb,'V');         for(cpt=1; cpt<nlstate;cpt++){
       Tvar[i]=atoi(strc);           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);
       strcpy(modelsav,stra);           }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);       for(cpt=1; cpt<=nlstate;cpt++) {
         scanf("%d",i);*/          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);
 }       }
         fprintf(fichtm,"\n<br>- Total life expectancy by age and
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  health expectancies in states (1) and (2): e%s%d.png<br>
   printf("cptcovprod=%d ", cptcovprod);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   scanf("%d ",i);*/     } /* end i1 */
     fclose(fic);   }/* End k1 */
    fprintf(fichtm,"</ul>");
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     /*-calculation of age at interview from date of interview and age at death -*/   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     agev=matrix(1,maxwav,1,imx);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
    - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
     for (i=1; i<=imx; i++) {   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
       for(m=2; (m<= maxwav); m++) {   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){   - 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);
          anint[m][i]=9999;  
          s[m][i]=-1;  /*  if(popforecast==1) fprintf(fichtm,"\n */
        }  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
       }  /*      <br>",fileres,fileres,fileres,fileres); */
     }  /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
     for (i=1; i<=imx; i++)  {  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){   m=cptcoveff;
         if(s[m][i] >0){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           if (s[m][i] >= nlstate+1) {  
             if(agedc[i]>0)   jj1=0;
               if(moisdc[i]!=99 && andc[i]!=9999)   for(k1=1; k1<=m;k1++){
                 agev[m][i]=agedc[i];     for(i1=1; i1<=ncodemax[k1];i1++){
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/       jj1++;
            else {       if (cptcovn > 0) {
               if (andc[i]!=9999){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
               printf("Warning negative age at death: %d line:%d\n",num[i],i);         for (cpt=1; cpt<=cptcoveff;cpt++) 
               agev[m][i]=-1;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
               }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
             }       }
           }       for(cpt=1; cpt<=nlstate;cpt++) {
           else if(s[m][i] !=9){ /* Should no more exist */         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  interval) in state (%d): v%s%d%d.png <br>
             if(mint[m][i]==99 || anint[m][i]==9999)  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
               agev[m][i]=1;       }
             else if(agev[m][i] <agemin){     } /* end i1 */
               agemin=agev[m][i];   }/* End k1 */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/   fprintf(fichtm,"</ul>");
             }  fclose(fichtm);
             else if(agev[m][i] >agemax){  }
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  /******************* Gnuplot file **************/
             }  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
           }    int ng;
           else { /* =9 */    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
             agev[m][i]=1;      printf("Problem with file %s",optionfilegnuplot);
             s[m][i]=-1;      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
           }    }
         }  
         else /*= 0 Unknown */    /*#ifdef windows */
           agev[m][i]=1;      fprintf(ficgp,"cd \"%s\" \n",pathc);
       }      /*#endif */
      m=pow(2,cptcoveff);
     }    
     for (i=1; i<=imx; i++)  {   /* 1eme*/
       for(m=1; (m<= maxwav); m++){    for (cpt=1; cpt<= nlstate ; cpt ++) {
         if (s[m][i] > (nlstate+ndeath)) {     for (k1=1; k1<= m ; k1 ++) {
           printf("Error: Wrong value in nlstate or ndeath\n");         fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           goto end;       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 (i=1; i<= nlstate ; i ++) {
     }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
     free_vector(severity,1,maxwav);       for (i=1; i<= nlstate ; i ++) {
     free_imatrix(outcome,1,maxwav+1,1,n);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     free_vector(moisnais,1,n);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     free_vector(annais,1,n);       } 
     /* free_matrix(mint,1,maxwav,1,n);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        free_matrix(anint,1,maxwav,1,n);*/       for (i=1; i<= nlstate ; i ++) {
     free_vector(moisdc,1,n);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     free_vector(andc,1,n);         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
           fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
     wav=ivector(1,imx);     }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    /*2 eme*/
        
     /* Concatenates waves */    for (k1=1; k1<= m ; k1 ++) { 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       Tcode=ivector(1,100);      for (i=1; i<= nlstate+1 ; i ++) {
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        k=2*i;
       ncodemax[1]=1;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        for (j=1; j<= nlstate+1 ; j ++) {
                if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
    codtab=imatrix(1,100,1,10);          else fprintf(ficgp," \%%*lf (\%%*lf)");
    h=0;        }   
    m=pow(2,cptcoveff);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
          else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
    for(k=1;k<=cptcoveff; k++){        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
      for(i=1; i <=(m/pow(2,k));i++){        for (j=1; j<= nlstate+1 ; j ++) {
        for(j=1; j <= ncodemax[k]; j++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
            h++;        }   
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        fprintf(ficgp,"\" t\"\" w l 0,");
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
          }        for (j=1; j<= nlstate+1 ; j ++) {
        }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
      }          else fprintf(ficgp," \%%*lf (\%%*lf)");
    }        }   
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       codtab[1][2]=1;codtab[2][2]=2; */        else fprintf(ficgp,"\" t\"\" w l 0,");
    /* for(i=1; i <=m ;i++){      }
       for(k=1; k <=cptcovn; k++){    }
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    
       }    /*3eme*/
       printf("\n");    
       }    for (k1=1; k1<= m ; k1 ++) { 
       scanf("%d",i);*/      for (cpt=1; cpt<= nlstate ; cpt ++) {
            k=2+nlstate*(2*cpt-2);
    /* Calculates basic frequencies. Computes observed prevalence at single age        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        and prints on file fileres'p'. */        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
              for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
              fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        */
              for (i=1; i< nlstate ; i ++) {
     /* For Powell, parameters are in a vector p[] starting at p[1]          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        } 
       }
     if(mle==1){    }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    
     }    /* CV preval stable (period) */
        for (k1=1; k1<= m ; k1 ++) { 
     /*--------- results files --------------*/      for (cpt=1; cpt<=nlstate ; cpt ++) {
     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);        k=3;
          fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
    jk=1;        
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        for (i=1; i<= nlstate ; i ++)
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          fprintf(ficgp,"+$%d",k+i+1);
    for(i=1,jk=1; i <=nlstate; i++){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
      for(k=1; k <=(nlstate+ndeath); k++){        
        if (k != i)        l=3+(nlstate+ndeath)*cpt;
          {        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
            printf("%d%d ",i,k);        for (i=1; i< nlstate ; i ++) {
            fprintf(ficres,"%1d%1d ",i,k);          l=3+(nlstate+ndeath)*cpt;
            for(j=1; j <=ncovmodel; j++){          fprintf(ficgp,"+$%d",l+i+1);
              printf("%f ",p[jk]);        }
              fprintf(ficres,"%f ",p[jk]);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
              jk++;      } 
            }    }  
            printf("\n");    
            fprintf(ficres,"\n");    /* proba elementaires */
          }    for(i=1,jk=1; i <=nlstate; i++){
      }      for(k=1; k <=(nlstate+ndeath); k++){
    }        if (k != i) {
  if(mle==1){          for(j=1; j <=ncovmodel; j++){
     /* Computing hessian and covariance matrix */            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     ftolhess=ftol; /* Usually correct */            jk++; 
     hesscov(matcov, p, npar, delti, ftolhess, func);            fprintf(ficgp,"\n");
  }          }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        }
     printf("# Scales (for hessian or gradient estimation)\n");      }
      for(i=1,jk=1; i <=nlstate; i++){     }
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
           fprintf(ficres,"%1d%1d",i,j);       for(jk=1; jk <=m; jk++) {
           printf("%1d%1d",i,j);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
           for(k=1; k<=ncovmodel;k++){         if (ng==2)
             printf(" %.5e",delti[jk]);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
             fprintf(ficres," %.5e",delti[jk]);         else
             jk++;           fprintf(ficgp,"\nset title \"Probability\"\n");
           }         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           printf("\n");         i=1;
           fprintf(ficres,"\n");         for(k2=1; k2<=nlstate; k2++) {
         }           k3=i;
       }           for(k=1; k<=(nlstate+ndeath); k++) {
      }             if (k != k2){
                   if(ng==2)
     k=1;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");               else
     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(ficgp," exp(p%d+p%d*x",i,i+1);
     for(i=1;i<=npar;i++){               ij=1;
       /*  if (k>nlstate) k=1;               for(j=3; j <=ncovmodel; j++) {
       i1=(i-1)/(ncovmodel*nlstate)+1;                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       printf("%s%d%d",alph[k],i1,tab[i]);*/                   ij++;
       fprintf(ficres,"%3d",i);                 }
       printf("%3d",i);                 else
       for(j=1; j<=i;j++){                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         fprintf(ficres," %.5e",matcov[i][j]);               }
         printf(" %.5e",matcov[i][j]);               fprintf(ficgp,")/(1");
       }               
       fprintf(ficres,"\n");               for(k1=1; k1 <=nlstate; k1++){   
       printf("\n");                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       k++;                 ij=1;
     }                 for(j=3; j <=ncovmodel; j++){
                       if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     while((c=getc(ficpar))=='#' && c!= EOF){                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       ungetc(c,ficpar);                     ij++;
       fgets(line, MAXLINE, ficpar);                   }
       puts(line);                   else
       fputs(line,ficparo);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     }                 }
     ungetc(c,ficpar);                 fprintf(ficgp,")");
     estepm=0;               }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     if (estepm==0 || estepm < stepm) estepm=stepm;               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     if (fage <= 2) {               i=i+ncovmodel;
       bage = ageminpar;             }
       fage = agemaxpar;           } /* end k */
     }         } /* end k2 */
           } /* end jk */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");     } /* end ng */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);     fclose(ficgp); 
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  }  /* end gnuplot */
    
     while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /*************** Moving average **************/
     fgets(line, MAXLINE, ficpar);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     puts(line);  
     fputs(line,ficparo);    int i, cpt, cptcod;
   }    int modcovmax =1;
   ungetc(c,ficpar);    int mobilavrange, mob;
      double age;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);  
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                             a covariate has 2 modalities */
          if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     fgets(line, MAXLINE, ficpar);      if(mobilav==1) mobilavrange=5; /* default */
     puts(line);      else mobilavrange=mobilav;
     fputs(line,ficparo);      for (age=bage; age<=fage; age++)
   }        for (i=1; i<=nlstate;i++)
   ungetc(c,ficpar);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
    dateprev2=anprev2+mprev2/12.+jprev2/365.;         we use a 5 terms etc. until the borders are no more concerned. 
       */ 
   fscanf(ficpar,"pop_based=%d\n",&popbased);      for (mob=3;mob <=mobilavrange;mob=mob+2){
   fprintf(ficparo,"pop_based=%d\n",popbased);          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   fprintf(ficres,"pop_based=%d\n",popbased);            for (i=1; i<=nlstate;i++){
              for (cptcod=1;cptcod<=modcovmax;cptcod++){
   while((c=getc(ficpar))=='#' && c!= EOF){              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
     ungetc(c,ficpar);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     fgets(line, MAXLINE, ficpar);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
     puts(line);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     fputs(line,ficparo);                }
   }              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   ungetc(c,ficpar);            }
           }
   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);        }/* end age */
 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);      }/* end mob */
 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);    }else return -1;
     return 0;
   }/* End movingaverage */
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  /************** Forecasting ******************/
     puts(line);  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     fputs(line,ficparo);    /* proj1, year, month, day of starting projection 
   }       agemin, agemax range of age
   ungetc(c,ficpar);       dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
   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);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    int *popage;
     double agec; /* generic age */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
 /*------------ gnuplot -------------*/    double ***p3mat;
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    double ***mobaverage;
      char fileresf[FILENAMELENGTH];
 /*------------ free_vector  -------------*/  
  chdir(path);    agelim=AGESUP;
      prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
  free_ivector(wav,1,imx);   
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    strcpy(fileresf,"f"); 
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      strcat(fileresf,fileres);
  free_ivector(num,1,n);    if((ficresf=fopen(fileresf,"w"))==NULL) {
  free_vector(agedc,1,n);      printf("Problem with forecast resultfile: %s\n", fileresf);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
  fclose(ficparo);    }
  fclose(ficres);    printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
 /*--------- index.htm --------*/  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);  
     if (mobilav!=0) {
        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*--------------- Prevalence limit --------------*/      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   strcpy(filerespl,"pl");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   strcat(filerespl,fileres);      }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }    stepsize=(int) (stepm+YEARM-1)/YEARM;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    if (stepm<=12) stepsize=1;
   fprintf(ficrespl,"#Prevalence limit\n");    if(estepm < stepm){
   fprintf(ficrespl,"#Age ");      printf ("Problem %d lower than %d\n",estepm, stepm);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    }
   fprintf(ficrespl,"\n");    else  hstepm=estepm;   
    
   prlim=matrix(1,nlstate,1,nlstate);    hstepm=hstepm/stepm; 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                                 fractional in yp1 */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    anprojmean=yp;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    yp2=modf((yp1*12),&yp);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    mprojmean=yp;
   k=0;    yp1=modf((yp2*30.5),&yp);
   agebase=ageminpar;    jprojmean=yp;
   agelim=agemaxpar;    if(jprojmean==0) jprojmean=1;
   ftolpl=1.e-10;    if(mprojmean==0) jprojmean=1;
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}    i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
         k=k+1;    
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    fprintf(ficresf,"#****** Routine prevforecast **\n");
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)  /*            if (h==(int)(YEARM*yearp)){ */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
         fprintf(ficrespl,"******\n");      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
                k=k+1;
         for (age=agebase; age<=agelim; age++){        fprintf(ficresf,"\n#******");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl,"%.0f",age );          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)        }
           fprintf(ficrespl," %.5f", prlim[i][i]);        fprintf(ficresf,"******\n");
           fprintf(ficrespl,"\n");        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         }        for(j=1; j<=nlstate+ndeath;j++){ 
       }          for(i=1; i<=nlstate;i++)              
     }            fprintf(ficresf," p%d%d",i,j);
   fclose(ficrespl);          fprintf(ficresf," p.%d",j);
         }
   /*------------- h Pij x at various ages ------------*/        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
            fprintf(ficresf,"\n");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          for (agec=fage; agec>=(ageminpar-1); agec--){ 
   }            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
   printf("Computing pij: result on file '%s' \n", filerespij);            nhstepm = nhstepm/hstepm; 
              p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   stepsize=(int) (stepm+YEARM-1)/YEARM;            oldm=oldms;savm=savms;
   /*if (stepm<=24) stepsize=2;*/            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
   agelim=AGESUP;            for (h=0; h<=nhstepm; h++){
   hstepm=stepsize*YEARM; /* Every year of age */              if (h*hstepm/YEARM*stepm ==yearp) {
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                fprintf(ficresf,"\n");
                  for(j=1;j<=cptcoveff;j++) 
   k=0;                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   for(cptcov=1;cptcov<=i1;cptcov++){                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              } 
       k=k+1;              for(j=1; j<=nlstate+ndeath;j++) {
         fprintf(ficrespij,"\n#****** ");                ppij=0.;
         for(j=1;j<=cptcoveff;j++)                for(i=1; i<=nlstate;i++) {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  if (mobilav==1) 
         fprintf(ficrespij,"******\n");                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                          else {
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                  }
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                  if (h*hstepm/YEARM*stepm== yearp) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
           oldm=oldms;savm=savms;                  }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  } /* end i */
           fprintf(ficrespij,"# Age");                if (h*hstepm/YEARM*stepm==yearp) {
           for(i=1; i<=nlstate;i++)                  fprintf(ficresf," %.3f", ppij);
             for(j=1; j<=nlstate+ndeath;j++)                }
               fprintf(ficrespij," %1d-%1d",i,j);              }/* end j */
           fprintf(ficrespij,"\n");            } /* end h */
            for (h=0; h<=nhstepm; h++){            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          } /* end agec */
             for(i=1; i<=nlstate;i++)        } /* end yearp */
               for(j=1; j<=nlstate+ndeath;j++)      } /* end cptcod */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    } /* end  cptcov */
             fprintf(ficrespij,"\n");         
              }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");    fclose(ficresf);
         }  }
     }  
   }  /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   fclose(ficrespij);    int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
   /*---------- Forecasting ------------------*/    double ***p3mat,***tabpop,***tabpopprev;
   if((stepm == 1) && (strcmp(model,".")==0)){    double ***mobaverage;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    char filerespop[FILENAMELENGTH];
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
     free_matrix(mint,1,maxwav,1,n);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_vector(weight,1,n);}    agelim=AGESUP;
   else{    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     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);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   }    
      
     strcpy(filerespop,"pop"); 
   /*---------- Health expectancies and variances ------------*/    strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
   strcpy(filerest,"t");      printf("Problem with forecast resultfile: %s\n", filerespop);
   strcat(filerest,fileres);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   if((ficrest=fopen(filerest,"w"))==NULL) {    }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    printf("Computing forecasting: result on file '%s' \n", filerespop);
   }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   strcpy(filerese,"e");    if (mobilav!=0) {
   strcat(filerese,fileres);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      }
     }
  strcpy(fileresv,"v");  
   strcat(fileresv,fileres);    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    if (stepm<=12) stepsize=1;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    
   }    agelim=AGESUP;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    
     hstepm=1;
   k=0;    hstepm=hstepm/stepm; 
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if (popforecast==1) {
       k=k+1;      if((ficpop=fopen(popfile,"r"))==NULL) {
       fprintf(ficrest,"\n#****** ");        printf("Problem with population file : %s\n",popfile);exit(0);
       for(j=1;j<=cptcoveff;j++)        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      } 
       fprintf(ficrest,"******\n");      popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       fprintf(ficreseij,"\n#****** ");      popcount=vector(0,AGESUP);
       for(j=1;j<=cptcoveff;j++)      
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      i=1;   
       fprintf(ficreseij,"******\n");      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       fprintf(ficresvij,"\n#****** ");      imx=i;
       for(j=1;j<=cptcoveff;j++)      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
       fprintf(ficresvij,"******\n");  
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       oldm=oldms;savm=savms;        k=k+1;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);          fprintf(ficrespop,"\n#******");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        for(j=1;j<=cptcoveff;j++) {
       oldm=oldms;savm=savms;          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        }
            fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
          for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        if (popforecast==1)  fprintf(ficrespop," [Population]");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        
       fprintf(ficrest,"\n");        for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
       epj=vector(1,nlstate+1);          
       for(age=bage; age <=fage ;age++){          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         if (popbased==1) {            nhstepm = nhstepm/hstepm; 
           for(i=1; i<=nlstate;i++)            
             prlim[i][i]=probs[(int)age][i][k];            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(ficrest," %4.0f",age);          
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            for (h=0; h<=nhstepm; h++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {              if (h==(int) (calagedatem+YEARM*cpt)) {
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
           }              } 
           epj[nlstate+1] +=epj[j];              for(j=1; j<=nlstate+ndeath;j++) {
         }                kk1=0.;kk2=0;
         for(i=1, vepp=0.;i <=nlstate;i++)                for(i=1; i<=nlstate;i++) {              
           for(j=1;j <=nlstate;j++)                  if (mobilav==1) 
             vepp += vareij[i][j][(int)age];                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));                  else {
         for(j=1;j <=nlstate;j++){                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                  }
         }                }
         fprintf(ficrest,"\n");                if (h==(int)(calagedatem+12*cpt)){
       }                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
     }                    /*fprintf(ficrespop," %.3f", kk1);
   }                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
   fclose(ficreseij);              }
   fclose(ficresvij);              for(i=1; i<=nlstate;i++){
   fclose(ficrest);                kk1=0.;
   fclose(ficpar);                  for(j=1; j<=nlstate;j++){
   free_vector(epj,1,nlstate+1);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                    }
   /*------- Variance limit prevalence------*/                      tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            }
     exit(0);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }          }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        }
    
   k=0;    /******/
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
       k=k+1;          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
       fprintf(ficresvpl,"\n#****** ");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
       for(j=1;j<=cptcoveff;j++)            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            nhstepm = nhstepm/hstepm; 
       fprintf(ficresvpl,"******\n");            
                  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);            oldm=oldms;savm=savms;
       oldm=oldms;savm=savms;            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            for (h=0; h<=nhstepm; h++){
     }              if (h==(int) (calagedatem+YEARM*cpt)) {
  }                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
   fclose(ficresvpl);              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
   /*---------- End : free ----------------*/                for(i=1; i<=nlstate;i++) {              
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                  }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);              }
              }
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   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);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_vector(delti,1,npar);  
   free_matrix(agev,1,maxwav,1,imx);    if (popforecast==1) {
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
   if(erreur >0)      free_vector(popcount,0,AGESUP);
     printf("End of Imach with error or warning %d\n",erreur);    }
   else   printf("End of Imach\n");    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fclose(ficrespop);
   /* 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 -----------*/  /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
  end:  
 #ifdef windows  int main(int argc, char *argv[])
   /* chdir(pathcd);*/  {
 #endif    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
  /*system("wgnuplot graph.plt");*/    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
  /*system("../gp37mgw/wgnuplot graph.plt");*/    double agedeb, agefin,hf;
  /*system("cd ../gp37mgw");*/    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    double fret;
  strcat(plotcmd," ");    double **xi,tmp,delta;
  strcat(plotcmd,optionfilegnuplot);  
  system(plotcmd);    double dum; /* Dummy variable */
     double ***p3mat;
 #ifdef windows    double ***mobaverage;
   while (z[0] != 'q') {    int *indx;
     /* chdir(path); */    char line[MAXLINE], linepar[MAXLINE];
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     scanf("%s",z);    int firstobs=1, lastobs=10;
     if (z[0] == 'c') system("./imach");    int sdeb, sfin; /* Status at beginning and end */
     else if (z[0] == 'e') system(optionfilehtm);    int c,  h , cpt,l;
     else if (z[0] == 'g') system(plotcmd);    int ju,jl, mi;
     else if (z[0] == 'q') exit(0);    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   }    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
 #endif    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
 }    int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1;
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.40  
changed lines
  Added in v.1.79


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>