Diff for /imach/src/imach.c between versions 1.51 and 1.78

version 1.51, 2002/07/19 12:22:25 version 1.78, 2003/05/27 17:26:53
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "gnuplot"    read datafile
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    concatwav
 #define FILENAMELENGTH 80    if (mle >= 1)
 /*#define DEBUG*/      mlikeli
 #define windows    print results files
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    if mle==1 
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */        begin-prev-date,...
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open gnuplot file
     open html file
 #define NINTERVMAX 8    stable prevalence
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */     for age prevalim()
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    h Pij x
 #define NCOVMAX 8 /* Maximum number of covariates */    variance of p varprob
 #define MAXN 20000    forecasting if prevfcast==1 prevforecast call prevalence()
 #define YEARM 12. /* Number of months per year */    health expectancies
 #define AGESUP 130    Variance-covariance of DFLE
 #define AGEBASE 40    prevalence()
 #ifdef windows     movingaverage()
 #define DIRSEPARATOR '\\'    varevsij() 
 #define ODIRSEPARATOR '/'    if popbased==1 varevsij(,popbased)
 #else    total life expectancies
 #define DIRSEPARATOR '/'    Variance of stable prevalence
 #define ODIRSEPARATOR '\\'   end
 #endif  */
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";  
 int erreur; /* Error number */  
 int nvar;   
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  #include <math.h>
 int npar=NPARMAX;  #include <stdio.h>
 int nlstate=2; /* Number of live states */  #include <stdlib.h>
 int ndeath=1; /* Number of dead states */  #include <unistd.h>
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 int *wav; /* Number of waves for this individuual 0 is possible */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 int maxwav; /* Maxim number of waves */  #define FILENAMELENGTH 80
 int jmin, jmax; /* min, max spacing between 2 waves */  /*#define DEBUG*/
 int mle, weightopt;  #define windows
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficlog;  #define NINTERVMAX 8
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 FILE *ficresprobmorprev;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 FILE *fichtm; /* Html File */  #define NCOVMAX 8 /* Maximum number of covariates */
 FILE *ficreseij;  #define MAXN 20000
 char filerese[FILENAMELENGTH];  #define YEARM 12. /* Number of months per year */
 FILE  *ficresvij;  #define AGESUP 130
 char fileresv[FILENAMELENGTH];  #define AGEBASE 40
 FILE  *ficresvpl;  #ifdef windows
 char fileresvpl[FILENAMELENGTH];  #define DIRSEPARATOR '\\'
 char title[MAXLINE];  #define ODIRSEPARATOR '/'
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  #else
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  #endif
 char filelog[FILENAMELENGTH]; /* Log file */  
 char filerest[FILENAMELENGTH];  char version[80]="Imach version 0.95a, May 2003, INED-EUROREVES ";
 char fileregp[FILENAMELENGTH];  int erreur; /* Error number */
 char popfile[FILENAMELENGTH];  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 #define NR_END 1  int ndeath=1; /* Number of dead states */
 #define FREE_ARG char*  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #define FTOL 1.0e-10  int popbased=0;
   
 #define NRANSI  int *wav; /* Number of waves for this individuual 0 is possible */
 #define ITMAX 200  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 #define TOL 2.0e-4  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #define CGOLD 0.3819660  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #define ZEPS 1.0e-10  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 #define GOLD 1.618034  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #define GLIMIT 100.0  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define TINY 1.0e-20  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 static double maxarg1,maxarg2;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  FILE *ficresprobmorprev;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  FILE *fichtm; /* Html File */
    FILE *ficreseij;
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char filerese[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 static double sqrarg;  FILE  *ficresvpl;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  char fileresvpl[FILENAMELENGTH];
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 int imx;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 int estepm;  char filerest[FILENAMELENGTH];
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;  #define NR_END 1
 double dateintmean=0;  #define FREE_ARG char*
   #define FTOL 1.0e-10
 double *weight;  
 int **s; /* Status */  #define NRANSI 
 double *agedc, **covar, idx;  #define ITMAX 200 
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   #define TOL 2.0e-4 
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /**************** split *************************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  #define GOLD 1.618034 
    char *s;                             /* pointer */  #define GLIMIT 100.0 
    int  l1, l2;                         /* length counters */  #define TINY 1.0e-20 
   
    l1 = strlen( path );                 /* length of path */  static double maxarg1,maxarg2;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    if ( s == NULL ) {                   /* no directory, so use current */    
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  #define rint(a) floor(a+0.5)
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       if ( getwd( dirc ) == NULL ) {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 #else  
       extern char       *getcwd( );  int imx; 
   int stepm;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  /* Stepm, step in month: minimum step interpolation*/
 #endif  
          return( GLOCK_ERROR_GETCWD );  int estepm;
       }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  int m,nb;
       s++;                              /* after this, the filename */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
       l2 = strlen( s );                 /* length of filename */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  double **pmmij, ***probs;
       strcpy( name, s );                /* save file name */  double dateintmean=0;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  double *weight;
    }  int **s; /* Status */
    l1 = strlen( dirc );                 /* length of directory */  double *agedc, **covar, idx;
 #ifdef windows  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  double ftolhess; /* Tolerance for computing hessian */
 #endif  
    s = strrchr( name, '.' );            /* find last / */  /**************** split *************************/
    s++;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    strcpy(ext,s);                       /* save extension */  {
    l1= strlen( name);    char  *ss;                            /* pointer */
    l2= strlen( s)+1;    int   l1, l2;                         /* length counters */
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    l1 = strlen(path );                   /* length of path */
    return( 0 );                         /* we're done */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 /******************************************/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* get current working directory */
 void replace(char *s, char*t)      /*    extern  char* getcwd ( char *buf , int len);*/
 {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   int i;        return( GLOCK_ERROR_GETCWD );
   int lg=20;      }
   i=0;      strcpy( name, path );               /* we've got it */
   lg=strlen(t);    } else {                              /* strip direcotry from path */
   for(i=0; i<= lg; i++) {      ss++;                               /* after this, the filename */
     (s[i] = t[i]);      l2 = strlen( ss );                  /* length of filename */
     if (t[i]== '\\') s[i]='/';      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   }      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 int nbocc(char *s, char occ)    }
 {    l1 = strlen( dirc );                  /* length of directory */
   int i,j=0;  #ifdef windows
   int lg=20;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   i=0;  #else
   lg=strlen(s);    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   for(i=0; i<= lg; i++) {  #endif
   if  (s[i] == occ ) j++;    ss = strrchr( name, '.' );            /* find last / */
   }    ss++;
   return j;    strcpy(ext,ss);                       /* save extension */
 }    l1= strlen( name);
     l2= strlen(ss)+1;
 void cutv(char *u,char *v, char*t, char occ)    strncpy( finame, name, l1-l2);
 {    finame[l1-l2]= 0;
   /* cuts string t into u and v where u is ended by char occ excluding it    return( 0 );                          /* we're done */
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  }
      gives u="abcedf" and v="ghi2j" */  
   int i,lg,j,p=0;  
   i=0;  /******************************************/
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  void replace(char *s, char*t)
   }  {
     int i;
   lg=strlen(t);    int lg=20;
   for(j=0; j<p; j++) {    i=0;
     (u[j] = t[j]);    lg=strlen(t);
   }    for(i=0; i<= lg; i++) {
      u[p]='\0';      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
    for(j=0; j<= lg; j++) {    }
     if (j>=(p+1))(v[j-p-1] = t[j]);  }
   }  
 }  int nbocc(char *s, char occ)
   {
 /********************** nrerror ********************/    int i,j=0;
     int lg=20;
 void nrerror(char error_text[])    i=0;
 {    lg=strlen(s);
   fprintf(stderr,"ERREUR ...\n");    for(i=0; i<= lg; i++) {
   fprintf(stderr,"%s\n",error_text);    if  (s[i] == occ ) j++;
   exit(1);    }
 }    return j;
 /*********************** vector *******************/  }
 double *vector(int nl, int nh)  
 {  void cutv(char *u,char *v, char*t, char occ)
   double *v;  {
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    /* cuts string t into u and v where u is ended by char occ excluding it
   if (!v) nrerror("allocation failure in vector");       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   return v-nl+NR_END;       gives u="abcedf" and v="ghi2j" */
 }    int i,lg,j,p=0;
     i=0;
 /************************ free vector ******************/    for(j=0; j<=strlen(t)-1; j++) {
 void free_vector(double*v, int nl, int nh)      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 {    }
   free((FREE_ARG)(v+nl-NR_END));  
 }    lg=strlen(t);
     for(j=0; j<p; j++) {
 /************************ivector *******************************/      (u[j] = t[j]);
 int *ivector(long nl,long nh)    }
 {       u[p]='\0';
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));     for(j=0; j<= lg; j++) {
   if (!v) nrerror("allocation failure in ivector");      if (j>=(p+1))(v[j-p-1] = t[j]);
   return v-nl+NR_END;    }
 }  }
   
 /******************free ivector **************************/  /********************** nrerror ********************/
 void free_ivector(int *v, long nl, long nh)  
 {  void nrerror(char error_text[])
   free((FREE_ARG)(v+nl-NR_END));  {
 }    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 /******************* imatrix *******************************/    exit(EXIT_FAILURE);
 int **imatrix(long nrl, long nrh, long ncl, long nch)  }
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  /*********************** vector *******************/
 {  double *vector(int nl, int nh)
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  {
   int **m;    double *v;
      v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   /* allocate pointers to rows */    if (!v) nrerror("allocation failure in vector");
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    return v-nl+NR_END;
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   m += NR_END;  
   m -= nrl;  /************************ free vector ******************/
    void free_vector(double*v, int nl, int nh)
    {
   /* allocate rows and set pointers to them */    free((FREE_ARG)(v+nl-NR_END));
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  /************************ivector *******************************/
   m[nrl] -= ncl;  char *cvector(long nl,long nh)
    {
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    char *v;
      v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   /* return pointer to array of pointers to rows */    if (!v) nrerror("allocation failure in cvector");
   return m;    return v-nl+NR_END;
 }  }
   
 /****************** free_imatrix *************************/  /******************free ivector **************************/
 void free_imatrix(m,nrl,nrh,ncl,nch)  void free_cvector(char *v, long nl, long nh)
       int **m;  {
       long nch,ncl,nrh,nrl;    free((FREE_ARG)(v+nl-NR_END));
      /* free an int matrix allocated by imatrix() */  }
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  /************************ivector *******************************/
   free((FREE_ARG) (m+nrl-NR_END));  int *ivector(long nl,long nh)
 }  {
     int *v;
 /******************* matrix *******************************/    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 double **matrix(long nrl, long nrh, long ncl, long nch)    if (!v) nrerror("allocation failure in ivector");
 {    return v-nl+NR_END;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+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; 
   return m;    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 /*************************free matrix ************************/    if (!m) nrerror("allocation failure 1 in matrix()"); 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    m += NR_END; 
 {    m -= nrl; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    
   free((FREE_ARG)(m+nrl-NR_END));    
 }    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 /******************* ma3x *******************************/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    m[nrl] += NR_END; 
 {    m[nrl] -= ncl; 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    
   double ***m;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    /* return pointer to array of pointers to rows */ 
   if (!m) nrerror("allocation failure 1 in matrix()");    return m; 
   m += NR_END;  } 
   m -= nrl;  
   /****************** free_imatrix *************************/
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  void free_imatrix(m,nrl,nrh,ncl,nch)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");        int **m;
   m[nrl] += NR_END;        long nch,ncl,nrh,nrl; 
   m[nrl] -= ncl;       /* free an int matrix allocated by imatrix() */ 
   { 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  } 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  /******************* matrix *******************************/
   m[nrl][ncl] -= nll;  double **matrix(long nrl, long nrh, long ncl, long nch)
   for (j=ncl+1; j<=nch; j++)  {
     m[nrl][j]=m[nrl][j-1]+nlay;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
      double **m;
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for (j=ncl+1; j<=nch; j++)    if (!m) nrerror("allocation failure 1 in matrix()");
       m[i][j]=m[i][j-1]+nlay;    m += NR_END;
   }    m -= nrl;
   return m;  
 }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 /*************************free ma3x ************************/    m[nrl] += NR_END;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m[nrl] -= ncl;
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    return m;
   free((FREE_ARG)(m+nrl-NR_END));    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
 }     */
   }
 /***************** f1dim *************************/  
 extern int ncom;  /*************************free matrix ************************/
 extern double *pcom,*xicom;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 extern double (*nrfunc)(double []);  {
      free((FREE_ARG)(m[nrl]+ncl-NR_END));
 double f1dim(double x)    free((FREE_ARG)(m+nrl-NR_END));
 {  }
   int j;  
   double f;  /******************* ma3x *******************************/
   double *xt;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
    {
   xt=vector(1,ncom);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    double ***m;
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   return f;    if (!m) nrerror("allocation failure 1 in matrix()");
 }    m += NR_END;
     m -= nrl;
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   int iter;    m[nrl] += NR_END;
   double a,b,d,etemp;    m[nrl] -= ncl;
   double fu,fv,fw,fx;  
   double ftemp;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
      if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   a=(ax < cx ? ax : cx);    m[nrl][ncl] += NR_END;
   b=(ax > cx ? ax : cx);    m[nrl][ncl] -= nll;
   x=w=v=bx;    for (j=ncl+1; j<=nch; j++) 
   fw=fv=fx=(*f)(x);      m[nrl][j]=m[nrl][j-1]+nlay;
   for (iter=1;iter<=ITMAX;iter++) {    
     xm=0.5*(a+b);    for (i=nrl+1; i<=nrh; i++) {
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      for (j=ncl+1; j<=nch; j++) 
     printf(".");fflush(stdout);        m[i][j]=m[i][j-1]+nlay;
     fprintf(ficlog,".");fflush(ficlog);    }
 #ifdef DEBUG    return m; 
     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);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    */
 #endif  }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /*************************free ma3x ************************/
       return fx;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     }  {
     ftemp=fu;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     if (fabs(e) > tol1) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       r=(x-w)*(fx-fv);    free((FREE_ARG)(m+nrl-NR_END));
       q=(x-v)*(fx-fw);  }
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  /***************** f1dim *************************/
       if (q > 0.0) p = -p;  extern int ncom; 
       q=fabs(q);  extern double *pcom,*xicom;
       etemp=e;  extern double (*nrfunc)(double []); 
       e=d;   
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  double f1dim(double x) 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  { 
       else {    int j; 
         d=p/q;    double f;
         u=x+d;    double *xt; 
         if (u-a < tol2 || b-u < tol2)   
           d=SIGN(tol1,xm-x);    xt=vector(1,ncom); 
       }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     } else {    f=(*nrfunc)(xt); 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    free_vector(xt,1,ncom); 
     }    return f; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  } 
     fu=(*f)(u);  
     if (fu <= fx) {  /*****************brent *************************/
       if (u >= x) a=x; else b=x;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       SHFT(v,w,x,u)  { 
         SHFT(fv,fw,fx,fu)    int iter; 
         } else {    double a,b,d,etemp;
           if (u < x) a=u; else b=u;    double fu,fv,fw,fx;
           if (fu <= fw || w == x) {    double ftemp;
             v=w;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
             w=u;    double e=0.0; 
             fv=fw;   
             fw=fu;    a=(ax < cx ? ax : cx); 
           } else if (fu <= fv || v == x || v == w) {    b=(ax > cx ? ax : cx); 
             v=u;    x=w=v=bx; 
             fv=fu;    fw=fv=fx=(*f)(x); 
           }    for (iter=1;iter<=ITMAX;iter++) { 
         }      xm=0.5*(a+b); 
   }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   nrerror("Too many iterations in brent");      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   *xmin=x;      printf(".");fflush(stdout);
   return fx;      fprintf(ficlog,".");fflush(ficlog);
 }  #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);
 /****************** mnbrak ***********************/      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #endif
             double (*func)(double))      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 {        *xmin=x; 
   double ulim,u,r,q, dum;        return fx; 
   double fu;      } 
        ftemp=fu;
   *fa=(*func)(*ax);      if (fabs(e) > tol1) { 
   *fb=(*func)(*bx);        r=(x-w)*(fx-fv); 
   if (*fb > *fa) {        q=(x-v)*(fx-fw); 
     SHFT(dum,*ax,*bx,dum)        p=(x-v)*q-(x-w)*r; 
       SHFT(dum,*fb,*fa,dum)        q=2.0*(q-r); 
       }        if (q > 0.0) p = -p; 
   *cx=(*bx)+GOLD*(*bx-*ax);        q=fabs(q); 
   *fc=(*func)(*cx);        etemp=e; 
   while (*fb > *fc) {        e=d; 
     r=(*bx-*ax)*(*fb-*fc);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     q=(*bx-*cx)*(*fb-*fa);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        else { 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));          d=p/q; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);          u=x+d; 
     if ((*bx-u)*(u-*cx) > 0.0) {          if (u-a < tol2 || b-u < tol2) 
       fu=(*func)(u);            d=SIGN(tol1,xm-x); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {        } 
       fu=(*func)(u);      } else { 
       if (fu < *fc) {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      } 
           SHFT(*fb,*fc,fu,(*func)(u))      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
           }      fu=(*f)(u); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      if (fu <= fx) { 
       u=ulim;        if (u >= x) a=x; else b=x; 
       fu=(*func)(u);        SHFT(v,w,x,u) 
     } else {          SHFT(fv,fw,fx,fu) 
       u=(*cx)+GOLD*(*cx-*bx);          } else { 
       fu=(*func)(u);            if (u < x) a=u; else b=u; 
     }            if (fu <= fw || w == x) { 
     SHFT(*ax,*bx,*cx,u)              v=w; 
       SHFT(*fa,*fb,*fc,fu)              w=u; 
       }              fv=fw; 
 }              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
 /*************** linmin ************************/              v=u; 
               fv=fu; 
 int ncom;            } 
 double *pcom,*xicom;          } 
 double (*nrfunc)(double []);    } 
      nrerror("Too many iterations in brent"); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    *xmin=x; 
 {    return fx; 
   double brent(double ax, double bx, double cx,  } 
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  /****************** mnbrak ***********************/
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   int j;              double (*func)(double)) 
   double xx,xmin,bx,ax;  { 
   double fx,fb,fa;    double ulim,u,r,q, dum;
      double fu; 
   ncom=n;   
   pcom=vector(1,n);    *fa=(*func)(*ax); 
   xicom=vector(1,n);    *fb=(*func)(*bx); 
   nrfunc=func;    if (*fb > *fa) { 
   for (j=1;j<=n;j++) {      SHFT(dum,*ax,*bx,dum) 
     pcom[j]=p[j];        SHFT(dum,*fb,*fa,dum) 
     xicom[j]=xi[j];        } 
   }    *cx=(*bx)+GOLD*(*bx-*ax); 
   ax=0.0;    *fc=(*func)(*cx); 
   xx=1.0;    while (*fb > *fc) { 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      r=(*bx-*ax)*(*fb-*fc); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      q=(*bx-*cx)*(*fb-*fa); 
 #ifdef DEBUG      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 #endif      if ((*bx-u)*(u-*cx) > 0.0) { 
   for (j=1;j<=n;j++) {        fu=(*func)(u); 
     xi[j] *= xmin;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     p[j] += xi[j];        fu=(*func)(u); 
   }        if (fu < *fc) { 
   free_vector(xicom,1,n);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   free_vector(pcom,1,n);            SHFT(*fb,*fc,fu,(*func)(u)) 
 }            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 /*************** powell ************************/        u=ulim; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,        fu=(*func)(u); 
             double (*func)(double []))      } else { 
 {        u=(*cx)+GOLD*(*cx-*bx); 
   void linmin(double p[], double xi[], int n, double *fret,        fu=(*func)(u); 
               double (*func)(double []));      } 
   int i,ibig,j;      SHFT(*ax,*bx,*cx,u) 
   double del,t,*pt,*ptt,*xit;        SHFT(*fa,*fb,*fc,fu) 
   double fp,fptt;        } 
   double *xits;  } 
   pt=vector(1,n);  
   ptt=vector(1,n);  /*************** linmin ************************/
   xit=vector(1,n);  
   xits=vector(1,n);  int ncom; 
   *fret=(*func)(p);  double *pcom,*xicom;
   for (j=1;j<=n;j++) pt[j]=p[j];  double (*nrfunc)(double []); 
   for (*iter=1;;++(*iter)) {   
     fp=(*fret);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     ibig=0;  { 
     del=0.0;    double brent(double ax, double bx, double cx, 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);                 double (*f)(double), double tol, double *xmin); 
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    double f1dim(double x); 
     for (i=1;i<=n;i++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       printf(" %d %.12f",i, p[i]);                double *fc, double (*func)(double)); 
     fprintf(ficlog," %d %.12f",i, p[i]);    int j; 
     printf("\n");    double xx,xmin,bx,ax; 
     fprintf(ficlog,"\n");    double fx,fb,fa;
     for (i=1;i<=n;i++) {   
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    ncom=n; 
       fptt=(*fret);    pcom=vector(1,n); 
 #ifdef DEBUG    xicom=vector(1,n); 
       printf("fret=%lf \n",*fret);    nrfunc=func; 
       fprintf(ficlog,"fret=%lf \n",*fret);    for (j=1;j<=n;j++) { 
 #endif      pcom[j]=p[j]; 
       printf("%d",i);fflush(stdout);      xicom[j]=xi[j]; 
       fprintf(ficlog,"%d",i);fflush(ficlog);    } 
       linmin(p,xit,n,fret,func);    ax=0.0; 
       if (fabs(fptt-(*fret)) > del) {    xx=1.0; 
         del=fabs(fptt-(*fret));    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         ibig=i;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       }  #ifdef DEBUG
 #ifdef DEBUG    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       printf("%d %.12e",i,(*fret));    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       fprintf(ficlog,"%d %.12e",i,(*fret));  #endif
       for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      xi[j] *= xmin; 
         printf(" x(%d)=%.12e",j,xit[j]);      p[j] += xi[j]; 
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);    } 
       }    free_vector(xicom,1,n); 
       for(j=1;j<=n;j++) {    free_vector(pcom,1,n); 
         printf(" p=%.12e",p[j]);  } 
         fprintf(ficlog," p=%.12e",p[j]);  
       }  /*************** powell ************************/
       printf("\n");  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       fprintf(ficlog,"\n");              double (*func)(double [])) 
 #endif  { 
     }    void linmin(double p[], double xi[], int n, double *fret, 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {                double (*func)(double [])); 
 #ifdef DEBUG    int i,ibig,j; 
       int k[2],l;    double del,t,*pt,*ptt,*xit;
       k[0]=1;    double fp,fptt;
       k[1]=-1;    double *xits;
       printf("Max: %.12e",(*func)(p));    pt=vector(1,n); 
       fprintf(ficlog,"Max: %.12e",(*func)(p));    ptt=vector(1,n); 
       for (j=1;j<=n;j++) {    xit=vector(1,n); 
         printf(" %.12e",p[j]);    xits=vector(1,n); 
         fprintf(ficlog," %.12e",p[j]);    *fret=(*func)(p); 
       }    for (j=1;j<=n;j++) pt[j]=p[j]; 
       printf("\n");    for (*iter=1;;++(*iter)) { 
       fprintf(ficlog,"\n");      fp=(*fret); 
       for(l=0;l<=1;l++) {      ibig=0; 
         for (j=1;j<=n;j++) {      del=0.0; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      fprintf(ficrespow,"%d %.12f",*iter,*fret);
         }      for (i=1;i<=n;i++) {
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        fprintf(ficlog," %d %.12lf",i, p[i]);
       }        fprintf(ficrespow," %.12lf", p[i]);
 #endif      }
       printf("\n");
       fprintf(ficlog,"\n");
       free_vector(xit,1,n);      fprintf(ficrespow,"\n");
       free_vector(xits,1,n);      for (i=1;i<=n;i++) { 
       free_vector(ptt,1,n);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       free_vector(pt,1,n);        fptt=(*fret); 
       return;  #ifdef DEBUG
     }        printf("fret=%lf \n",*fret);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        fprintf(ficlog,"fret=%lf \n",*fret);
     for (j=1;j<=n;j++) {  #endif
       ptt[j]=2.0*p[j]-pt[j];        printf("%d",i);fflush(stdout);
       xit[j]=p[j]-pt[j];        fprintf(ficlog,"%d",i);fflush(ficlog);
       pt[j]=p[j];        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
     fptt=(*func)(ptt);          del=fabs(fptt-(*fret)); 
     if (fptt < fp) {          ibig=i; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        } 
       if (t < 0.0) {  #ifdef DEBUG
         linmin(p,xit,n,fret,func);        printf("%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {        fprintf(ficlog,"%d %.12e",i,(*fret));
           xi[j][ibig]=xi[j][n];        for (j=1;j<=n;j++) {
           xi[j][n]=xit[j];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         }          printf(" x(%d)=%.12e",j,xit[j]);
 #ifdef DEBUG          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        }
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        for(j=1;j<=n;j++) {
         for(j=1;j<=n;j++){          printf(" p=%.12e",p[j]);
           printf(" %.12e",xit[j]);          fprintf(ficlog," p=%.12e",p[j]);
           fprintf(ficlog," %.12e",xit[j]);        }
         }        printf("\n");
         printf("\n");        fprintf(ficlog,"\n");
         fprintf(ficlog,"\n");  #endif
 #endif      } 
       }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
   }        int k[2],l;
 }        k[0]=1;
         k[1]=-1;
 /**** Prevalence limit ****************/        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        for (j=1;j<=n;j++) {
 {          printf(" %.12e",p[j]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          fprintf(ficlog," %.12e",p[j]);
      matrix by transitions matrix until convergence is reached */        }
         printf("\n");
   int i, ii,j,k;        fprintf(ficlog,"\n");
   double min, max, maxmin, maxmax,sumnew=0.;        for(l=0;l<=1;l++) {
   double **matprod2();          for (j=1;j<=n;j++) {
   double **out, cov[NCOVMAX], **pmij();            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   double **newm;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double agefin, delaymax=50 ; /* Max number of years to converge */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
   for (ii=1;ii<=nlstate+ndeath;ii++)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (j=1;j<=nlstate+ndeath;j++){          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        }
     }  #endif
   
    cov[1]=1.;  
          free_vector(xit,1,n); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        free_vector(xits,1,n); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        free_vector(ptt,1,n); 
     newm=savm;        free_vector(pt,1,n); 
     /* Covariates have to be included here again */        return; 
      cov[2]=agefin;      } 
        if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (k=1; k<=cptcovn;k++) {      for (j=1;j<=n;j++) { 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        ptt[j]=2.0*p[j]-pt[j]; 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/        xit[j]=p[j]-pt[j]; 
       }        pt[j]=p[j]; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      } 
       for (k=1; k<=cptcovprod;k++)      fptt=(*func)(ptt); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        if (t < 0.0) { 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          linmin(p,xit,n,fret,func); 
       /*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);            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
     savm=oldm;          }
     oldm=newm;  #ifdef DEBUG
     maxmax=0.;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(j=1;j<=nlstate;j++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       min=1.;          for(j=1;j<=n;j++){
       max=0.;            printf(" %.12e",xit[j]);
       for(i=1; i<=nlstate; i++) {            fprintf(ficlog," %.12e",xit[j]);
         sumnew=0;          }
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          printf("\n");
         prlim[i][j]= newm[i][j]/(1-sumnew);          fprintf(ficlog,"\n");
         max=FMAX(max,prlim[i][j]);  #endif
         min=FMIN(min,prlim[i][j]);        }
       }      } 
       maxmin=max-min;    } 
       maxmax=FMAX(maxmax,maxmin);  } 
     }  
     if(maxmax < ftolpl){  /**** Prevalence limit (stable prevalence)  ****************/
       return prlim;  
     }  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 */
 /*************** transition probabilities ***************/  
     int i, ii,j,k;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    double min, max, maxmin, maxmax,sumnew=0.;
 {    double **matprod2();
   double s1, s2;    double **out, cov[NCOVMAX], **pmij();
   /*double t34;*/    double **newm;
   int i,j,j1, nc, ii, jj;    double agefin, delaymax=50 ; /* Max number of years to converge */
   
     for(i=1; i<= nlstate; i++){    for (ii=1;ii<=nlstate+ndeath;ii++)
     for(j=1; j<i;j++){      for (j=1;j<=nlstate+ndeath;j++){
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         /*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);*/     cov[1]=1.;
       }   
       ps[i][j]=s2;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     }      newm=savm;
     for(j=i+1; j<=nlstate+ndeath;j++){      /* Covariates have to be included here again */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       cov[2]=agefin;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        for (k=1; k<=cptcovn;k++) {
       }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       ps[i][j]=s2;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     }        }
   }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     /*ps[3][2]=1;*/        for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for(i=1; i<= nlstate; i++){  
      s1=0;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for(j=1; j<i; j++)        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       s1+=exp(ps[i][j]);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     for(j=i+1; j<=nlstate+ndeath; j++)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);      savm=oldm;
     for(j=1; j<i; j++)      oldm=newm;
       ps[i][j]= exp(ps[i][j])*ps[i][i];      maxmax=0.;
     for(j=i+1; j<=nlstate+ndeath; j++)      for(j=1;j<=nlstate;j++){
       ps[i][j]= exp(ps[i][j])*ps[i][i];        min=1.;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        max=0.;
   } /* end i */        for(i=1; i<=nlstate; i++) {
           sumnew=0;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for(jj=1; jj<= nlstate+ndeath; jj++){          prlim[i][j]= newm[i][j]/(1-sumnew);
       ps[ii][jj]=0;          max=FMAX(max,prlim[i][j]);
       ps[ii][ii]=1;          min=FMIN(min,prlim[i][j]);
     }        }
   }        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
       }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      if(maxmax < ftolpl){
     for(jj=1; jj<= nlstate+ndeath; jj++){        return prlim;
      printf("%lf ",ps[ii][jj]);      }
    }    }
     printf("\n ");  }
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  /*************** transition probabilities ***************/ 
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   goto end;*/  {
     return ps;    double s1, s2;
 }    /*double t34;*/
     int i,j,j1, nc, ii, jj;
 /**************** Product of 2 matrices ******************/  
       for(i=1; i<= nlstate; i++){
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      for(j=1; j<i;j++){
 {        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          /*s2 += param[i][j][nc]*cov[nc];*/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   /* in, b, out are matrice of pointers which should have been initialized          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
      before: only the contents of out is modified. The function returns        }
      a pointer to pointers identical to out */        ps[i][j]=s2;
   long i, j, k;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   for(i=nrl; i<= nrh; i++)      }
     for(k=ncolol; k<=ncoloh; k++)      for(j=i+1; j<=nlstate+ndeath;j++){
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         out[i][k] +=in[i][j]*b[j][k];          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   return out;        }
 }        ps[i][j]=s2;
       }
     }
 /************* Higher Matrix Product ***************/      /*ps[3][2]=1;*/
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    for(i=1; i<= nlstate; i++){
 {       s1=0;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      for(j=1; j<i; j++)
      duration (i.e. until        s1+=exp(ps[i][j]);
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      for(j=i+1; j<=nlstate+ndeath; j++)
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        s1+=exp(ps[i][j]);
      (typically every 2 years instead of every month which is too big).      ps[i][i]=1./(s1+1.);
      Model is determined by parameters x and covariates have to be      for(j=1; j<i; j++)
      included manually here.        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
      */        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   int i, j, d, h, k;    } /* end i */
   double **out, cov[NCOVMAX];  
   double **newm;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
   /* Hstepm could be zero and should return the unit matrix */        ps[ii][jj]=0;
   for (i=1;i<=nlstate+ndeath;i++)        ps[ii][ii]=1;
     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 */    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   for(h=1; h <=nhstepm; h++){      for(jj=1; jj<= nlstate+ndeath; jj++){
     for(d=1; d <=hstepm; d++){       printf("%lf ",ps[ii][jj]);
       newm=savm;     }
       /* Covariates have to be included here again */      printf("\n ");
       cov[1]=1.;      }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      printf("\n ");printf("%lf ",cov[2]);*/
       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<= npar; i++) printf("%f ",x[i]);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    goto end;*/
       for (k=1; k<=cptcovprod;k++)      return ps;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  }
   
   /**************** Product of 2 matrices ******************/
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  {
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       savm=oldm;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       oldm=newm;    /* in, b, out are matrice of pointers which should have been initialized 
     }       before: only the contents of out is modified. The function returns
     for(i=1; i<=nlstate+ndeath; i++)       a pointer to pointers identical to out */
       for(j=1;j<=nlstate+ndeath;j++) {    long i, j, k;
         po[i][j][h]=newm[i][j];    for(i=nrl; i<= nrh; i++)
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      for(k=ncolol; k<=ncoloh; k++)
          */        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       }          out[i][k] +=in[i][j]*b[j][k];
   } /* end h */  
   return po;    return out;
 }  }
   
   
 /*************** log-likelihood *************/  /************* Higher Matrix Product ***************/
 double func( double *x)  
 {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   int i, ii, j, k, mi, d, kk;  {
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    /* Computes the transition matrix starting at age 'age' over 
   double **out;       'nhstepm*hstepm*stepm' months (i.e. until
   double sw; /* Sum of weights */       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   double lli; /* Individual log likelihood */       nhstepm*hstepm matrices. 
   long ipmx;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   /*extern weight */       (typically every 2 years instead of every month which is too big 
   /* We are differentiating ll according to initial status */       for the memory).
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/       Model is determined by parameters x and covariates have to be 
   /*for(i=1;i<imx;i++)       included manually here. 
     printf(" %d\n",s[4][i]);  
   */       */
   cov[1]=1.;  
     int i, j, d, h, k;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    double **out, cov[NCOVMAX];
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    double **newm;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  
     for(mi=1; mi<= wav[i]-1; mi++){    /* Hstepm could be zero and should return the unit matrix */
       for (ii=1;ii<=nlstate+ndeath;ii++)    for (i=1;i<=nlstate+ndeath;i++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      for (j=1;j<=nlstate+ndeath;j++){
       for(d=0; d<dh[mi][i]; d++){        oldm[i][j]=(i==j ? 1.0 : 0.0);
         newm=savm;        po[i][j][0]=(i==j ? 1.0 : 0.0);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      }
         for (kk=1; kk<=cptcovage;kk++) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    for(h=1; h <=nhstepm; h++){
         }      for(d=1; d <=hstepm; d++){
                newm=savm;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        /* Covariates have to be included here again */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        cov[1]=1.;
         savm=oldm;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         oldm=newm;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                for (k=1; k<=cptcovage;k++)
                  cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       } /* end mult */        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]]];
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       sw += weight[i];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     } /* end of wave */                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   } /* end of individual */        savm=oldm;
         oldm=newm;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      for(i=1; i<=nlstate+ndeath; i++)
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        for(j=1;j<=nlstate+ndeath;j++) {
   return -l;          po[i][j][h]=newm[i][j];
 }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
            */
         }
 /*********** Maximum Likelihood Estimation ***************/    } /* end h */
     return po;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  }
 {  
   int i,j, iter;  
   double **xi,*delti;  /*************** log-likelihood *************/
   double fret;  double func( double *x)
   xi=matrix(1,npar,1,npar);  {
   for (i=1;i<=npar;i++)    int i, ii, j, k, mi, d, kk;
     for (j=1;j<=npar;j++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       xi[i][j]=(i==j ? 1.0 : 0.0);    double **out;
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    double sw; /* Sum of weights */
   powell(p,xi,npar,ftol,&iter,&fret,func);    double lli; /* Individual log likelihood */
     int s1, s2;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    double bbh, survp;
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    long ipmx;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    /*extern weight */
     /* We are differentiating ll according to initial status */
 }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
 /**** Computes Hessian and covariance matrix ***/      printf(" %d\n",s[4][i]);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    */
 {    cov[1]=1.;
   double  **a,**y,*x,pd;  
   double **hess;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   int i, j,jk;  
   int *indx;    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double hessii(double p[], double delta, int theta, double delti[]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double hessij(double p[], double delti[], int i, int j);        for(mi=1; mi<= wav[i]-1; mi++){
   void lubksb(double **a, int npar, int *indx, double b[]) ;          for (ii=1;ii<=nlstate+ndeath;ii++)
   void ludcmp(double **a, int npar, int *indx, double *d) ;            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   hess=matrix(1,npar,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   printf("\nCalculation of the hessian matrix. Wait...\n");          for(d=0; d<dh[mi][i]; d++){
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");            newm=savm;
   for (i=1;i<=npar;i++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     printf("%d",i);fflush(stdout);            for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficlog,"%d",i);fflush(ficlog);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     hess[i][i]=hessii(p,ftolhess,i,delti);            }
     /*printf(" %f ",p[i]);*/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     /*printf(" %lf ",hess[i][i]);*/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
              oldm=newm;
   for (i=1;i<=npar;i++) {          } /* end mult */
     for (j=1;j<=npar;j++)  {        
       if (j>i) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         printf(".%d%d",i,j);fflush(stdout);          /* But now since version 0.9 we anticipate for bias and large stepm.
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         hess[i][j]=hessij(p,delti,i,j);           * (in months) between two waves is not a multiple of stepm, we rounded to 
         hess[j][i]=hess[i][j];               * the nearest (and in case of equal distance, to the lowest) interval but now
         /*printf(" %lf ",hess[i][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
     }           * 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
   printf("\n");           * -stepm/2 to stepm/2 .
   fprintf(ficlog,"\n");           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");           */
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   a=matrix(1,npar,1,npar);          bbh=(double)bh[mi][i]/(double)stepm; 
   y=matrix(1,npar,1,npar);          /* bias is positive if real duration
   x=vector(1,npar);           * is higher than the multiple of stepm and negative otherwise.
   indx=ivector(1,npar);           */
   for (i=1;i<=npar;i++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          if( s2 > nlstate){ 
   ludcmp(a,npar,indx,&pd);            /* i.e. if s2 is a death state and if the date of death is known then the contribution
                to the likelihood is the probability to die between last step unit time and current 
   for (j=1;j<=npar;j++) {               step unit time, which is also the differences between probability to die before dh 
     for (i=1;i<=npar;i++) x[i]=0;               and probability to die before dh-stepm . 
     x[j]=1;               In version up to 0.92 likelihood was computed
     lubksb(a,npar,indx,x);          as if date of death was unknown. Death was treated as any other
     for (i=1;i<=npar;i++){          health state: the date of the interview describes the actual state
       matcov[i][j]=x[i];          and not the date of a change in health state. The former idea was
     }          to consider that at each interview the state was recorded
   }          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
   printf("\n#Hessian matrix#\n");          the contribution of an exact death to the likelihood. This new
   fprintf(ficlog,"\n#Hessian matrix#\n");          contribution is smaller and very dependent of the step unit
   for (i=1;i<=npar;i++) {          stepm. It is no more the probability to die between last interview
     for (j=1;j<=npar;j++) {          and month of death but the probability to survive from last
       printf("%.3e ",hess[i][j]);          interview up to one month before death multiplied by the
       fprintf(ficlog,"%.3e ",hess[i][j]);          probability to die within a month. Thanks to Chris
     }          Jackson for correcting this bug.  Former versions increased
     printf("\n");          mortality artificially. The bad side is that we add another loop
     fprintf(ficlog,"\n");          which slows down the processing. The difference can be up to 10%
   }          lower mortality.
             */
   /* Recompute Inverse */            lli=log(out[s1][s2] - savm[s1][s2]);
   for (i=1;i<=npar;i++)          }else{
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   ludcmp(a,npar,indx,&pd);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
   /*  printf("\n#Hessian matrix recomputed#\n");          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
   for (j=1;j<=npar;j++) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     for (i=1;i<=npar;i++) x[i]=0;          ipmx +=1;
     x[j]=1;          sw += weight[i];
     lubksb(a,npar,indx,x);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1;i<=npar;i++){        } /* end of wave */
       y[i][j]=x[i];      } /* end of individual */
       printf("%.3e ",y[i][j]);    }  else if(mle==2){
       fprintf(ficlog,"%.3e ",y[i][j]);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     printf("\n");        for(mi=1; mi<= wav[i]-1; mi++){
     fprintf(ficlog,"\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_matrix(a,1,npar,1,npar);            }
   free_matrix(y,1,npar,1,npar);          for(d=0; d<=dh[mi][i]; d++){
   free_vector(x,1,npar);            newm=savm;
   free_ivector(indx,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_matrix(hess,1,npar,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /*************** hessian matrix ****************/            savm=oldm;
 double hessii( double x[], double delta, int theta, double delti[])            oldm=newm;
 {          } /* end mult */
   int i;        
   int l=1, lmax=20;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double k1,k2;          /* But now since version 0.9 we anticipate for bias and large stepm.
   double p2[NPARMAX+1];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double res;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double fx;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int k=0,kmax=10;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   double l1;           * 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
   fx=func(x);           * -stepm/2 to stepm/2 .
   for (i=1;i<=npar;i++) p2[i]=x[i];           * For stepm=1 the results are the same as for previous versions of Imach.
   for(l=0 ; l <=lmax; l++){           * For stepm > 1 the results are less biased than in previous versions. 
     l1=pow(10,l);           */
     delts=delt;          s1=s[mw[mi][i]][i];
     for(k=1 ; k <kmax; k=k+1){          s2=s[mw[mi+1][i]][i];
       delt = delta*(l1*k);          bbh=(double)bh[mi][i]/(double)stepm; 
       p2[theta]=x[theta] +delt;          /* bias is positive if real duration
       k1=func(p2)-fx;           * is higher than the multiple of stepm and negative otherwise.
       p2[theta]=x[theta]-delt;           */
       k2=func(p2)-fx;          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 */
       /*res= (k1-2.0*fx+k2)/delt/delt; */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          /*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]);*/
 #ifdef DEBUG          /*if(lli ==000.0)*/
       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);          /*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); */
       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);          ipmx +=1;
 #endif          sw += weight[i];
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        } /* end of wave */
         k=kmax;      } /* end of individual */
       }    }  else if(mle==3){  /* exponential inter-extrapolation */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         k=kmax; l=lmax*10.;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          for (ii=1;ii<=nlstate+ndeath;ii++)
         delts=delt;            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   delti[theta]=delts;          for(d=0; d<dh[mi][i]; d++){
   return res;            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 double hessij( double x[], double delti[], int thetai,int thetaj)            }
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int l=1, l1, lmax=20;            savm=oldm;
   double k1,k2,k3,k4,res,fx;            oldm=newm;
   double p2[NPARMAX+1];          } /* end mult */
   int k;        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   fx=func(x);          /* But now since version 0.9 we anticipate for bias and large stepm.
   for (k=1; k<=2; k++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (i=1;i<=npar;i++) p2[i]=x[i];           * (in months) between two waves is not a multiple of stepm, we rounded to 
     p2[thetai]=x[thetai]+delti[thetai]/k;           * the nearest (and in case of equal distance, to the lowest) interval but now
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     k1=func(p2)-fx;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
             * probability in order to take into account the bias as a fraction of the way
     p2[thetai]=x[thetai]+delti[thetai]/k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * -stepm/2 to stepm/2 .
     k2=func(p2)-fx;           * 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. 
     p2[thetai]=x[thetai]-delti[thetai]/k;           */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          s1=s[mw[mi][i]][i];
     k3=func(p2)-fx;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
     p2[thetai]=x[thetai]-delti[thetai]/k;          /* bias is positive if real duration
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * is higher than the multiple of stepm and negative otherwise.
     k4=func(p2)-fx;           */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          /* 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 */
 #ifdef DEBUG          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 */
     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);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);          /*if(lli ==000.0)*/
 #endif          /*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;
   return res;          sw += weight[i];
 }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
 /************** Inverse of matrix **************/      } /* end of individual */
 void ludcmp(double **a, int n, int *indx, double *d)    }else{  /* ml=4 no inter-extrapolation */
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i,imax,j,k;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double big,dum,sum,temp;        for(mi=1; mi<= wav[i]-1; mi++){
   double *vv;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   vv=vector(1,n);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   *d=1.0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=n;i++) {            }
     big=0.0;          for(d=0; d<dh[mi][i]; d++){
     for (j=1;j<=n;j++)            newm=savm;
       if ((temp=fabs(a[i][j])) > big) big=temp;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            for (kk=1; kk<=cptcovage;kk++) {
     vv[i]=1.0/big;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   for (j=1;j<=n;j++) {          
     for (i=1;i<j;i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       sum=a[i][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            savm=oldm;
       a[i][j]=sum;            oldm=newm;
     }          } /* end mult */
     big=0.0;        
     for (i=j;i<=n;i++) {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       sum=a[i][j];          ipmx +=1;
       for (k=1;k<j;k++)          sw += weight[i];
         sum -= a[i][k]*a[k][j];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       a[i][j]=sum;        } /* end of wave */
       if ( (dum=vv[i]*fabs(sum)) >= big) {      } /* end of individual */
         big=dum;    } /* End of if */
         imax=i;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* 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 */
     if (j != imax) {    return -l;
       for (k=1;k<=n;k++) {  }
         dum=a[imax][k];  
         a[imax][k]=a[j][k];  
         a[j][k]=dum;  /*********** Maximum Likelihood Estimation ***************/
       }  
       *d = -(*d);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       vv[imax]=vv[j];  {
     }    int i,j, iter;
     indx[j]=imax;    double **xi;
     if (a[j][j] == 0.0) a[j][j]=TINY;    double fret;
     if (j != n) {    char filerespow[FILENAMELENGTH];
       dum=1.0/(a[j][j]);    xi=matrix(1,npar,1,npar);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++)
   }        xi[i][j]=(i==j ? 1.0 : 0.0);
   free_vector(vv,1,n);  /* Doesn't work */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
 ;    strcpy(filerespow,"pow"); 
 }    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
 void lubksb(double **a, int n, int *indx, double b[])      printf("Problem with resultfile: %s\n", filerespow);
 {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   int i,ii=0,ip,j;    }
   double sum;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
      for (i=1;i<=nlstate;i++)
   for (i=1;i<=n;i++) {      for(j=1;j<=nlstate+ndeath;j++)
     ip=indx[i];        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     sum=b[ip];    fprintf(ficrespow,"\n");
     b[ip]=b[i];    powell(p,xi,npar,ftol,&iter,&fret,func);
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    fclose(ficrespow);
     else if (sum) ii=i;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     b[i]=sum;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   for (i=n;i>=1;i--) {  
     sum=b[i];  }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];  /**** 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;
 /************ Frequencies ********************/    double **hess;
 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)    int i, j,jk;
 {  /* Some frequencies */    int *indx;
    
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    double hessii(double p[], double delta, int theta, double delti[]);
   int first;    double hessij(double p[], double delti[], int i, int j);
   double ***freq; /* Frequencies */    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double *pp;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double pos, k2, dateintsum=0,k2cpt=0;  
   FILE *ficresp;    hess=matrix(1,npar,1,npar);
   char fileresp[FILENAMELENGTH];  
      printf("\nCalculation of the hessian matrix. Wait...\n");
   pp=vector(1,nlstate);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (i=1;i<=npar;i++){
   strcpy(fileresp,"p");      printf("%d",i);fflush(stdout);
   strcat(fileresp,fileres);      fprintf(ficlog,"%d",i);fflush(ficlog);
   if((ficresp=fopen(fileresp,"w"))==NULL) {      hess[i][i]=hessii(p,ftolhess,i,delti);
     printf("Problem with prevalence resultfile: %s\n", fileresp);      /*printf(" %f ",p[i]);*/
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      /*printf(" %lf ",hess[i][i]);*/
     exit(0);    }
   }    
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    for (i=1;i<=npar;i++) {
   j1=0;      for (j=1;j<=npar;j++)  {
          if (j>i) { 
   j=cptcoveff;          printf(".%d%d",i,j);fflush(stdout);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j);
   first=1;          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
   for(k1=1; k1<=j;k1++){        }
     for(i1=1; i1<=ncodemax[k1];i1++){      }
       j1++;    }
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    printf("\n");
         scanf("%d", i);*/    fprintf(ficlog,"\n");
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)      printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           for(m=agemin; m <= agemax+3; m++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
             freq[i][jk][m]=0;    
          a=matrix(1,npar,1,npar);
       dateintsum=0;    y=matrix(1,npar,1,npar);
       k2cpt=0;    x=vector(1,npar);
       for (i=1; i<=imx; i++) {    indx=ivector(1,npar);
         bool=1;    for (i=1;i<=npar;i++)
         if  (cptcovn>0) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           for (z1=1; z1<=cptcoveff; z1++)    ludcmp(a,npar,indx,&pd);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;    for (j=1;j<=npar;j++) {
         }      for (i=1;i<=npar;i++) x[i]=0;
         if (bool==1) {      x[j]=1;
           for(m=firstpass; m<=lastpass; m++){      lubksb(a,npar,indx,x);
             k2=anint[m][i]+(mint[m][i]/12.);      for (i=1;i<=npar;i++){ 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        matcov[i][j]=x[i];
               if(agev[m][i]==0) agev[m][i]=agemax+1;      }
               if(agev[m][i]==1) agev[m][i]=agemax+2;    }
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    printf("\n#Hessian matrix#\n");
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    fprintf(ficlog,"\n#Hessian matrix#\n");
               }    for (i=1;i<=npar;i++) { 
                    for (j=1;j<=npar;j++) { 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        printf("%.3e ",hess[i][j]);
                 dateintsum=dateintsum+k2;        fprintf(ficlog,"%.3e ",hess[i][j]);
                 k2cpt++;      }
               }      printf("\n");
             }      fprintf(ficlog,"\n");
           }    }
         }  
       }    /* Recompute Inverse */
            for (i=1;i<=npar;i++)
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
       if  (cptcovn>0) {  
         fprintf(ficresp, "\n#********** Variable ");    /*  printf("\n#Hessian matrix recomputed#\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresp, "**********\n#");    for (j=1;j<=npar;j++) {
       }      for (i=1;i<=npar;i++) x[i]=0;
       for(i=1; i<=nlstate;i++)      x[j]=1;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      lubksb(a,npar,indx,x);
       fprintf(ficresp, "\n");      for (i=1;i<=npar;i++){ 
              y[i][j]=x[i];
       for(i=(int)agemin; i <= (int)agemax+3; i++){        printf("%.3e ",y[i][j]);
         if(i==(int)agemax+3){        fprintf(ficlog,"%.3e ",y[i][j]);
           fprintf(ficlog,"Total");      }
         }else{      printf("\n");
           if(first==1){      fprintf(ficlog,"\n");
             first=0;    }
             printf("See log file for details...\n");    */
           }  
           fprintf(ficlog,"Age %d", i);    free_matrix(a,1,npar,1,npar);
         }    free_matrix(y,1,npar,1,npar);
         for(jk=1; jk <=nlstate ; jk++){    free_vector(x,1,npar);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    free_ivector(indx,1,npar);
             pp[jk] += freq[jk][m][i];    free_matrix(hess,1,npar,1,npar);
         }  
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)  }
             pos += freq[jk][m][i];  
           if(pp[jk]>=1.e-10){  /*************** hessian matrix ****************/
             if(first==1){  double hessii( double x[], double delta, int theta, double delti[])
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  {
             }    int i;
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    int l=1, lmax=20;
           }else{    double k1,k2;
             if(first==1)    double p2[NPARMAX+1];
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    double res;
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           }    double fx;
         }    int k=0,kmax=10;
     double l1;
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    fx=func(x);
             pp[jk] += freq[jk][m][i];    for (i=1;i<=npar;i++) p2[i]=x[i];
         }    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
         for(jk=1,pos=0; jk <=nlstate ; jk++)      delts=delt;
           pos += pp[jk];      for(k=1 ; k <kmax; k=k+1){
         for(jk=1; jk <=nlstate ; jk++){        delt = delta*(l1*k);
           if(pos>=1.e-5){        p2[theta]=x[theta] +delt;
             if(first==1)        k1=func(p2)-fx;
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        p2[theta]=x[theta]-delt;
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        k2=func(p2)-fx;
           }else{        /*res= (k1-2.0*fx+k2)/delt/delt; */
             if(first==1)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  #ifdef DEBUG
           }        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);
           if( i <= (int) agemax){        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
             if(pos>=1.e-5){  #endif
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
               probs[i][jk][j1]= pp[jk]/pos;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          k=kmax;
             }        }
             else        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          k=kmax; l=lmax*10.;
           }        }
         }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
                  delts=delt;
         for(jk=-1; jk <=nlstate+ndeath; jk++)        }
           for(m=-1; m <=nlstate+ndeath; m++)      }
             if(freq[jk][m][i] !=0 ) {    }
             if(first==1)    delti[theta]=delts;
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    return res; 
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);    
             }  }
         if(i <= (int) agemax)  
           fprintf(ficresp,"\n");  double hessij( double x[], double delti[], int thetai,int thetaj)
         if(first==1)  {
           printf("Others in log...\n");    int i;
         fprintf(ficlog,"\n");    int l=1, l1, lmax=20;
       }    double k1,k2,k3,k4,res,fx;
     }    double p2[NPARMAX+1];
   }    int k;
   dateintmean=dateintsum/k2cpt;  
      fx=func(x);
   fclose(ficresp);    for (k=1; k<=2; k++) {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (i=1;i<=npar;i++) p2[i]=x[i];
   free_vector(pp,1,nlstate);      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   /* End of Freq */      k1=func(p2)-fx;
 }    
       p2[thetai]=x[thetai]+delti[thetai]/k;
 /************ Prevalence ********************/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 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)      k2=func(p2)-fx;
 {  /* Some frequencies */    
        p2[thetai]=x[thetai]-delti[thetai]/k;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double ***freq; /* Frequencies */      k3=func(p2)-fx;
   double *pp;    
   double pos, k2;      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   pp=vector(1,nlstate);      k4=func(p2)-fx;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    #ifdef DEBUG
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      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);
   j1=0;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
    #endif
   j=cptcoveff;    }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    return res;
    }
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){  /************** Inverse of matrix **************/
       j1++;  void ludcmp(double **a, int n, int *indx, double *d) 
        { 
       for (i=-1; i<=nlstate+ndeath; i++)      int i,imax,j,k; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double big,dum,sum,temp; 
           for(m=agemin; m <= agemax+3; m++)    double *vv; 
             freq[i][jk][m]=0;   
          vv=vector(1,n); 
       for (i=1; i<=imx; i++) {    *d=1.0; 
         bool=1;    for (i=1;i<=n;i++) { 
         if  (cptcovn>0) {      big=0.0; 
           for (z1=1; z1<=cptcoveff; z1++)      for (j=1;j<=n;j++) 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        if ((temp=fabs(a[i][j])) > big) big=temp; 
               bool=0;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         }      vv[i]=1.0/big; 
         if (bool==1) {    } 
           for(m=firstpass; m<=lastpass; m++){    for (j=1;j<=n;j++) { 
             k2=anint[m][i]+(mint[m][i]/12.);      for (i=1;i<j;i++) { 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        sum=a[i][j]; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;        a[i][j]=sum; 
               if (m<lastpass) {      } 
                 if (calagedate>0)      big=0.0; 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      for (i=j;i<=n;i++) { 
                 else        sum=a[i][j]; 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for (k=1;k<j;k++) 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          sum -= a[i][k]*a[k][j]; 
               }        a[i][j]=sum; 
             }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           }          big=dum; 
         }          imax=i; 
       }        } 
       for(i=(int)agemin; i <= (int)agemax+3; i++){      } 
         for(jk=1; jk <=nlstate ; jk++){      if (j != imax) { 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for (k=1;k<=n;k++) { 
             pp[jk] += freq[jk][m][i];          dum=a[imax][k]; 
         }          a[imax][k]=a[j][k]; 
         for(jk=1; jk <=nlstate ; jk++){          a[j][k]=dum; 
           for(m=-1, pos=0; m <=0 ; m++)        } 
             pos += freq[jk][m][i];        *d = -(*d); 
         }        vv[imax]=vv[j]; 
              } 
         for(jk=1; jk <=nlstate ; jk++){      indx[j]=imax; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
             pp[jk] += freq[jk][m][i];      if (j != n) { 
         }        dum=1.0/(a[j][j]); 
                for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      } 
            } 
         for(jk=1; jk <=nlstate ; jk++){        free_vector(vv,1,n);  /* Doesn't work */
           if( i <= (int) agemax){  ;
             if(pos>=1.e-5){  } 
               probs[i][jk][j1]= pp[jk]/pos;  
             }  void lubksb(double **a, int n, int *indx, double b[]) 
           }  { 
         }/* end jk */    int i,ii=0,ip,j; 
       }/* end i */    double sum; 
     } /* end i1 */   
   } /* end k1 */    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
        sum=b[ip]; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      b[ip]=b[i]; 
   free_vector(pp,1,nlstate);      if (ii) 
          for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 }  /* End of Freq */      else if (sum) ii=i; 
       b[i]=sum; 
 /************* Waves Concatenation ***************/    } 
     for (i=n;i>=1;i--) { 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      sum=b[i]; 
 {      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      b[i]=sum/a[i][i]; 
      Death is a valid wave (if date is known).    } 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  } 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  
      and mw[mi+1][i]. dh depends on stepm.  /************ Frequencies ********************/
      */  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
   {  /* Some frequencies */
   int i, mi, m;    
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
      double sum=0., jmean=0.;*/    int first;
   int first;    double ***freq; /* Frequencies */
   int j, k=0,jk, ju, jl;    double *pp, **prop;
   double sum=0.;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   first=0;    FILE *ficresp;
   jmin=1e+5;    char fileresp[FILENAMELENGTH];
   jmax=-1;    
   jmean=0.;    pp=vector(1,nlstate);
   for(i=1; i<=imx; i++){    prop=matrix(1,nlstate,iagemin,iagemax+3);
     mi=0;    strcpy(fileresp,"p");
     m=firstpass;    strcat(fileresp,fileres);
     while(s[m][i] <= nlstate){    if((ficresp=fopen(fileresp,"w"))==NULL) {
       if(s[m][i]>=1)      printf("Problem with prevalence resultfile: %s\n", fileresp);
         mw[++mi][i]=m;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       if(m >=lastpass)      exit(0);
         break;    }
       else    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
         m++;    j1=0;
     }/* end while */    
     if (s[m][i] > nlstate){    j=cptcoveff;
       mi++;     /* Death is another wave */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       /* if(mi==0)  never been interviewed correctly before death */  
          /* Only death is a correct wave */    first=1;
       mw[mi][i]=m;  
     }    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
     wav[i]=mi;        j1++;
     if(mi==0){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       if(first==0){          scanf("%d", i);*/
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);        for (i=-1; i<=nlstate+ndeath; i++)  
         first=1;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       }            for(m=iagemin; m <= iagemax+3; m++)
       if(first==1){              freq[i][jk][m]=0;
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);  
       }      for (i=1; i<=nlstate; i++)  
     } /* end mi==0 */        for(m=iagemin; m <= iagemax+3; m++)
   }          prop[i][m]=0;
         
   for(i=1; i<=imx; i++){        dateintsum=0;
     for(mi=1; mi<wav[i];mi++){        k2cpt=0;
       if (stepm <=0)        for (i=1; i<=imx; i++) {
         dh[mi][i]=1;          bool=1;
       else{          if  (cptcovn>0) {
         if (s[mw[mi+1][i]][i] > nlstate) {            for (z1=1; z1<=cptcoveff; z1++) 
           if (agedc[i] < 2*AGESUP) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                bool=0;
           if(j==0) j=1;  /* Survives at least one month after exam */          }
           k=k+1;          if (bool==1){
           if (j >= jmax) jmax=j;            for(m=firstpass; m<=lastpass; m++){
           if (j <= jmin) jmin=j;              k2=anint[m][i]+(mint[m][i]/12.);
           sum=sum+j;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
           /*if (j<0) printf("j=%d num=%d \n",j,i); */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         else{                if (m<lastpass) {
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           k=k+1;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           if (j >= jmax) jmax=j;                }
           else if (j <= jmin)jmin=j;                
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           sum=sum+j;                  dateintsum=dateintsum+k2;
         }                  k2cpt++;
         jk= j/stepm;                }
         jl= j -jk*stepm;              }
         ju= j -(jk+1)*stepm;            }
         if(jl <= -ju)          }
           dh[mi][i]=jk;        }
         else         
           dh[mi][i]=jk+1;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */        if  (cptcovn>0) {
       }          fprintf(ficresp, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresp, "**********\n#");
   jmean=sum/k;        }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        for(i=1; i<=nlstate;i++) 
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
  }        fprintf(ficresp, "\n");
         
 /*********** Tricode ****************************/        for(i=iagemin; i <= iagemax+3; i++){
 void tricode(int *Tvar, int **nbcode, int imx)          if(i==iagemax+3){
 {            fprintf(ficlog,"Total");
   int Ndum[20],ij=1, k, j, i;          }else{
   int cptcode=0;            if(first==1){
   cptcoveff=0;              first=0;
                printf("See log file for details...\n");
   for (k=0; k<19; k++) Ndum[k]=0;            }
   for (k=1; k<=7; k++) ncodemax[k]=0;            fprintf(ficlog,"Age %d", i);
           }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          for(jk=1; jk <=nlstate ; jk++){
     for (i=1; i<=imx; i++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       ij=(int)(covar[Tvar[j]][i]);              pp[jk] += freq[jk][m][i]; 
       Ndum[ij]++;          }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          for(jk=1; jk <=nlstate ; jk++){
       if (ij > cptcode) cptcode=ij;            for(m=-1, pos=0; m <=0 ; m++)
     }              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
     for (i=0; i<=cptcode; i++) {              if(first==1){
       if(Ndum[i]!=0) ncodemax[j]++;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     }              }
     ij=1;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
               if(first==1)
     for (i=1; i<=ncodemax[j]; i++) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for (k=0; k<=19; k++) {              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         if (Ndum[k] != 0) {            }
           nbcode[Tvar[j]][ij]=k;          }
            
           ij++;          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         if (ij > ncodemax[j]) break;              pp[jk] += freq[jk][m][i];
       }            }       
     }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   }              pos += pp[jk];
             posprop += prop[jk][i];
  for (k=0; k<19; k++) Ndum[k]=0;          }
           for(jk=1; jk <=nlstate ; jk++){
  for (i=1; i<=ncovmodel-2; i++) {            if(pos>=1.e-5){
    ij=Tvar[i];              if(first==1)
    Ndum[ij]++;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
  ij=1;              if(first==1)
  for (i=1; i<=10; i++) {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
    if((Ndum[i]!=0) && (i<=ncovcol)){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      Tvaraff[ij]=i;            }
      ij++;            if( i <= iagemax){
    }              if(pos>=1.e-5){
  }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                  probs[i][jk][j1]= pp[jk]/pos;
  cptcoveff=ij-1;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 }              }
               else
 /*********** Health Expectancies ****************/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )          }
           
 {          for(jk=-1; jk <=nlstate+ndeath; jk++)
   /* Health expectancies */            for(m=-1; m <=nlstate+ndeath; m++)
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;              if(freq[jk][m][i] !=0 ) {
   double age, agelim, hf;              if(first==1)
   double ***p3mat,***varhe;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double **dnewm,**doldm;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   double *xp;              }
   double **gp, **gm;          if(i <= iagemax)
   double ***gradg, ***trgradg;            fprintf(ficresp,"\n");
   int theta;          if(first==1)
             printf("Others in log...\n");
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          fprintf(ficlog,"\n");
   xp=vector(1,npar);        }
   dnewm=matrix(1,nlstate*2,1,npar);      }
   doldm=matrix(1,nlstate*2,1,nlstate*2);    }
      dateintmean=dateintsum/k2cpt; 
   fprintf(ficreseij,"# Health expectancies\n");   
   fprintf(ficreseij,"# Age");    fclose(ficresp);
   for(i=1; i<=nlstate;i++)    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     for(j=1; j<=nlstate;j++)    free_vector(pp,1,nlstate);
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   fprintf(ficreseij,"\n");    /* End of Freq */
   }
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  /************ Prevalence ********************/
   }  void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   else  hstepm=estepm;    {  
   /* We compute the life expectancy from trapezoids spaced every estepm months    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
    * This is mainly to measure the difference between two models: for example       in each health status at the date of interview (if between dateprev1 and dateprev2).
    * if stepm=24 months pijx are given only every 2 years and by summing them       We still use firstpass and lastpass as another selection.
    * we are calculating an estimate of the Life Expectancy assuming a linear    */
    * progression inbetween and thus overestimating or underestimating according   
    * to the curvature of the survival function. If, for the same date, we    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    double ***freq; /* Frequencies */
    * to compare the new estimate of Life expectancy with the same linear    double *pp, **prop;
    * hypothesis. A more precise result, taking into account a more precise    double pos,posprop; 
    * curvature will be obtained if estepm is as small as stepm. */    double  y2; /* in fractional years */
     int iagemin, iagemax;
   /* 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.    iagemin= (int) agemin;
      nhstepm is the number of hstepm from age to agelim    iagemax= (int) agemax;
      nstepm is the number of stepm from age to agelin.    /*pp=vector(1,nlstate);*/
      Look at hpijx to understand the reason of that which relies in memory size    prop=matrix(1,nlstate,iagemin,iagemax+3); 
      and note for a fixed period like estepm months */    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    j1=0;
      survival function given by stepm (the optimization length). Unfortunately it    
      means that if the survival funtion is printed only each two years of age and if    j=cptcoveff;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      results. So we changed our mind and took the option of the best precision.    
   */    for(k1=1; k1<=j;k1++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
   agelim=AGESUP;        
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for (i=1; i<=nlstate; i++)  
     /* nhstepm age range expressed in number of stepm */          for(m=iagemin; m <= iagemax+3; m++)
     nstepm=(int) rint((agelim-age)*YEARM/stepm);            prop[i][m]=0.0;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */       
     /* if (stepm >= YEARM) hstepm=1;*/        for (i=1; i<=imx; i++) { /* Each individual */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          bool=1;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if  (cptcovn>0) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);            for (z1=1; z1<=cptcoveff; z1++) 
     gp=matrix(0,nhstepm,1,nlstate*2);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     gm=matrix(0,nhstepm,1,nlstate*2);                bool=0;
           } 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          if (bool==1) { 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                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); 
     /* Computing Variances of health expectancies */                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*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(theta=1; theta <=npar; theta++){                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       for(i=1; i<=npar; i++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                } 
       }              }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              } /* end selection of waves */
            }
       cptj=0;        }
       for(j=1; j<= nlstate; j++){        for(i=iagemin; i <= iagemax+3; i++){  
         for(i=1; i<=nlstate; i++){          
           cptj=cptj+1;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){            posprop += prop[jk][i]; 
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          } 
           }  
         }          for(jk=1; jk <=nlstate ; jk++){     
       }            if( i <=  iagemax){ 
                    if(posprop>=1.e-5){ 
                      probs[i][jk][j1]= prop[jk][i]/posprop;
       for(i=1; i<=npar; i++)              } 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            } 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            }/* end jk */ 
              }/* end i */ 
       cptj=0;      } /* end i1 */
       for(j=1; j<= nlstate; j++){    } /* end k1 */
         for(i=1;i<=nlstate;i++){    
           cptj=cptj+1;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    /*free_vector(pp,1,nlstate);*/
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           }  }  /* End of prevalence */
         }  
       }  /************* Waves Concatenation ***************/
       for(j=1; j<= nlstate*2; j++)  
         for(h=0; h<=nhstepm-1; h++){  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)
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  {
         }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
      }       Death is a valid wave (if date is known).
           mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 /* End theta */       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);       */
   
      for(h=0; h<=nhstepm-1; h++)    int i, mi, m;
       for(j=1; j<=nlstate*2;j++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         for(theta=1; theta <=npar; theta++)       double sum=0., jmean=0.;*/
           trgradg[h][j][theta]=gradg[h][theta][j];    int first;
          int j, k=0,jk, ju, jl;
     double sum=0.;
      for(i=1;i<=nlstate*2;i++)    first=0;
       for(j=1;j<=nlstate*2;j++)    jmin=1e+5;
         varhe[i][j][(int)age] =0.;    jmax=-1;
     jmean=0.;
      printf("%d|",(int)age);fflush(stdout);    for(i=1; i<=imx; i++){
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);      mi=0;
      for(h=0;h<=nhstepm-1;h++){      m=firstpass;
       for(k=0;k<=nhstepm-1;k++){      while(s[m][i] <= nlstate){
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        if(s[m][i]>=1)
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          mw[++mi][i]=m;
         for(i=1;i<=nlstate*2;i++)        if(m >=lastpass)
           for(j=1;j<=nlstate*2;j++)          break;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;        else
       }          m++;
     }      }/* end while */
     /* Computing expectancies */      if (s[m][i] > nlstate){
     for(i=1; i<=nlstate;i++)        mi++;     /* Death is another wave */
       for(j=1; j<=nlstate;j++)        /* if(mi==0)  never been interviewed correctly before death */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){           /* Only death is a correct wave */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        mw[mi][i]=m;
                }
 /* 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]);*/  
       wav[i]=mi;
         }      if(mi==0){
         if(first==0){
     fprintf(ficreseij,"%3.0f",age );          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
     cptj=0;          first=1;
     for(i=1; i<=nlstate;i++)        }
       for(j=1; j<=nlstate;j++){        if(first==1){
         cptj++;          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        }
       }      } /* end mi==0 */
     fprintf(ficreseij,"\n");    } /* End individuals */
      
     free_matrix(gm,0,nhstepm,1,nlstate*2);    for(i=1; i<=imx; i++){
     free_matrix(gp,0,nhstepm,1,nlstate*2);      for(mi=1; mi<wav[i];mi++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        if (stepm <=0)
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          dh[mi][i]=1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        else{
   }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   printf("\n");            if (agedc[i] < 2*AGESUP) {
   fprintf(ficlog,"\n");            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(j==0) j=1;  /* Survives at least one month after exam */
   free_vector(xp,1,npar);            k=k+1;
   free_matrix(dnewm,1,nlstate*2,1,npar);            if (j >= jmax) jmax=j;
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);            if (j <= jmin) jmin=j;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);            sum=sum+j;
 }            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
             /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 /************ Variance ******************/            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]);
 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)            }
 {          }
   /* Variance of health expectancies */          else{
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /* double **newm;*/            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   double **dnewm,**doldm;            k=k+1;
   double **dnewmp,**doldmp;            if (j >= jmax) jmax=j;
   int i, j, nhstepm, hstepm, h, nstepm ;            else if (j <= jmin)jmin=j;
   int k, cptcode;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   double *xp;            /*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]);*/
   double **gp, **gm;  /* for var eij */            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]);
   double ***gradg, ***trgradg; /*for var eij */            sum=sum+j;
   double **gradgp, **trgradgp; /* for var p point j */          }
   double *gpp, *gmp; /* for var p point j */          jk= j/stepm;
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */          jl= j -jk*stepm;
   double ***p3mat;          ju= j -(jk+1)*stepm;
   double age,agelim, hf;          if(mle <=1){ 
   int theta;            if(jl==0){
   char digit[4];              dh[mi][i]=jk;
   char digitp[16];              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
   char fileresprobmorprev[FILENAMELENGTH];                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
   if(popbased==1)              bh[mi][i]=ju;
     strcpy(digitp,"-populbased-");            }
   else          }else{
     strcpy(digitp,"-stablbased-");            if(jl <= -ju){
               dh[mi][i]=jk;
   strcpy(fileresprobmorprev,"prmorprev");              bh[mi][i]=jl;       /* bias is positive if real duration
   sprintf(digit,"%-d",ij);                                   * is higher than the multiple of stepm and negative otherwise.
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/                                   */
   strcat(fileresprobmorprev,digit); /* Tvar to be done */            }
   strcat(fileresprobmorprev,digitp); /* Popbased or not */            else{
   strcat(fileresprobmorprev,fileres);              dh[mi][i]=jk+1;
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {              bh[mi][i]=ju;
     printf("Problem with resultfile: %s\n", fileresprobmorprev);            }
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);            if(dh[mi][i]==0){
   }              dh[mi][i]=1; /* At least one step */
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);              bh[mi][i]=ju; /* At least one step */
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);              /*  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);*/
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");            }
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);          }
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){        } /* end if mle */
     fprintf(ficresprobmorprev," p.%-d SE",j);      } /* end wave */
     for(i=1; i<=nlstate;i++)    }
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);    jmean=sum/k;
   }      printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   fprintf(ficresprobmorprev,"\n");    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {   }
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);  
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);  /*********** Tricode ****************************/
     exit(0);  void tricode(int *Tvar, int **nbcode, int imx)
   }  {
   else{    
     fprintf(ficgp,"\n# Routine varevsij");    int Ndum[20],ij=1, k, j, i, maxncov=19;
   }    int cptcode=0;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    cptcoveff=0; 
     printf("Problem with html file: %s\n", optionfilehtm);   
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     exit(0);    for (k=1; k<=7; k++) ncodemax[k]=0;
   }  
   else{    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   }                                 modality*/ 
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   fprintf(ficresvij,"# Age");        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   for(i=1; i<=nlstate;i++)                                         Tvar[j]. If V=sex and male is 0 and 
     for(j=1; j<=nlstate;j++)                                         female is 1, then  cptcode=1.*/
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      }
   fprintf(ficresvij,"\n");  
       for (i=0; i<=cptcode; i++) {
   xp=vector(1,npar);        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 */
   dnewm=matrix(1,nlstate,1,npar);      }
   doldm=matrix(1,nlstate,1,nlstate);  
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);      ij=1; 
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<= maxncov; k++) {
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);          if (Ndum[k] != 0) {
   gpp=vector(nlstate+1,nlstate+ndeath);            nbcode[Tvar[j]][ij]=k; 
   gmp=vector(nlstate+1,nlstate+ndeath);            /* 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; */
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/            
              ij++;
   if(estepm < stepm){          }
     printf ("Problem %d lower than %d\n",estepm, stepm);          if (ij > ncodemax[j]) break; 
   }        }  
   else  hstepm=estepm;        } 
   /* 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   for (k=0; k< maxncov; k++) Ndum[k]=0;
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size   for (i=1; i<=ncovmodel-2; i++) { 
      and note for a fixed period like k years */     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the     ij=Tvar[i];
      survival function given by stepm (the optimization length). Unfortunately it     Ndum[ij]++;
      means that if the survival funtion is printed only each two years of age and if   }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.   ij=1;
   */   for (i=1; i<= maxncov; i++) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */     if((Ndum[i]!=0) && (i<=ncovcol)){
   agelim = AGESUP;       Tvaraff[ij]=i; /*For printing */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       ij++;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */     }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */   }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);   cptcoveff=ij-1; /*Number of simple covariates*/
     gp=matrix(0,nhstepm,1,nlstate);  }
     gm=matrix(0,nhstepm,1,nlstate);  
   /*********** Health Expectancies ****************/
   
     for(theta=1; theta <=npar; theta++){  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    /* Health expectancies */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double age, agelim, hf;
     double ***p3mat,***varhe;
       if (popbased==1) {    double **dnewm,**doldm;
         for(i=1; i<=nlstate;i++)    double *xp;
           prlim[i][i]=probs[(int)age][i][ij];    double **gp, **gm;
       }    double ***gradg, ***trgradg;
      int theta;
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    xp=vector(1,npar);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    dnewm=matrix(1,nlstate*nlstate,1,npar);
         }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       }    
       /* This for computing forces of mortality (h=1)as a weighted average */    fprintf(ficreseij,"# Health expectancies\n");
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    fprintf(ficreseij,"# Age");
         for(i=1; i<= nlstate; i++)    for(i=1; i<=nlstate;i++)
           gpp[j] += prlim[i][i]*p3mat[i][j][1];      for(j=1; j<=nlstate;j++)
       }            fprintf(ficreseij," %1d-%1d (SE)",i,j);
       /* end force of mortality */    fprintf(ficreseij,"\n");
   
       for(i=1; i<=npar; i++) /* Computes gradient */    if(estepm < stepm){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      printf ("Problem %d lower than %d\n",estepm, stepm);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    else  hstepm=estepm;   
      /* We compute the life expectancy from trapezoids spaced every estepm months
       if (popbased==1) {     * This is mainly to measure the difference between two models: for example
         for(i=1; i<=nlstate;i++)     * if stepm=24 months pijx are given only every 2 years and by summing them
           prlim[i][i]=probs[(int)age][i][ij];     * we are calculating an estimate of the Life Expectancy assuming a linear 
       }     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
       for(j=1; j<= nlstate; j++){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         for(h=0; h<=nhstepm; h++){     * to compare the new estimate of Life expectancy with the same linear 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)     * hypothesis. A more precise result, taking into account a more precise
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];     * curvature will be obtained if estepm is as small as stepm. */
         }  
       }    /* For example we decided to compute the life expectancy with the smallest unit */
       /* This for computing force of mortality (h=1)as a weighted average */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){       nhstepm is the number of hstepm from age to agelim 
         for(i=1; i<= nlstate; i++)       nstepm is the number of stepm from age to agelin. 
           gmp[j] += prlim[i][i]*p3mat[i][j][1];       Look at hpijx to understand the reason of that which relies in memory size
       }           and note for a fixed period like estepm months */
       /* end force of mortality */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
       for(j=1; j<= nlstate; j++) /* vareij */       means that if the survival funtion is printed only each two years of age and if
         for(h=0; h<=nhstepm; h++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];       results. So we changed our mind and took the option of the best precision.
         }    */
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];  
       }    agelim=AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     } /* End theta */      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
     for(h=0; h<=nhstepm; h++) /* veij */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for(j=1; j<=nlstate;j++)      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(theta=1; theta <=npar; theta++)      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           trgradg[h][j][theta]=gradg[h][theta][j];      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       gm=matrix(0,nhstepm,1,nlstate*nlstate);
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */  
       for(theta=1; theta <=npar; theta++)      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         trgradgp[j][theta]=gradgp[theta][j];         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */   
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         vareij[i][j][(int)age] =0.;  
       /* Computing Variances of health expectancies */
     for(h=0;h<=nhstepm;h++){  
       for(k=0;k<=nhstepm;k++){       for(theta=1; theta <=npar; theta++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        for(i=1; i<=npar; i++){ 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         for(i=1;i<=nlstate;i++)        }
           for(j=1;j<=nlstate;j++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    
       }        cptj=0;
     }        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
     /* pptj */            cptj=cptj+1;
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     for(j=nlstate+1;j<=nlstate+ndeath;j++)            }
       for(i=nlstate+1;i<=nlstate+ndeath;i++)          }
         varppt[j][i]=doldmp[j][i];        }
     /* end ppptj */       
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);         
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);        for(i=1; i<=npar; i++) 
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
     if (popbased==1) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for(i=1; i<=nlstate;i++)        
         prlim[i][i]=probs[(int)age][i][ij];        cptj=0;
     }        for(j=1; j<= nlstate; j++){
              for(i=1;i<=nlstate;i++){
     /* This for computing force of mortality (h=1)as a weighted average */            cptj=cptj+1;
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       for(i=1; i<= nlstate; i++)  
         gmp[j] += prlim[i][i]*p3mat[i][j][1];              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     }                }
     /* end force of mortality */          }
         }
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);        for(j=1; j<= nlstate*nlstate; j++)
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){          for(h=0; h<=nhstepm-1; h++){
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       for(i=1; i<=nlstate;i++){          }
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);       } 
       }     
     }  /* End theta */
     fprintf(ficresprobmorprev,"\n");  
        trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)       for(h=0; h<=nhstepm-1; h++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate*nlstate;j++)
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          for(theta=1; theta <=npar; theta++)
       }            trgradg[h][j][theta]=gradg[h][theta][j];
     fprintf(ficresvij,"\n");       
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);       for(i=1;i<=nlstate*nlstate;i++)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for(j=1;j<=nlstate*nlstate;j++)
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          varhe[i][j][(int)age] =0.;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */       printf("%d|",(int)age);fflush(stdout);
   free_vector(gpp,nlstate+1,nlstate+ndeath);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   free_vector(gmp,nlstate+1,nlstate+ndeath);       for(h=0;h<=nhstepm-1;h++){
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);        for(k=0;k<=nhstepm-1;k++){
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */          for(i=1;i<=nlstate*nlstate;i++)
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");            for(j=1;j<=nlstate*nlstate;j++)
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);        }
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);      }
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);      /* Computing expectancies */
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);      for(i=1; i<=nlstate;i++)
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   free_vector(xp,1,npar);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   free_matrix(doldm,1,nlstate,1,nlstate);            
   free_matrix(dnewm,1,nlstate,1,npar);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);          }
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  
   fclose(ficresprobmorprev);      fprintf(ficreseij,"%3.0f",age );
   fclose(ficgp);      cptj=0;
   fclose(fichtm);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
 }          cptj++;
           fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
 /************ 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)      fprintf(ficreseij,"\n");
 {     
   /* Variance of prevalence limit */      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   double **newm;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   double **dnewm,**doldm;      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   int i, j, nhstepm, hstepm;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int k, cptcode;    }
   double *xp;    printf("\n");
   double *gp, *gm;    fprintf(ficlog,"\n");
   double **gradg, **trgradg;  
   double age,agelim;    free_vector(xp,1,npar);
   int theta;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
        free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   fprintf(ficresvpl,"# Age");  }
   for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %1d-%1d",i,i);  /************ Variance ******************/
   fprintf(ficresvpl,"\n");  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
   {
   xp=vector(1,npar);    /* Variance of health expectancies */
   dnewm=matrix(1,nlstate,1,npar);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   doldm=matrix(1,nlstate,1,nlstate);    /* double **newm;*/
      double **dnewm,**doldm;
   hstepm=1*YEARM; /* Every year of age */    double **dnewmp,**doldmp;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    int i, j, nhstepm, hstepm, h, nstepm ;
   agelim = AGESUP;    int k, cptcode;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double *xp;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double **gp, **gm;  /* for var eij */
     if (stepm >= YEARM) hstepm=1;    double ***gradg, ***trgradg; /*for var eij */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double **gradgp, **trgradgp; /* for var p point j */
     gradg=matrix(1,npar,1,nlstate);    double *gpp, *gmp; /* for var p point j */
     gp=vector(1,nlstate);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     gm=vector(1,nlstate);    double ***p3mat;
     double age,agelim, hf;
     for(theta=1; theta <=npar; theta++){    double ***mobaverage;
       for(i=1; i<=npar; i++){ /* Computes gradient */    int theta;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    char digit[4];
       }    char digitp[25];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    char fileresprobmorprev[FILENAMELENGTH];
         gp[i] = prlim[i][i];  
        if(popbased==1){
       for(i=1; i<=npar; i++) /* Computes gradient */      if(mobilav!=0)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        strcpy(digitp,"-populbased-mobilav-");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      else strcpy(digitp,"-populbased-nomobil-");
       for(i=1;i<=nlstate;i++)    }
         gm[i] = prlim[i][i];    else 
       strcpy(digitp,"-stablbased-");
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    if (mobilav!=0) {
     } /* End theta */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     trgradg =matrix(1,nlstate,1,npar);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
     for(j=1; j<=nlstate;j++)      }
       for(theta=1; theta <=npar; theta++)    }
         trgradg[j][theta]=gradg[theta][j];  
     strcpy(fileresprobmorprev,"prmorprev"); 
     for(i=1;i<=nlstate;i++)    sprintf(digit,"%-d",ij);
       varpl[i][(int)age] =0.;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     for(i=1;i<=nlstate;i++)    strcat(fileresprobmorprev,fileres);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
     fprintf(ficresvpl,"%.0f ",age );      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     for(i=1; i<=nlstate;i++)    }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficresvpl,"\n");    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     free_vector(gp,1,nlstate);    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);
     free_vector(gm,1,nlstate);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     free_matrix(gradg,1,npar,1,nlstate);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     free_matrix(trgradg,1,nlstate,1,npar);      fprintf(ficresprobmorprev," p.%-d SE",j);
   } /* End age */      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   free_vector(xp,1,npar);    }  
   free_matrix(doldm,1,nlstate,1,npar);    fprintf(ficresprobmorprev,"\n");
   free_matrix(dnewm,1,nlstate,1,nlstate);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
 }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
 /************ 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)    else{
 {      fprintf(ficgp,"\n# Routine varevsij");
   int i, j=0,  i1, k1, l1, t, tj;    }
   int k2, l2, j1,  z1;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   int k=0,l, cptcode;      printf("Problem with html file: %s\n", optionfilehtm);
   int first=1, first1;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;      exit(0);
   double **dnewm,**doldm;    }
   double *xp;    else{
   double *gp, *gm;      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");
   double **gradg, **trgradg;      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   double **mu;    }
   double age,agelim, cov[NCOVMAX];    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */  
   int theta;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   char fileresprob[FILENAMELENGTH];    fprintf(ficresvij,"# Age");
   char fileresprobcov[FILENAMELENGTH];    for(i=1; i<=nlstate;i++)
   char fileresprobcor[FILENAMELENGTH];      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   double ***varpij;    fprintf(ficresvij,"\n");
   
   strcpy(fileresprob,"prob");    xp=vector(1,npar);
   strcat(fileresprob,fileres);    dnewm=matrix(1,nlstate,1,npar);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    doldm=matrix(1,nlstate,1,nlstate);
     printf("Problem with resultfile: %s\n", fileresprob);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }  
   strcpy(fileresprobcov,"probcov");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   strcat(fileresprobcov,fileres);    gpp=vector(nlstate+1,nlstate+ndeath);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    gmp=vector(nlstate+1,nlstate+ndeath);
     printf("Problem with resultfile: %s\n", fileresprobcov);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    
   }    if(estepm < stepm){
   strcpy(fileresprobcor,"probcor");      printf ("Problem %d lower than %d\n",estepm, stepm);
   strcat(fileresprobcor,fileres);    }
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    else  hstepm=estepm;   
     printf("Problem with resultfile: %s\n", fileresprobcor);    /* For example we decided to compute the life expectancy with the smallest unit */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);    /* 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 
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);       nstepm is the number of stepm from age to agelin. 
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);       Look at hpijx to understand the reason of that which relies in memory size
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);       and note for a fixed period like k years */
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);       survival function given by stepm (the optimization length). Unfortunately it
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);       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 
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");       results. So we changed our mind and took the option of the best precision.
   fprintf(ficresprob,"# Age");    */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fprintf(ficresprobcov,"# Age");    agelim = AGESUP;
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fprintf(ficresprobcov,"# Age");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   for(i=1; i<=nlstate;i++)      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     for(j=1; j<=(nlstate+ndeath);j++){      gp=matrix(0,nhstepm,1,nlstate);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      gm=matrix(0,nhstepm,1,nlstate);
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  
     }        for(theta=1; theta <=npar; theta++){
   fprintf(ficresprob,"\n");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   fprintf(ficresprobcov,"\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   fprintf(ficresprobcor,"\n");        }
   xp=vector(1,npar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));  
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);        if (popbased==1) {
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);          if(mobilav ==0){
   first=1;            for(i=1; i<=nlstate;i++)
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {              prlim[i][i]=probs[(int)age][i][ij];
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          }else{ /* mobilav */ 
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);            for(i=1; i<=nlstate;i++)
     exit(0);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   else{        }
     fprintf(ficgp,"\n# Routine varprob");    
   }        for(j=1; j<= nlstate; j++){
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {          for(h=0; h<=nhstepm; h++){
     printf("Problem with html file: %s\n", optionfilehtm);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     exit(0);          }
   }        }
   else{        /* This for computing probability of death (h=1 means
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");           computed over hstepm matrices product = hstepm*stepm months) 
     fprintf(fichtm,"\n");           as a weighted average of prlim.
         */
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     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");          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     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");            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   }        /* end probability of death */
   
          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   cov[1]=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   tj=cptcoveff;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   j1=0;   
   for(t=1; t<=tj;t++){        if (popbased==1) {
     for(i1=1; i1<=ncodemax[t];i1++){          if(mobilav ==0){
       j1++;            for(i=1; i<=nlstate;i++)
                    prlim[i][i]=probs[(int)age][i][ij];
       if  (cptcovn>0) {          }else{ /* mobilav */ 
         fprintf(ficresprob, "\n#********** Variable ");            for(i=1; i<=nlstate;i++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              prlim[i][i]=mobaverage[(int)age][i][ij];
         fprintf(ficresprob, "**********\n#");          }
         fprintf(ficresprobcov, "\n#********** Variable ");        }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresprobcov, "**********\n#");        for(j=1; j<= nlstate; j++){
                  for(h=0; h<=nhstepm; h++){
         fprintf(ficgp, "\n#********** Variable ");            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         fprintf(ficgp, "**********\n#");          }
                }
                /* This for computing probability of death (h=1 means
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");           computed over hstepm matrices product = hstepm*stepm months) 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);           as a weighted average of prlim.
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");        */
                for(j=nlstate+1;j<=nlstate+ndeath;j++){
         fprintf(ficresprobcor, "\n#********** Variable ");              for(i=1,gmp[j]=0.; i<= nlstate; i++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         fprintf(ficgp, "**********\n#");            }    
       }        /* end probability of death */
        
       for (age=bage; age<=fage; age ++){        for(j=1; j<= nlstate; j++) /* vareij */
         cov[2]=age;          for(h=0; h<=nhstepm; h++){
         for (k=1; k<=cptcovn;k++) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          }
         }  
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         for (k=1; k<=cptcovprod;k++)          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        }
          
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));      } /* End theta */
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
         gp=vector(1,(nlstate)*(nlstate+ndeath));      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
         gm=vector(1,(nlstate)*(nlstate+ndeath));  
          for(h=0; h<=nhstepm; h++) /* veij */
         for(theta=1; theta <=npar; theta++){        for(j=1; j<=nlstate;j++)
           for(i=1; i<=npar; i++)          for(theta=1; theta <=npar; theta++)
             xp[i] = x[i] + (i==theta ?delti[theta]:0);            trgradg[h][j][theta]=gradg[h][theta][j];
            
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                  for(theta=1; theta <=npar; theta++)
           k=0;          trgradgp[j][theta]=gradgp[theta][j];
           for(i=1; i<= (nlstate); i++){    
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               gp[k]=pmmij[i][j];      for(i=1;i<=nlstate;i++)
             }        for(j=1;j<=nlstate;j++)
           }          vareij[i][j][(int)age] =0.;
            
           for(i=1; i<=npar; i++)      for(h=0;h<=nhstepm;h++){
             xp[i] = x[i] - (i==theta ?delti[theta]:0);        for(k=0;k<=nhstepm;k++){
              matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           k=0;          for(i=1;i<=nlstate;i++)
           for(i=1; i<=(nlstate); i++){            for(j=1;j<=nlstate;j++)
             for(j=1; j<=(nlstate+ndeath);j++){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
               k=k+1;        }
               gm[k]=pmmij[i][j];      }
             }    
           }      /* pptj */
            matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        for(j=nlstate+1;j<=nlstate+ndeath;j++)
         }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)      /* end ppptj */
           for(theta=1; theta <=npar; theta++)      /*  x centered again */
             trgradg[j][theta]=gradg[theta][j];      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
              prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);   
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);      if (popbased==1) {
                if(mobilav ==0){
         pmij(pmmij,cov,ncovmodel,x,nlstate);          for(i=1; i<=nlstate;i++)
                    prlim[i][i]=probs[(int)age][i][ij];
         k=0;        }else{ /* mobilav */ 
         for(i=1; i<=(nlstate); i++){          for(i=1; i<=nlstate;i++)
           for(j=1; j<=(nlstate+ndeath);j++){            prlim[i][i]=mobaverage[(int)age][i][ij];
             k=k+1;        }
             mu[k][(int) age]=pmmij[i][j];      }
           }               
         }      /* This for computing probability of death (h=1 means
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)         as a weighted average of prlim.
             varpij[i][j][(int)age] = doldm[i][j];      */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         /*printf("\n%d ",(int)age);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      }    
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      /* end probability of death */
      }*/  
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         fprintf(ficresprob,"\n%d ",(int)age);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobcov,"\n%d ",(int)age);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         fprintf(ficresprobcor,"\n%d ",(int)age);        for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)        }
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));      } 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){      fprintf(ficresprobmorprev,"\n");
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);  
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);      fprintf(ficresvij,"%.0f ",age );
         }      for(i=1; i<=nlstate;i++)
         i=0;        for(j=1; j<=nlstate;j++){
         for (k=1; k<=(nlstate);k++){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           for (l=1; l<=(nlstate+ndeath);l++){        }
             i=i++;      fprintf(ficresvij,"\n");
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);      free_matrix(gp,0,nhstepm,1,nlstate);
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);      free_matrix(gm,0,nhstepm,1,nlstate);
             for (j=1; j<=i;j++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             }    } /* End age */
           }    free_vector(gpp,nlstate+1,nlstate+ndeath);
         }/* end of loop for state */    free_vector(gmp,nlstate+1,nlstate+ndeath);
       } /* end of loop for age */    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       /* Confidence intervalle of pij  */    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       /*    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       fprintf(ficgp,"\nset noparametric;unset label");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);    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);
     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);
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    /*  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);
       first1=1;  */
       for (k2=1; k2<=(nlstate);k2++){    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
         for (l2=1; l2<=(nlstate+ndeath);l2++){  
           if(l2==k2) continue;    free_vector(xp,1,npar);
           j=(k2-1)*(nlstate+ndeath)+l2;    free_matrix(doldm,1,nlstate,1,nlstate);
           for (k1=1; k1<=(nlstate);k1++){    free_matrix(dnewm,1,nlstate,1,npar);
             for (l1=1; l1<=(nlstate+ndeath);l1++){    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               if(l1==k1) continue;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
               i=(k1-1)*(nlstate+ndeath)+l1;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               if(i<=j) continue;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               for (age=bage; age<=fage; age ++){    fclose(ficresprobmorprev);
                 if ((int)age %5==0){    fclose(ficgp);
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    fclose(fichtm);
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;  }  
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;  
                   mu1=mu[i][(int) age]/stepm*YEARM ;  /************ Variance of prevlim ******************/
                   mu2=mu[j][(int) age]/stepm*YEARM;  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)
                   c12=cv12/sqrt(v1*v2);  {
                   /* Computing eigen value of matrix of covariance */    /* Variance of prevalence limit */
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;    double **newm;
                   /* Eigen vectors */    double **dnewm,**doldm;
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    int i, j, nhstepm, hstepm;
                   /*v21=sqrt(1.-v11*v11); *//* error */    int k, cptcode;
                   v21=(lc1-v1)/cv12*v11;    double *xp;
                   v12=-v21;    double *gp, *gm;
                   v22=v11;    double **gradg, **trgradg;
                   tnalp=v21/v11;    double age,agelim;
                   if(first1==1){    int theta;
                     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);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
                   }    fprintf(ficresvpl,"# Age");
                   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);    for(i=1; i<=nlstate;i++)
                   /*printf(fignu*/        fprintf(ficresvpl," %1d-%1d",i,i);
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    fprintf(ficresvpl,"\n");
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */  
                   if(first==1){    xp=vector(1,npar);
                     first=0;    dnewm=matrix(1,nlstate,1,npar);
                     fprintf(ficgp,"\nset parametric;unset label");    doldm=matrix(1,nlstate,1,nlstate);
                     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);    
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    hstepm=1*YEARM; /* Every year of age */
                     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);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);    agelim = AGESUP;
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);      if (stepm >= YEARM) hstepm=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",\      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\      gradg=matrix(1,npar,1,nlstate);
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));      gp=vector(1,nlstate);
                   }else{      gm=vector(1,nlstate);
                     first=0;  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);      for(theta=1; theta <=npar; theta++){
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);        for(i=1; i<=npar; i++){ /* Computes gradient */
                     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",\          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\        }
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   }/* if first */        for(i=1;i<=nlstate;i++)
                 } /* age mod 5 */          gp[i] = prlim[i][i];
               } /* end loop age */      
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);        for(i=1; i<=npar; i++) /* Computes gradient */
               first=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             } /*l12 */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           } /* k12 */        for(i=1;i<=nlstate;i++)
         } /*l1 */          gm[i] = prlim[i][i];
       }/* k1 */  
     } /* loop covariates */        for(i=1;i<=nlstate;i++)
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      } /* End theta */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);      trgradg =matrix(1,nlstate,1,npar);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for(j=1; j<=nlstate;j++)
   }        for(theta=1; theta <=npar; theta++)
   free_vector(xp,1,npar);          trgradg[j][theta]=gradg[theta][j];
   fclose(ficresprob);  
   fclose(ficresprobcov);      for(i=1;i<=nlstate;i++)
   fclose(ficresprobcor);        varpl[i][(int)age] =0.;
   fclose(ficgp);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   fclose(fichtm);      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 */
   
 /******************* Printing html file ***********/      fprintf(ficresvpl,"%.0f ",age );
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      for(i=1; i<=nlstate;i++)
                   int lastpass, int stepm, int weightopt, char model[],\        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\      fprintf(ficresvpl,"\n");
                   int popforecast, int estepm ,\      free_vector(gp,1,nlstate);
                   double jprev1, double mprev1,double anprev1, \      free_vector(gm,1,nlstate);
                   double jprev2, double mprev2,double anprev2){      free_matrix(gradg,1,npar,1,nlstate);
   int jj1, k1, i1, cpt;      free_matrix(trgradg,1,nlstate,1,npar);
   /*char optionfilehtm[FILENAMELENGTH];*/    } /* End age */
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);    free_vector(xp,1,npar);
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);    free_matrix(doldm,1,nlstate,1,npar);
   }    free_matrix(dnewm,1,nlstate,1,nlstate);
   
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n  }
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n  
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n  /************ Variance of one-step probabilities  ******************/
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
  - Life expectancies by age and initial health status (estepm=%2d months):  {
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    int i, j=0,  i1, k1, l1, t, tj;
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");    int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
  m=cptcoveff;    double **dnewm,**doldm;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double *xp;
     double *gp, *gm;
  jj1=0;    double **gradg, **trgradg;
  for(k1=1; k1<=m;k1++){    double **mu;
    for(i1=1; i1<=ncodemax[k1];i1++){    double age,agelim, cov[NCOVMAX];
      jj1++;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
      if (cptcovn > 0) {    int theta;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    char fileresprob[FILENAMELENGTH];
        for (cpt=1; cpt<=cptcoveff;cpt++)    char fileresprobcov[FILENAMELENGTH];
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    char fileresprobcor[FILENAMELENGTH];
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
      }    double ***varpij;
      /* Pij */  
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>    strcpy(fileresprob,"prob"); 
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        strcat(fileresprob,fileres);
      /* Quasi-incidences */    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      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("Problem with resultfile: %s\n", fileresprob);
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
        /* Stable prevalence in each health state */    }
        for(cpt=1; cpt<nlstate;cpt++){    strcpy(fileresprobcov,"probcov"); 
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    strcat(fileresprobcov,fileres);
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        }      printf("Problem with resultfile: %s\n", fileresprobcov);
      for(cpt=1; cpt<=nlstate;cpt++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    }
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    strcpy(fileresprobcor,"probcor"); 
      }    strcat(fileresprobcor,fileres);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
 health expectancies in states (1) and (2): e%s%d.png<br>      printf("Problem with resultfile: %s\n", fileresprobcor);
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
    } /* end i1 */    }
  }/* End k1 */    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
  fprintf(fichtm,"</ul>");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    fprintf(ficresprob,"# Age");
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    fprintf(ficresprobcov,"# Age");
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
  if(popforecast==1) fprintf(fichtm,"\n  
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n  
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    for(i=1; i<=nlstate;i++)
         <br>",fileres,fileres,fileres,fileres);      for(j=1; j<=(nlstate+ndeath);j++){
  else        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
  m=cptcoveff;   /* fprintf(ficresprob,"\n");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
  jj1=0;   */
  for(k1=1; k1<=m;k1++){   xp=vector(1,npar);
    for(i1=1; i1<=ncodemax[k1];i1++){    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      jj1++;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      if (cptcovn > 0) {    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
        for (cpt=1; cpt<=cptcoveff;cpt++)    first=1;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
      }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
      for(cpt=1; cpt<=nlstate;cpt++) {      exit(0);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    }
 interval) in state (%d): v%s%d%d.png <br>    else{
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        fprintf(ficgp,"\n# Routine varprob");
      }    }
    } /* end i1 */    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
  }/* End k1 */      printf("Problem with html file: %s\n", optionfilehtm);
  fprintf(fichtm,"</ul>");      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
 fclose(fichtm);      exit(0);
 }    }
     else{
 /******************* Gnuplot file **************/      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      fprintf(fichtm,"\n");
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   int ng;      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");
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      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");
     printf("Problem with file %s",optionfilegnuplot);  
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);    }
   }  
     cov[1]=1;
 #ifdef windows    tj=cptcoveff;
     fprintf(ficgp,"cd \"%s\" \n",pathc);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
 #endif    j1=0;
 m=pow(2,cptcoveff);    for(t=1; t<=tj;t++){
        for(i1=1; i1<=ncodemax[t];i1++){ 
  /* 1eme*/        j1++;
   for (cpt=1; cpt<= nlstate ; cpt ++) {        if  (cptcovn>0) {
    for (k1=1; k1<= m ; k1 ++) {          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 #ifdef windows          fprintf(ficresprob, "**********\n#\n");
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          fprintf(ficresprobcov, "\n#********** Variable "); 
      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 (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 #endif          fprintf(ficresprobcov, "**********\n#\n");
 #ifdef unix          
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          fprintf(ficgp, "\n#********** Variable "); 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 #endif          fprintf(ficgp, "**********\n#\n");
           
 for (i=1; i<= nlstate ; i ++) {          
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          
     for (i=1; i<= nlstate ; i ++) {          fprintf(ficresprobcor, "\n#********** Variable ");    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficresprobcor, "**********\n#");    
 }        }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        
      for (i=1; i<= nlstate ; i ++) {        for (age=bage; age<=fage; age ++){ 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          cov[2]=age;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (k=1; k<=cptcovn;k++) {
 }              cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          }
 #ifdef unix          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");          for (k=1; k<=cptcovprod;k++)
 #endif            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    }          
   }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   /*2 eme*/          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
   for (k1=1; k1<= m ; k1 ++) {          gm=vector(1,(nlstate)*(nlstate+ndeath));
     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);          for(theta=1; theta <=npar; theta++){
                for(i=1; i<=npar; i++)
     for (i=1; i<= nlstate+1 ; i ++) {              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       k=2*i;            
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {            
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            k=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1; i<= (nlstate); i++){
 }                for(j=1; j<=(nlstate+ndeath);j++){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                k=k+1;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                gp[k]=pmmij[i][j];
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              }
       for (j=1; j<= nlstate+1 ; j ++) {            }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            
         else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1; i<=npar; i++)
 }                xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       fprintf(ficgp,"\" t\"\" w l 0,");      
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {            k=0;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(i=1; i<=(nlstate); i++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");              for(j=1; j<=(nlstate+ndeath);j++){
 }                  k=k+1;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                gm[k]=pmmij[i][j];
       else fprintf(ficgp,"\" t\"\" w l 0,");              }
     }            }
   }       
              for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   /*3eme*/              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       k=2+nlstate*(2*cpt-2);            for(theta=1; theta <=npar; theta++)
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);              trgradg[j][theta]=gradg[theta][j];
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
 */          pmij(pmmij,cov,ncovmodel,x,nlstate);
       for (i=1; i< nlstate ; i ++) {          
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);          k=0;
           for(i=1; i<=(nlstate); i++){
       }            for(j=1; j<=(nlstate+ndeath);j++){
     }              k=k+1;
   }              mu[k][(int) age]=pmmij[i][j];
              }
   /* CV preval stat */          }
     for (k1=1; k1<= m ; k1 ++) {          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     for (cpt=1; cpt<nlstate ; cpt ++) {            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       k=3;              varpij[i][j][(int)age] = doldm[i][j];
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       for (i=1; i< nlstate ; i ++)            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         fprintf(ficgp,"+$%d",k+i+1);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            }*/
        
       l=3+(nlstate+ndeath)*cpt;          fprintf(ficresprob,"\n%d ",(int)age);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          fprintf(ficresprobcov,"\n%d ",(int)age);
       for (i=1; i< nlstate ; i ++) {          fprintf(ficresprobcor,"\n%d ",(int)age);
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       }            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   }              fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
            }
   /* proba elementaires */          i=0;
    for(i=1,jk=1; i <=nlstate; i++){          for (k=1; k<=(nlstate);k++){
     for(k=1; k <=(nlstate+ndeath); k++){            for (l=1; l<=(nlstate+ndeath);l++){ 
       if (k != i) {              i=i++;
         for(j=1; j <=ncovmodel; j++){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
           jk++;              for (j=1; j<=i;j++){
           fprintf(ficgp,"\n");                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       }              }
     }            }
    }          }/* end of loop for state */
         } /* end of loop for age */
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/  
      for(jk=1; jk <=m; jk++) {        /* Confidence intervalle of pij  */
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);        /*
        if (ng==2)          fprintf(ficgp,"\nset noparametric;unset label");
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
        else          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
          fprintf(ficgp,"\nset title \"Probability\"\n");          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
        i=1;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
        for(k2=1; k2<=nlstate; k2++) {          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
          k3=i;        */
          for(k=1; k<=(nlstate+ndeath); k++) {  
            if (k != k2){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
              if(ng==2)        first1=1;
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);        for (k2=1; k2<=(nlstate);k2++){
              else          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            if(l2==k2) continue;
              ij=1;            j=(k2-1)*(nlstate+ndeath)+l2;
              for(j=3; j <=ncovmodel; j++) {            for (k1=1; k1<=(nlstate);k1++){
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                if(l1==k1) continue;
                  ij++;                i=(k1-1)*(nlstate+ndeath)+l1;
                }                if(i<=j) continue;
                else                for (age=bage; age<=fage; age ++){ 
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                  if ((int)age %5==0){
              }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
              fprintf(ficgp,")/(1");                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                                  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
              for(k1=1; k1 <=nlstate; k1++){                      mu1=mu[i][(int) age]/stepm*YEARM ;
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                    mu2=mu[j][(int) age]/stepm*YEARM;
                ij=1;                    c12=cv12/sqrt(v1*v2);
                for(j=3; j <=ncovmodel; j++){                    /* Computing eigen value of matrix of covariance */
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                    ij++;                    /* Eigen vectors */
                  }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                  else                    /*v21=sqrt(1.-v11*v11); *//* error */
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                    v21=(lc1-v1)/cv12*v11;
                }                    v12=-v21;
                fprintf(ficgp,")");                    v22=v11;
              }                    tnalp=v21/v11;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);                    if(first1==1){
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                      first1=0;
              i=i+ncovmodel;                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
            }                    }
          } /* end k */                    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);
        } /* end k2 */                    /*printf(fignu*/
      } /* end jk */                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
    } /* end ng */                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
    fclose(ficgp);                    if(first==1){
 }  /* end gnuplot */                      first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       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);
 /*************** Moving average **************/                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   int i, cpt, cptcod;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
       for (i=1; i<=nlstate;i++)                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           mobaverage[(int)agedeb][i][cptcod]=0.;                      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),\
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       for (i=1; i<=nlstate;i++){                    }else{
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                      first=0;
           for (cpt=0;cpt<=4;cpt++){                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
         }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     }                    }/* if first */
                      } /* age mod 5 */
 }                } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
 /************** Forecasting ******************/              } /*l12 */
 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){            } /* k12 */
            } /*l1 */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }/* k1 */
   int *popage;      } /* loop covariates */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    }
   double *popeffectif,*popcount;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   double ***p3mat;    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   char fileresf[FILENAMELENGTH];    free_vector(xp,1,npar);
     fclose(ficresprob);
  agelim=AGESUP;    fclose(ficresprobcov);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    fclose(ficresprobcor);
     fclose(ficgp);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    fclose(fichtm);
    }
    
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);  /******************* Printing html file ***********/
   if((ficresf=fopen(fileresf,"w"))==NULL) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     printf("Problem with forecast resultfile: %s\n", fileresf);                    int lastpass, int stepm, int weightopt, char model[],\
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   }                    int popforecast, int estepm ,\
   printf("Computing forecasting: result on file '%s' \n", fileresf);                    double jprev1, double mprev1,double anprev1, \
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    /*char optionfilehtm[FILENAMELENGTH];*/
     if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   if (mobilav==1) {      printf("Problem with %s \n",optionfilehtm), exit(0);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    }
   }  
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   stepsize=(int) (stepm+YEARM-1)/YEARM;   - 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
   if (stepm<=12) stepsize=1;   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
     - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   agelim=AGESUP;   - Life expectancies by age and initial health status (estepm=%2d months): 
       <a href=\"e%s\">e%s</a> <br>\n</li>", \
   hstepm=1;    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   anprojmean=yp;  
   yp2=modf((yp1*12),&yp);   m=cptcoveff;
   mprojmean=yp;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;   jj1=0;
   if(jprojmean==0) jprojmean=1;   for(k1=1; k1<=m;k1++){
   if(mprojmean==0) jprojmean=1;     for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);       if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   for(cptcov=1;cptcov<=i2;cptcov++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       k=k+1;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       fprintf(ficresf,"\n#******");       }
       for(j=1;j<=cptcoveff;j++) {       /* Pij */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       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);     
       fprintf(ficresf,"******\n");       /* Quasi-incidences */
       fprintf(ficresf,"# StartingAge FinalAge");       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>
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
               /* Stable prevalence in each health state */
               for(cpt=1; cpt<nlstate;cpt++){
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
         fprintf(ficresf,"\n");  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);           }
        for(cpt=1; cpt<=nlstate;cpt++) {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           nhstepm = nhstepm/hstepm;       }
                 fprintf(fichtm,"\n<br>- Total life expectancy by age and
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  health expectancies in states (1) and (2): e%s%d.png<br>
           oldm=oldms;savm=savms;  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       } /* end i1 */
           }/* End k1 */
           for (h=0; h<=nhstepm; h++){   fprintf(fichtm,"</ul>");
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  
             }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
             for(j=1; j<=nlstate+ndeath;j++) {   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
               kk1=0.;kk2=0;   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
               for(i=1; i<=nlstate;i++) {                 - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
                 if (mobilav==1)   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
                 else {   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
                 }  
                  /*  if(popforecast==1) fprintf(fichtm,"\n */
               }  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
               if (h==(int)(calagedate+12*cpt)){  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
                 fprintf(ficresf," %.3f", kk1);  /*      <br>",fileres,fileres,fileres,fileres); */
                          /*  else  */
               }  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
             }  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   m=cptcoveff;
         }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       }  
     }   jj1=0;
   }   for(k1=1; k1<=m;k1++){
             for(i1=1; i1<=ncodemax[k1];i1++){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       jj1++;
        if (cptcovn > 0) {
   fclose(ficresf);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 }         for (cpt=1; cpt<=cptcoveff;cpt++) 
 /************** Forecasting ******************/           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       for(cpt=1; cpt<=nlstate;cpt++) {
   int *popage;         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  interval) in state (%d): v%s%d%d.png <br>
   double *popeffectif,*popcount;  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
   double ***p3mat,***tabpop,***tabpopprev;       }
   char filerespop[FILENAMELENGTH];     } /* end i1 */
    }/* End k1 */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   fprintf(fichtm,"</ul>");
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  fclose(fichtm);
   agelim=AGESUP;  }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  
    /******************* Gnuplot file **************/
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    
      int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   strcpy(filerespop,"pop");    int ng;
   strcat(filerespop,fileres);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      printf("Problem with file %s",optionfilegnuplot);
     printf("Problem with forecast resultfile: %s\n", filerespop);      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);    }
   }  
   printf("Computing forecasting: result on file '%s' \n", filerespop);    /*#ifdef windows */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);      fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  m=pow(2,cptcoveff);
     
   if (mobilav==1) {   /* 1eme*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (cpt=1; cpt<= nlstate ; cpt ++) {
     movingaverage(agedeb, fage, ageminpar, mobaverage);     for (k1=1; k1<= m ; k1 ++) {
   }       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;       for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   agelim=AGESUP;         else fprintf(ficgp," \%%*lf (\%%*lf)");
         }
   hstepm=1;       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);
   hstepm=hstepm/stepm;       for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   if (popforecast==1) {         else fprintf(ficgp," \%%*lf (\%%*lf)");
     if((ficpop=fopen(popfile,"r"))==NULL) {       } 
       printf("Problem with population file : %s\n",popfile);exit(0);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);       for (i=1; i<= nlstate ; i ++) {
     }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     popage=ivector(0,AGESUP);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     popeffectif=vector(0,AGESUP);       }  
     popcount=vector(0,AGESUP);       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
         }
     i=1;      }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    /*2 eme*/
        
     imx=i;    for (k1=1; k1<= m ; k1 ++) { 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      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);
       
   for(cptcov=1;cptcov<=i2;cptcov++){      for (i=1; i<= nlstate+1 ; i ++) {
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        k=2*i;
       k=k+1;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
       fprintf(ficrespop,"\n#******");        for (j=1; j<= nlstate+1 ; j ++) {
       for(j=1;j<=cptcoveff;j++) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       }        }   
       fprintf(ficrespop,"******\n");        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       fprintf(ficrespop,"# Age");        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
       if (popforecast==1)  fprintf(ficrespop," [Population]");        for (j=1; j<= nlstate+1 ; j ++) {
                if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       for (cpt=0; cpt<=0;cpt++) {          else fprintf(ficgp," \%%*lf (\%%*lf)");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          }   
                fprintf(ficgp,"\" t\"\" w l 0,");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for (j=1; j<= nlstate+1 ; j ++) {
           nhstepm = nhstepm/hstepm;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                    else fprintf(ficgp," \%%*lf (\%%*lf)");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }   
           oldm=oldms;savm=savms;        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          else fprintf(ficgp,"\" t\"\" w l 0,");
              }
           for (h=0; h<=nhstepm; h++){    }
             if (h==(int) (calagedate+YEARM*cpt)) {    
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    /*3eme*/
             }    
             for(j=1; j<=nlstate+ndeath;j++) {    for (k1=1; k1<= m ; k1 ++) { 
               kk1=0.;kk2=0;      for (cpt=1; cpt<= nlstate ; cpt ++) {
               for(i=1; i<=nlstate;i++) {                      k=2+nlstate*(2*cpt-2);
                 if (mobilav==1)        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
                 else {        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                 }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
               }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
               if (h==(int)(calagedate+12*cpt)){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   /*fprintf(ficrespop," %.3f", kk1);          
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        */
               }        for (i=1; i< nlstate ; i ++) {
             }          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
             for(i=1; i<=nlstate;i++){          
               kk1=0.;        } 
                 for(j=1; j<=nlstate;j++){      }
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    }
                 }    
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    /* CV preval stable (period) */
             }    for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        k=3;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
         }        for (i=1; i<= nlstate ; i ++)
       }          fprintf(ficgp,"+$%d",k+i+1);
          fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   /******/        
         l=3+(nlstate+ndeath)*cpt;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          for (i=1; i< nlstate ; i ++) {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          l=3+(nlstate+ndeath)*cpt;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          fprintf(ficgp,"+$%d",l+i+1);
           nhstepm = nhstepm/hstepm;        }
                  fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } 
           oldm=oldms;savm=savms;    }  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      
           for (h=0; h<=nhstepm; h++){    /* proba elementaires */
             if (h==(int) (calagedate+YEARM*cpt)) {    for(i=1,jk=1; i <=nlstate; i++){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      for(k=1; k <=(nlstate+ndeath); k++){
             }        if (k != i) {
             for(j=1; j<=nlstate+ndeath;j++) {          for(j=1; j <=ncovmodel; j++){
               kk1=0.;kk2=0;            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
               for(i=1; i<=nlstate;i++) {                          jk++; 
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                fprintf(ficgp,"\n");
               }          }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        }
             }      }
           }     }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       }       for(jk=1; jk <=m; jk++) {
    }         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
   }         if (ng==2)
             fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         else
            fprintf(ficgp,"\nset title \"Probability\"\n");
   if (popforecast==1) {         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     free_ivector(popage,0,AGESUP);         i=1;
     free_vector(popeffectif,0,AGESUP);         for(k2=1; k2<=nlstate; k2++) {
     free_vector(popcount,0,AGESUP);           k3=i;
   }           for(k=1; k<=(nlstate+ndeath); k++) {
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);             if (k != k2){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);               if(ng==2)
   fclose(ficrespop);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
 }               else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
 /***********************************************/               ij=1;
 /**************** Main Program *****************/               for(j=3; j <=ncovmodel; j++) {
 /***********************************************/                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
 int main(int argc, char *argv[])                   ij++;
 {                 }
                  else
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   double agedeb, agefin,hf;               }
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;               fprintf(ficgp,")/(1");
                
   double fret;               for(k1=1; k1 <=nlstate; k1++){   
   double **xi,tmp,delta;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
   double dum; /* Dummy variable */                 for(j=3; j <=ncovmodel; j++){
   double ***p3mat;                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   int *indx;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   char line[MAXLINE], linepar[MAXLINE];                     ij++;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];                   }
   int firstobs=1, lastobs=10;                   else
   int sdeb, sfin; /* Status at beginning and end */                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   int c,  h , cpt,l;                 }
   int ju,jl, mi;                 fprintf(ficgp,")");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;               }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   int mobilav=0,popforecast=0;               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   int hstepm, nhstepm;               i=i+ncovmodel;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;             }
            } /* end k */
   double bage, fage, age, agelim, agebase;         } /* end k2 */
   double ftolpl=FTOL;       } /* end jk */
   double **prlim;     } /* end ng */
   double *severity;     fclose(ficgp); 
   double ***param; /* Matrix of parameters */  }  /* end gnuplot */
   double  *p;  
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */  /*************** Moving average **************/
   double *delti; /* Scale */  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */    int i, cpt, cptcod;
   double *epj, vepp;    int modcovmax =1;
   double kk1, kk2;    int mobilavrange, mob;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    double age;
    
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   char *alph[]={"a","a","b","c","d","e"}, str[4];                             a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   char z[1]="c", occ;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
 #include <sys/time.h>      if(mobilav==1) mobilavrange=5; /* default */
 #include <time.h>      else mobilavrange=mobilav;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      for (age=bage; age<=fage; age++)
          for (i=1; i<=nlstate;i++)
   /* long total_usecs;          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   struct timeval start_time, end_time;            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        /* We keep the original values on the extreme ages bage, fage and for 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   getcwd(pathcd, size);         we use a 5 terms etc. until the borders are no more concerned. 
       */ 
   printf("\n%s",version);      for (mob=3;mob <=mobilavrange;mob=mob+2){
   if(argc <=1){        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     printf("\nEnter the parameter file name: ");          for (i=1; i<=nlstate;i++){
     scanf("%s",pathtot);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   else{                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     strcpy(pathtot,argv[1]);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                }
   /*cygwin_split_path(pathtot,path,optionfile);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/            }
   /* cutv(path,optionfile,pathtot,'\\');*/          }
         }/* end age */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      }/* end mob */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    }else return -1;
   chdir(path);    return 0;
   replace(pathc,path);  }/* End movingaverage */
   
 /*-------- arguments in the command line --------*/  
   /************** Forecasting ******************/
   /* Log file */  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){
   strcat(filelog, optionfilefiname);    /* proj1, year, month, day of starting projection 
   strcat(filelog,".log");    /* */       agemin, agemax range of age
   if((ficlog=fopen(filelog,"w"))==NULL)    {       dateprev1 dateprev2 range of dates during which prevalence is computed
     printf("Problem with logfile %s\n",filelog);       anproj2 year of en of projection (same day and month as proj1).
     goto end;    */
   }    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   fprintf(ficlog,"Log filename:%s\n",filelog);    int *popage;
   fprintf(ficlog,"\n%s",version);    double agec; /* generic age */
   fprintf(ficlog,"\nEnter the parameter file name: ");    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    double *popeffectif,*popcount;
   fflush(ficlog);    double ***p3mat;
     double ***mobaverage;
   /* */    char fileresf[FILENAMELENGTH];
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);    agelim=AGESUP;
   strcat(fileres,".txt");    /* Other files have txt extension */    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
   /*---------arguments file --------*/    strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    if((ficresf=fopen(fileresf,"w"))==NULL) {
     printf("Problem with optionfile %s\n",optionfile);      printf("Problem with forecast resultfile: %s\n", fileresf);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     goto end;    }
   }    printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   strcpy(filereso,"o");  
   strcat(filereso,fileres);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);    if (mobilav!=0) {
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     goto end;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
   /* Reads comments: lines beginning with '#' */      }
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     puts(line);    if (stepm<=12) stepsize=1;
     fputs(line,ficparo);    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   ungetc(c,ficpar);    }
     else  hstepm=estepm;   
   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);    hstepm=hstepm/stepm; 
   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);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
 while((c=getc(ficpar))=='#' && c!= EOF){                                 fractional in yp1 */
     ungetc(c,ficpar);    anprojmean=yp;
     fgets(line, MAXLINE, ficpar);    yp2=modf((yp1*12),&yp);
     puts(line);    mprojmean=yp;
     fputs(line,ficparo);    yp1=modf((yp2*30.5),&yp);
   }    jprojmean=yp;
   ungetc(c,ficpar);    if(jprojmean==0) jprojmean=1;
      if(mprojmean==0) jprojmean=1;
      
   covar=matrix(0,NCOVMAX,1,n);    i1=cptcoveff;
   cptcovn=0;    if (cptcovn < 1){i1=1;}
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   ncovmodel=2+cptcovn;    
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    fprintf(ficresf,"#****** Routine prevforecast **\n");
    
   /* Read guess parameters */  /*            if (h==(int)(YEARM*yearp)){ */
   /* Reads comments: lines beginning with '#' */    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   while((c=getc(ficpar))=='#' && c!= EOF){      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     ungetc(c,ficpar);        k=k+1;
     fgets(line, MAXLINE, ficpar);        fprintf(ficresf,"\n#******");
     puts(line);        for(j=1;j<=cptcoveff;j++) {
     fputs(line,ficparo);          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]]);
   }        }
   ungetc(c,ficpar);        fprintf(ficresf,"******\n");
          fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        for(j=1; j<=nlstate+ndeath;j++){ 
     for(i=1; i <=nlstate; i++)          for(i=1; i<=nlstate;i++)              
     for(j=1; j <=nlstate+ndeath-1; j++){            fprintf(ficresf," p%d%d",i,j);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          fprintf(ficresf," p.%d",j);
       fprintf(ficparo,"%1d%1d",i1,j1);        }
       if(mle==1)        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
         printf("%1d%1d",i,j);          fprintf(ficresf,"\n");
       fprintf(ficlog,"%1d%1d",i,j);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
         if(mle==1){            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
           printf(" %lf",param[i][j][k]);            nhstepm = nhstepm/hstepm; 
           fprintf(ficlog," %lf",param[i][j][k]);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }            oldm=oldms;savm=savms;
         else            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficlog," %lf",param[i][j][k]);          
         fprintf(ficparo," %lf",param[i][j][k]);            for (h=0; h<=nhstepm; h++){
       }              if (h*hstepm/YEARM*stepm ==yearp) {
       fscanf(ficpar,"\n");                fprintf(ficresf,"\n");
       if(mle==1)                for(j=1;j<=cptcoveff;j++) 
         printf("\n");                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficlog,"\n");                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
       fprintf(ficparo,"\n");              } 
     }              for(j=1; j<=nlstate+ndeath;j++) {
                  ppij=0.;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
   p=param[1][1];                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                    else {
   /* Reads comments: lines beginning with '#' */                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   while((c=getc(ficpar))=='#' && c!= EOF){                  }
     ungetc(c,ficpar);                  if (h*hstepm/YEARM*stepm== yearp) {
     fgets(line, MAXLINE, ficpar);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
     puts(line);                  }
     fputs(line,ficparo);                } /* end i */
   }                if (h*hstepm/YEARM*stepm==yearp) {
   ungetc(c,ficpar);                  fprintf(ficresf," %.3f", ppij);
                 }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              }/* end j */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            } /* end h */
   for(i=1; i <=nlstate; i++){            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(j=1; j <=nlstate+ndeath-1; j++){          } /* end agec */
       fscanf(ficpar,"%1d%1d",&i1,&j1);        } /* end yearp */
       printf("%1d%1d",i,j);      } /* end cptcod */
       fprintf(ficparo,"%1d%1d",i1,j1);    } /* end  cptcov */
       for(k=1; k<=ncovmodel;k++){         
         fscanf(ficpar,"%le",&delti3[i][j][k]);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);    fclose(ficresf);
       }  }
       fscanf(ficpar,"\n");  
       printf("\n");  /************** Forecasting *****not tested NB*************/
       fprintf(ficparo,"\n");  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     }    
   }    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   delti=delti3[1][1];    int *popage;
      double calagedatem, agelim, kk1, kk2;
   /* Reads comments: lines beginning with '#' */    double *popeffectif,*popcount;
   while((c=getc(ficpar))=='#' && c!= EOF){    double ***p3mat,***tabpop,***tabpopprev;
     ungetc(c,ficpar);    double ***mobaverage;
     fgets(line, MAXLINE, ficpar);    char filerespop[FILENAMELENGTH];
     puts(line);  
     fputs(line,ficparo);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   ungetc(c,ficpar);    agelim=AGESUP;
      calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   matcov=matrix(1,npar,1,npar);    
   for(i=1; i <=npar; i++){    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     fscanf(ficpar,"%s",&str);    
     if(mle==1)    
       printf("%s",str);    strcpy(filerespop,"pop"); 
     fprintf(ficlog,"%s",str);    strcat(filerespop,fileres);
     fprintf(ficparo,"%s",str);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     for(j=1; j <=i; j++){      printf("Problem with forecast resultfile: %s\n", filerespop);
       fscanf(ficpar," %le",&matcov[i][j]);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
       if(mle==1){    }
         printf(" %.5le",matcov[i][j]);    printf("Computing forecasting: result on file '%s' \n", filerespop);
         fprintf(ficlog," %.5le",matcov[i][j]);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
       }  
       else    if (cptcoveff==0) ncodemax[cptcoveff]=1;
         fprintf(ficlog," %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);    if (mobilav!=0) {
     }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fscanf(ficpar,"\n");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     if(mle==1)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       printf("\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     fprintf(ficlog,"\n");      }
     fprintf(ficparo,"\n");    }
   }  
   for(i=1; i <=npar; i++)    stepsize=(int) (stepm+YEARM-1)/YEARM;
     for(j=i+1;j<=npar;j++)    if (stepm<=12) stepsize=1;
       matcov[i][j]=matcov[j][i];    
        agelim=AGESUP;
   if(mle==1)    
     printf("\n");    hstepm=1;
   fprintf(ficlog,"\n");    hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
     /*-------- Rewriting paramater file ----------*/      if((ficpop=fopen(popfile,"r"))==NULL) {
      strcpy(rfileres,"r");    /* "Rparameterfile */        printf("Problem with population file : %s\n",popfile);exit(0);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
      strcat(rfileres,".");    /* */      } 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      popage=ivector(0,AGESUP);
     if((ficres =fopen(rfileres,"w"))==NULL) {      popeffectif=vector(0,AGESUP);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      popcount=vector(0,AGESUP);
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;      
     }      i=1;   
     fprintf(ficres,"#%s\n",version);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
         
     /*-------- data file ----------*/      imx=i;
     if((fic=fopen(datafile,"r"))==NULL)    {      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
       printf("Problem with datafile: %s\n", datafile);goto end;    }
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;  
     }    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     n= lastobs;        k=k+1;
     severity = vector(1,maxwav);        fprintf(ficrespop,"\n#******");
     outcome=imatrix(1,maxwav+1,1,n);        for(j=1;j<=cptcoveff;j++) {
     num=ivector(1,n);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     moisnais=vector(1,n);        }
     annais=vector(1,n);        fprintf(ficrespop,"******\n");
     moisdc=vector(1,n);        fprintf(ficrespop,"# Age");
     andc=vector(1,n);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     agedc=vector(1,n);        if (popforecast==1)  fprintf(ficrespop," [Population]");
     cod=ivector(1,n);        
     weight=vector(1,n);        for (cpt=0; cpt<=0;cpt++) { 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     mint=matrix(1,maxwav,1,n);          
     anint=matrix(1,maxwav,1,n);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     s=imatrix(1,maxwav+1,1,n);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     adl=imatrix(1,maxwav+1,1,n);                nhstepm = nhstepm/hstepm; 
     tab=ivector(1,NCOVMAX);            
     ncodemax=ivector(1,8);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
     i=1;            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     while (fgets(line, MAXLINE, fic) != NULL)    {          
       if ((i >= firstobs) && (i <=lastobs)) {            for (h=0; h<=nhstepm; h++){
                      if (h==(int) (calagedatem+YEARM*cpt)) {
         for (j=maxwav;j>=1;j--){                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              } 
           strcpy(line,stra);              for(j=1; j<=nlstate+ndeath;j++) {
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                kk1=0.;kk2=0;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                for(i=1; i<=nlstate;i++) {              
         }                  if (mobilav==1) 
                            kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                  else {
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                    /*fprintf(ficrespop," %.3f", kk1);
         for (j=ncovcol;j>=1;j--){                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                }
         }              }
         num[i]=atol(stra);              for(i=1; i<=nlstate;i++){
                        kk1=0.;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                  for(j=1; j<=nlstate;j++){
           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;}*/                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
         i=i+1;                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
       }              }
     }  
     /* printf("ii=%d", ij);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
        scanf("%d",i);*/                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   imx=i-1; /* Number of individuals */            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* 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++){        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
      if (s[4][i]==9)  s[4][i]=-1;          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
      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 (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
              nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
              nhstepm = nhstepm/hstepm; 
   /* 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 */            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   Tprod=ivector(1,15);            oldm=oldms;savm=savms;
   Tvaraff=ivector(1,15);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   Tvard=imatrix(1,15,1,2);            for (h=0; h<=nhstepm; h++){
   Tage=ivector(1,15);                    if (h==(int) (calagedatem+YEARM*cpt)) {
                    fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   if (strlen(model) >1){              } 
     j=0, j1=0, k1=1, k2=1;              for(j=1; j<=nlstate+ndeath;j++) {
     j=nbocc(model,'+');                kk1=0.;kk2=0;
     j1=nbocc(model,'*');                for(i=1; i<=nlstate;i++) {              
     cptcovn=j+1;                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
     cptcovprod=j1;                }
                    if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
     strcpy(modelsav,model);              }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            }
       printf("Error. Non available option model=%s ",model);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficlog,"Error. Non available option model=%s ",model);          }
       goto end;        }
     }     } 
        }
     for(i=(j+1); i>=1;i--){   
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    if (popforecast==1) {
       /*scanf("%d",i);*/      free_ivector(popage,0,AGESUP);
       if (strchr(strb,'*')) {  /* Model includes a product */      free_vector(popeffectif,0,AGESUP);
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/      free_vector(popcount,0,AGESUP);
         if (strcmp(strc,"age")==0) { /* Vn*age */    }
           cptcovprod--;    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           cutv(strb,stre,strd,'V');    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/    fclose(ficrespop);
           cptcovage++;  }
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/  /***********************************************/
         }  /**************** Main Program *****************/
         else if (strcmp(strd,"age")==0) { /* or age*Vn */  /***********************************************/
           cptcovprod--;  
           cutv(strb,stre,strc,'V');  int main(int argc, char *argv[])
           Tvar[i]=atoi(stre);  {
           cptcovage++;    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
           Tage[cptcovage]=i;    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
         }    double agedeb, agefin,hf;
         else {  /* Age is not in the model */    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/  
           Tvar[i]=ncovcol+k1;    double fret;
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */    double **xi,tmp,delta;
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc); /* m*/    double dum; /* Dummy variable */
           Tvard[k1][2]=atoi(stre); /* n */    double ***p3mat;
           Tvar[cptcovn+k2]=Tvard[k1][1];    double ***mobaverage;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    int *indx;
           for (k=1; k<=lastobs;k++)    char line[MAXLINE], linepar[MAXLINE];
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
           k1++;    int firstobs=1, lastobs=10;
           k2=k2+2;    int sdeb, sfin; /* Status at beginning and end */
         }    int c,  h , cpt,l;
       }    int ju,jl, mi;
       else { /* no more sum */    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
        /*  scanf("%d",i);*/    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
       cutv(strd,strc,strb,'V');    int mobilav=0,popforecast=0;
       Tvar[i]=atoi(strc);    int hstepm, nhstepm;
       }    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
       strcpy(modelsav,stra);      double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/    double bage, fage, age, agelim, agebase;
     } /* end of loop + */    double ftolpl=FTOL;
   } /* end model */    double **prlim;
      double *severity;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    double ***param; /* Matrix of parameters */
   printf("cptcovprod=%d ", cptcovprod);    double  *p;
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    double **matcov; /* Matrix of covariance */
   scanf("%d ",i);*/    double ***delti3; /* Scale */
     fclose(fic);    double *delti; /* Scale */
     double ***eij, ***vareij;
     /*  if(mle==1){*/    double **varpl; /* Variances of prevalence limits by age */
     if (weightopt != 1) { /* Maximisation without weights*/    double *epj, vepp;
       for(i=1;i<=n;i++) weight[i]=1.0;    double kk1, kk2;
     }    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
     for (i=1; i<=imx; i++) {  
       for(m=2; (m<= maxwav); m++) {    char z[1]="c", occ;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  #include <sys/time.h>
          anint[m][i]=9999;  #include <time.h>
          s[m][i]=-1;    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
        }   
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    /* long total_usecs;
       }       struct timeval start_time, end_time;
     }    
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     for (i=1; i<=imx; i++)  {    getcwd(pathcd, size);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){    printf("\n%s",version);
         if(s[m][i] >0){    if(argc <=1){
           if (s[m][i] >= nlstate+1) {      printf("\nEnter the parameter file name: ");
             if(agedc[i]>0)      scanf("%s",pathtot);
               if(moisdc[i]!=99 && andc[i]!=9999)    }
                 agev[m][i]=agedc[i];    else{
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      strcpy(pathtot,argv[1]);
            else {    }
               if (andc[i]!=9999){    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    /*cygwin_split_path(pathtot,path,optionfile);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
               agev[m][i]=-1;    /* 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);
           else if(s[m][i] !=9){ /* Should no more exist */    chdir(path);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    replace(pathc,path);
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;    /*-------- arguments in the command line --------*/
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];    /* Log file */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    strcat(filelog, optionfilefiname);
             }    strcat(filelog,".log");    /* */
             else if(agev[m][i] >agemax){    if((ficlog=fopen(filelog,"w"))==NULL)    {
               agemax=agev[m][i];      printf("Problem with logfile %s\n",filelog);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      goto end;
             }    }
             /*agev[m][i]=anint[m][i]-annais[i];*/    fprintf(ficlog,"Log filename:%s\n",filelog);
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(ficlog,"\n%s",version);
           }    fprintf(ficlog,"\nEnter the parameter file name: ");
           else { /* =9 */    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
             agev[m][i]=1;    fflush(ficlog);
             s[m][i]=-1;  
           }    /* */
         }    strcpy(fileres,"r");
         else /*= 0 Unknown */    strcat(fileres, optionfilefiname);
           agev[m][i]=1;    strcat(fileres,".txt");    /* Other files have txt extension */
       }  
        /*---------arguments file --------*/
     }  
     for (i=1; i<=imx; i++)  {    if((ficpar=fopen(optionfile,"r"))==NULL)    {
       for(m=1; (m<= maxwav); m++){      printf("Problem with optionfile %s\n",optionfile);
         if (s[m][i] > (nlstate+ndeath)) {      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
           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);        goto end;
           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;  
         }    strcpy(filereso,"o");
       }    strcat(filereso,fileres);
     }    if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      goto end;
     }
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);    /* Reads comments: lines beginning with '#' */
     free_vector(moisnais,1,n);    while((c=getc(ficpar))=='#' && c!= EOF){
     free_vector(annais,1,n);      ungetc(c,ficpar);
     /* free_matrix(mint,1,maxwav,1,n);      fgets(line, MAXLINE, ficpar);
        free_matrix(anint,1,maxwav,1,n);*/      puts(line);
     free_vector(moisdc,1,n);      fputs(line,ficparo);
     free_vector(andc,1,n);    }
     ungetc(c,ficpar);
      
     wav=ivector(1,imx);    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);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    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);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    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){
     /* Concatenates waves */      ungetc(c,ficpar);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
       Tcode=ivector(1,100);    }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    ungetc(c,ficpar);
       ncodemax[1]=1;    
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);     
          covar=matrix(0,NCOVMAX,1,n); 
    codtab=imatrix(1,100,1,10);    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
    h=0;    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
    m=pow(2,cptcoveff);  
      ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
    for(k=1;k<=cptcoveff; k++){    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
      for(i=1; i <=(m/pow(2,k));i++){    
        for(j=1; j <= ncodemax[k]; j++){    /* Read guess parameters */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    /* Reads comments: lines beginning with '#' */
            h++;    while((c=getc(ficpar))=='#' && c!= EOF){
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;      ungetc(c,ficpar);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      fgets(line, MAXLINE, ficpar);
          }      puts(line);
        }      fputs(line,ficparo);
      }    }
    }    ungetc(c,ficpar);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    
       codtab[1][2]=1;codtab[2][2]=2; */    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
    /* for(i=1; i <=m ;i++){    for(i=1; i <=nlstate; i++)
       for(k=1; k <=cptcovn; k++){      for(j=1; j <=nlstate+ndeath-1; j++){
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);        fscanf(ficpar,"%1d%1d",&i1,&j1);
       }        fprintf(ficparo,"%1d%1d",i1,j1);
       printf("\n");        if(mle==1)
       }          printf("%1d%1d",i,j);
       scanf("%d",i);*/        fprintf(ficlog,"%1d%1d",i,j);
            for(k=1; k<=ncovmodel;k++){
    /* Calculates basic frequencies. Computes observed prevalence at single age          fscanf(ficpar," %lf",&param[i][j][k]);
        and prints on file fileres'p'. */          if(mle==1){
             printf(" %lf",param[i][j][k]);
                fprintf(ficlog," %lf",param[i][j][k]);
              }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          else
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            fprintf(ficlog," %lf",param[i][j][k]);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficparo," %lf",param[i][j][k]);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        fscanf(ficpar,"\n");
              if(mle==1)
     /* For Powell, parameters are in a vector p[] starting at p[1]          printf("\n");
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        fprintf(ficlog,"\n");
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        fprintf(ficparo,"\n");
       }
     if(mle==1){    
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
     }  
        p=param[1][1];
     /*--------- 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);    /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
    jk=1;      fgets(line, MAXLINE, ficpar);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      puts(line);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fputs(line,ficparo);
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    }
    for(i=1,jk=1; i <=nlstate; i++){    ungetc(c,ficpar);
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
          {    /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
            printf("%d%d ",i,k);    for(i=1; i <=nlstate; i++){
            fprintf(ficlog,"%d%d ",i,k);      for(j=1; j <=nlstate+ndeath-1; j++){
            fprintf(ficres,"%1d%1d ",i,k);        fscanf(ficpar,"%1d%1d",&i1,&j1);
            for(j=1; j <=ncovmodel; j++){        printf("%1d%1d",i,j);
              printf("%f ",p[jk]);        fprintf(ficparo,"%1d%1d",i1,j1);
              fprintf(ficlog,"%f ",p[jk]);        for(k=1; k<=ncovmodel;k++){
              fprintf(ficres,"%f ",p[jk]);          fscanf(ficpar,"%le",&delti3[i][j][k]);
              jk++;          printf(" %le",delti3[i][j][k]);
            }          fprintf(ficparo," %le",delti3[i][j][k]);
            printf("\n");        }
            fprintf(ficlog,"\n");        fscanf(ficpar,"\n");
            fprintf(ficres,"\n");        printf("\n");
          }        fprintf(ficparo,"\n");
      }      }
    }    }
    if(mle==1){    delti=delti3[1][1];
      /* Computing hessian and covariance matrix */  
      ftolhess=ftol; /* Usually correct */  
      hesscov(matcov, p, npar, delti, ftolhess, func);    /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
    }    
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    /* Reads comments: lines beginning with '#' */
    printf("# Scales (for hessian or gradient estimation)\n");    while((c=getc(ficpar))=='#' && c!= EOF){
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");      ungetc(c,ficpar);
    for(i=1,jk=1; i <=nlstate; i++){      fgets(line, MAXLINE, ficpar);
      for(j=1; j <=nlstate+ndeath; j++){      puts(line);
        if (j!=i) {      fputs(line,ficparo);
          fprintf(ficres,"%1d%1d",i,j);    }
          printf("%1d%1d",i,j);    ungetc(c,ficpar);
          fprintf(ficlog,"%1d%1d",i,j);    
          for(k=1; k<=ncovmodel;k++){    matcov=matrix(1,npar,1,npar);
            printf(" %.5e",delti[jk]);    for(i=1; i <=npar; i++){
            fprintf(ficlog," %.5e",delti[jk]);      fscanf(ficpar,"%s",&str);
            fprintf(ficres," %.5e",delti[jk]);      if(mle==1)
            jk++;        printf("%s",str);
          }      fprintf(ficlog,"%s",str);
          printf("\n");      fprintf(ficparo,"%s",str);
          fprintf(ficlog,"\n");      for(j=1; j <=i; j++){
          fprintf(ficres,"\n");        fscanf(ficpar," %le",&matcov[i][j]);
        }        if(mle==1){
      }          printf(" %.5le",matcov[i][j]);
    }          fprintf(ficlog," %.5le",matcov[i][j]);
            }
    k=1;        else
    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");          fprintf(ficlog," %.5le",matcov[i][j]);
    if(mle==1)        fprintf(ficparo," %.5le",matcov[i][j]);
      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");      fscanf(ficpar,"\n");
    for(i=1;i<=npar;i++){      if(mle==1)
      /*  if (k>nlstate) k=1;        printf("\n");
          i1=(i-1)/(ncovmodel*nlstate)+1;      fprintf(ficlog,"\n");
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      fprintf(ficparo,"\n");
          printf("%s%d%d",alph[k],i1,tab[i]);*/    }
      fprintf(ficres,"%3d",i);    for(i=1; i <=npar; i++)
      if(mle==1)      for(j=i+1;j<=npar;j++)
        printf("%3d",i);        matcov[i][j]=matcov[j][i];
      fprintf(ficlog,"%3d",i);     
      for(j=1; j<=i;j++){    if(mle==1)
        fprintf(ficres," %.5e",matcov[i][j]);      printf("\n");
        if(mle==1)    fprintf(ficlog,"\n");
          printf(" %.5e",matcov[i][j]);  
        fprintf(ficlog," %.5e",matcov[i][j]);  
      }    /*-------- Rewriting paramater file ----------*/
      fprintf(ficres,"\n");    strcpy(rfileres,"r");    /* "Rparameterfile */
      if(mle==1)    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
        printf("\n");    strcat(rfileres,".");    /* */
      fprintf(ficlog,"\n");    strcat(rfileres,optionfilext);    /* Other files have txt extension */
      k++;    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;
    while((c=getc(ficpar))=='#' && c!= EOF){    }
      ungetc(c,ficpar);    fprintf(ficres,"#%s\n",version);
      fgets(line, MAXLINE, ficpar);      
      puts(line);    /*-------- data file ----------*/
      fputs(line,ficparo);    if((fic=fopen(datafile,"r"))==NULL)    {
    }      printf("Problem with datafile: %s\n", datafile);goto end;
    ungetc(c,ficpar);      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
    estepm=0;    }
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);  
    if (estepm==0 || estepm < stepm) estepm=stepm;    n= lastobs;
    if (fage <= 2) {    severity = vector(1,maxwav);
      bage = ageminpar;    outcome=imatrix(1,maxwav+1,1,n);
      fage = agemaxpar;    num=ivector(1,n);
    }    moisnais=vector(1,n);
        annais=vector(1,n);
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    moisdc=vector(1,n);
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    andc=vector(1,n);
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    agedc=vector(1,n);
        cod=ivector(1,n);
    while((c=getc(ficpar))=='#' && c!= EOF){    weight=vector(1,n);
      ungetc(c,ficpar);    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
      fgets(line, MAXLINE, ficpar);    mint=matrix(1,maxwav,1,n);
      puts(line);    anint=matrix(1,maxwav,1,n);
      fputs(line,ficparo);    s=imatrix(1,maxwav+1,1,n);
    }    tab=ivector(1,NCOVMAX);
    ungetc(c,ficpar);    ncodemax=ivector(1,8);
    
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    i=1;
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    while (fgets(line, MAXLINE, fic) != NULL)    {
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      if ((i >= firstobs) && (i <=lastobs)) {
              
    while((c=getc(ficpar))=='#' && c!= EOF){        for (j=maxwav;j>=1;j--){
      ungetc(c,ficpar);          cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
      fgets(line, MAXLINE, ficpar);          strcpy(line,stra);
      puts(line);          cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
      fputs(line,ficparo);          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
    }        }
    ungetc(c,ficpar);          
          cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
   fprintf(ficparo,"pop_based=%d\n",popbased);          cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
   fprintf(ficres,"pop_based=%d\n",popbased);          for (j=ncovcol;j>=1;j--){
            cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
   while((c=getc(ficpar))=='#' && c!= EOF){        } 
     ungetc(c,ficpar);        num[i]=atol(stra);
     fgets(line, MAXLINE, ficpar);          
     puts(line);        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
     fputs(line,ficparo);          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;}*/
   }  
   ungetc(c,ficpar);        i=i+1;
       }
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);    }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    /* printf("ii=%d", ij);
 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);       scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
 while((c=getc(ficpar))=='#' && c!= EOF){    /* for (i=1; i<=imx; i++){
     ungetc(c,ficpar);      if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
     fgets(line, MAXLINE, ficpar);      if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
     puts(line);      if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
     fputs(line,ficparo);      }*/
   }     /*  for (i=1; i<=imx; i++){
   ungetc(c,ficpar);       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]));}*/
   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);   for (i=1; i<=imx; i++)
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);   
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       else weight[i]=1;*/
   
 /*------------ gnuplot -------------*/    /* Calculation of the number of parameter from char model*/
   strcpy(optionfilegnuplot,optionfilefiname);    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
   strcat(optionfilegnuplot,".gp");    Tprod=ivector(1,15); 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    Tvaraff=ivector(1,15); 
     printf("Problem with file %s",optionfilegnuplot);    Tvard=imatrix(1,15,1,2);
   }    Tage=ivector(1,15);      
   fclose(ficgp);     
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    if (strlen(model) >1){ /* If there is at least 1 covariate */
 /*--------- index.htm --------*/      j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
   strcpy(optionfilehtm,optionfile);      j1=nbocc(model,'*'); /* j1=Number of '*' */
   strcat(optionfilehtm,".htm");      cptcovn=j+1; 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      cptcovprod=j1; /*Number of products */
     printf("Problem with %s \n",optionfilehtm), exit(0);      
   }      strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n        printf("Error. Non available option model=%s ",model);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        fprintf(ficlog,"Error. Non available option model=%s ",model);
 \n        goto end;
 Total number of observations=%d <br>\n      }
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      
 <hr  size=\"2\" color=\"#EC5E5E\">      /* This loop fills the array Tvar from the string 'model'.*/
  <ul><li><h4>Parameter files</h4>\n  
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      for(i=(j+1); i>=1;i--){
  - Log file of the run: <a href=\"%s\">%s</a><br>\n        cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
   fclose(fichtm);        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);        if (strchr(strb,'*')) {  /* Model includes a product */
            cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
 /*------------ free_vector  -------------*/          if (strcmp(strc,"age")==0) { /* Vn*age */
  chdir(path);            cptcovprod--;
              cutv(strb,stre,strd,'V');
  free_ivector(wav,1,imx);            Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            cptcovage++;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                Tage[cptcovage]=i;
  free_ivector(num,1,n);              /*printf("stre=%s ", stre);*/
  free_vector(agedc,1,n);          }
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          else if (strcmp(strd,"age")==0) { /* or age*Vn */
  fclose(ficparo);            cptcovprod--;
  fclose(ficres);            cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
   /*--------------- Prevalence limit --------------*/            Tage[cptcovage]=i;
            }
   strcpy(filerespl,"pl");          else {  /* Age is not in the model */
   strcat(filerespl,fileres);            cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            Tvar[i]=ncovcol+k1;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;            Tprod[k1]=i;
   }            Tvard[k1][1]=atoi(strc); /* m*/
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            Tvard[k1][2]=atoi(stre); /* n */
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);            Tvar[cptcovn+k2]=Tvard[k1][1];
   fprintf(ficrespl,"#Prevalence limit\n");            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
   fprintf(ficrespl,"#Age ");            for (k=1; k<=lastobs;k++) 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
   fprintf(ficrespl,"\n");            k1++;
              k2=k2+2;
   prlim=matrix(1,nlstate,1,nlstate);          }
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        else { /* no more sum */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         /*  scanf("%d",i);*/
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        cutv(strd,strc,strb,'V');
   k=0;        Tvar[i]=atoi(strc);
   agebase=ageminpar;        }
   agelim=agemaxpar;        strcpy(modelsav,stra);  
   ftolpl=1.e-10;        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
   i1=cptcoveff;          scanf("%d",i);*/
   if (cptcovn < 1){i1=1;}      } /* end of loop + */
     } /* end model */
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
         k=k+1;      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
         printf("\n#******");    printf("cptcovprod=%d ", cptcovprod);
         fprintf(ficlog,"\n#******");    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
         for(j=1;j<=cptcoveff;j++) {  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    scanf("%d ",i);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fclose(fic);*/
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         }      /*  if(mle==1){*/
         fprintf(ficrespl,"******\n");    if (weightopt != 1) { /* Maximisation without weights*/
         printf("******\n");      for(i=1;i<=n;i++) weight[i]=1.0;
         fprintf(ficlog,"******\n");    }
              /*-calculation of age at interview from date of interview and age at death -*/
         for (age=agebase; age<=agelim; age++){    agev=matrix(1,maxwav,1,imx);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );    for (i=1; i<=imx; i++) {
           for(i=1; i<=nlstate;i++)      for(m=2; (m<= maxwav); m++) {
           fprintf(ficrespl," %.5f", prlim[i][i]);        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           fprintf(ficrespl,"\n");          anint[m][i]=9999;
         }          s[m][i]=-1;
       }        }
     }        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
   fclose(ficrespl);          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);
   /*------------- h Pij x at various ages ------------*/          s[m][i]=-1;
          }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          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]); 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          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]); 
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;          s[m][i]=-1;
   }        }
   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;    for (i=1; i<=imx; i++)  {
   /*if (stepm<=24) stepsize=2;*/      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
   agelim=AGESUP;        if(s[m][i] >0){
   hstepm=stepsize*YEARM; /* Every year of age */          if (s[m][i] >= nlstate+1) {
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
   /* hstepm=1;   aff par mois*/                agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
   k=0;              else {
   for(cptcov=1;cptcov<=i1;cptcov++){                if ((int)andc[i]!=9999){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                  printf("Warning negative age at death: %d line:%d\n",num[i],i);
       k=k+1;                  fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
         fprintf(ficrespij,"\n#****** ");                  agev[m][i]=-1;
         for(j=1;j<=cptcoveff;j++)                }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              }
         fprintf(ficrespij,"******\n");          }
                  else if(s[m][i] !=9){ /* Standard case, age in fractional
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                                   years but with the precision of a
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                                   month */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            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)
           /*      nhstepm=nhstepm*YEARM; aff par mois*/              agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              agemin=agev[m][i];
           oldm=oldms;savm=savms;              /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              }
           fprintf(ficrespij,"# Age");            else if(agev[m][i] >agemax){
           for(i=1; i<=nlstate;i++)              agemax=agev[m][i];
             for(j=1; j<=nlstate+ndeath;j++)              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
               fprintf(ficrespij," %1d-%1d",i,j);            }
           fprintf(ficrespij,"\n");            /*agev[m][i]=anint[m][i]-annais[i];*/
            for (h=0; h<=nhstepm; h++){            /*     agev[m][i] = age[i]+2*m;*/
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          }
             for(i=1; i<=nlstate;i++)          else { /* =9 */
               for(j=1; j<=nlstate+ndeath;j++)            agev[m][i]=1;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            s[m][i]=-1;
             fprintf(ficrespij,"\n");          }
              }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        else /*= 0 Unknown */
           fprintf(ficrespij,"\n");          agev[m][i]=1;
         }      }
     }      
   }    }
     for (i=1; i<=imx; i++)  {
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
   fclose(ficrespij);          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;
   /*---------- Forecasting ------------------*/        }
   if((stepm == 1) && (strcmp(model,".")==0)){      }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    }
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
   }    /*for (i=1; i<=imx; i++){
   else{    for (m=firstpass; (m<lastpass); m++){
     erreur=108;       printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
     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);  
   }  }*/
    
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
   /*---------- Health expectancies and variances ------------*/    fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
   strcpy(filerest,"t");    free_vector(severity,1,maxwav);
   strcat(filerest,fileres);    free_imatrix(outcome,1,maxwav+1,1,n);
   if((ficrest=fopen(filerest,"w"))==NULL) {    free_vector(moisnais,1,n);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    free_vector(annais,1,n);
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;    /* free_matrix(mint,1,maxwav,1,n);
   }       free_matrix(anint,1,maxwav,1,n);*/
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    free_vector(moisdc,1,n);
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);    free_vector(andc,1,n);
   
      
   strcpy(filerese,"e");    wav=ivector(1,imx);
   strcat(filerese,fileres);    dh=imatrix(1,lastpass-firstpass+1,1,imx);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    bh=imatrix(1,lastpass-firstpass+1,1,imx);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    mw=imatrix(1,lastpass-firstpass+1,1,imx);
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);     
   }    /* Concatenates waves */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);  
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   strcpy(fileresv,"v");  
   strcat(fileresv,fileres);    Tcode=ivector(1,100);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    ncodemax[1]=1;
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);    if (cptcovn > 0) tricode(Tvar,nbcode,imx);
   }        
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                                   the estimations*/
   calagedate=-1;    h=0;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    m=pow(2,cptcoveff);
    
   k=0;    for(k=1;k<=cptcoveff; k++){
   for(cptcov=1;cptcov<=i1;cptcov++){      for(i=1; i <=(m/pow(2,k));i++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(j=1; j <= ncodemax[k]; j++){
       k=k+1;          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
       fprintf(ficrest,"\n#****** ");            h++;
       for(j=1;j<=cptcoveff;j++)            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[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]);*/
       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]]);    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
       fprintf(ficreseij,"******\n");       codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
       fprintf(ficresvij,"\n#****** ");       for(k=1; k <=cptcovn; k++){
       for(j=1;j<=cptcoveff;j++)       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       }
       fprintf(ficresvij,"******\n");       printf("\n");
        }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       scanf("%d",i);*/
       oldm=oldms;savm=savms;      
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      /* Calculates basic frequencies. Computes observed prevalence at single age
         and prints on file fileres'p'. */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;      pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       if(popbased==1){      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
        }      oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
       
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    /* For Powell, parameters are in a vector p[] starting at p[1]
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
       fprintf(ficrest,"\n");    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
       epj=vector(1,nlstate+1);    if(mle>=1){ /* Could be 1 or 2 */
       for(age=bage; age <=fage ;age++){      mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    }
         if (popbased==1) {      
           for(i=1; i<=nlstate;i++)    /*--------- results files --------------*/
             prlim[i][i]=probs[(int)age][i][k];    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);
         }    
          
         fprintf(ficrest," %4.0f",age);    jk=1;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    for(i=1,jk=1; i <=nlstate; i++){
           }      for(k=1; k <=(nlstate+ndeath); k++){
           epj[nlstate+1] +=epj[j];        if (k != i) 
         }          {
             printf("%d%d ",i,k);
         for(i=1, vepp=0.;i <=nlstate;i++)            fprintf(ficlog,"%d%d ",i,k);
           for(j=1;j <=nlstate;j++)            fprintf(ficres,"%1d%1d ",i,k);
             vepp += vareij[i][j][(int)age];            for(j=1; j <=ncovmodel; j++){
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));              printf("%f ",p[jk]);
         for(j=1;j <=nlstate;j++){              fprintf(ficlog,"%f ",p[jk]);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));              fprintf(ficres,"%f ",p[jk]);
         }              jk++; 
         fprintf(ficrest,"\n");            }
       }            printf("\n");
     }            fprintf(ficlog,"\n");
   }            fprintf(ficres,"\n");
 free_matrix(mint,1,maxwav,1,n);          }
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      }
     free_vector(weight,1,n);    }
   fclose(ficreseij);    if(mle==1){
   fclose(ficresvij);      /* Computing hessian and covariance matrix */
   fclose(ficrest);      ftolhess=ftol; /* Usually correct */
   fclose(ficpar);      hesscov(matcov, p, npar, delti, ftolhess, func);
   free_vector(epj,1,nlstate+1);    }
      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
   /*------- Variance limit prevalence------*/      printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
   strcpy(fileresvpl,"vpl");    for(i=1,jk=1; i <=nlstate; i++){
   strcat(fileresvpl,fileres);      for(j=1; j <=nlstate+ndeath; j++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        if (j!=i) {
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          fprintf(ficres,"%1d%1d",i,j);
     exit(0);          printf("%1d%1d",i,j);
   }          fprintf(ficlog,"%1d%1d",i,j);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
   k=0;            fprintf(ficlog," %.5e",delti[jk]);
   for(cptcov=1;cptcov<=i1;cptcov++){            fprintf(ficres," %.5e",delti[jk]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            jk++;
       k=k+1;          }
       fprintf(ficresvpl,"\n#****** ");          printf("\n");
       for(j=1;j<=cptcoveff;j++)          fprintf(ficlog,"\n");
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficres,"\n");
       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);    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");
   fclose(ficresvpl);    for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
   /*---------- End : free ----------------*/          i1=(i-1)/(ncovmodel*nlstate)+1; 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
            printf("%s%d%d",alph[k],i1,tab[i]);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      fprintf(ficres,"%3d",i);
        if(mle==1)
          printf("%3d",i);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficlog,"%3d",i);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      for(j=1; j<=i;j++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficres," %.5e",matcov[i][j]);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        if(mle==1)
            printf(" %.5e",matcov[i][j]);
   free_matrix(matcov,1,npar,1,npar);        fprintf(ficlog," %.5e",matcov[i][j]);
   free_vector(delti,1,npar);      }
   free_matrix(agev,1,maxwav,1,imx);      fprintf(ficres,"\n");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      if(mle==1)
         printf("\n");
   fprintf(fichtm,"\n</body>");      fprintf(ficlog,"\n");
   fclose(fichtm);      k++;
   fclose(ficgp);    }
       
     while((c=getc(ficpar))=='#' && c!= EOF){
   if(erreur >0){      ungetc(c,ficpar);
     printf("End of Imach with error or warning %d\n",erreur);      fgets(line, MAXLINE, ficpar);
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);      puts(line);
   }else{      fputs(line,ficparo);
    printf("End of Imach\n");    }
    fprintf(ficlog,"End of Imach\n");    ungetc(c,ficpar);
   }  
   printf("See log file on %s\n",filelog);    estepm=0;
   fclose(ficlog);    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    if (estepm==0 || estepm < stepm) estepm=stepm;
      if (fage <= 2) {
   /* 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);*/      bage = ageminpar;
   /*printf("Total time was %d uSec.\n", total_usecs);*/      fage = agemaxpar;
   /*------ End -----------*/    }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
  end:    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
 #ifdef windows    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
   /* chdir(pathcd);*/     
 #endif    while((c=getc(ficpar))=='#' && c!= EOF){
  /*system("wgnuplot graph.plt");*/      ungetc(c,ficpar);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      fgets(line, MAXLINE, ficpar);
  /*system("cd ../gp37mgw");*/      puts(line);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      fputs(line,ficparo);
  strcpy(plotcmd,GNUPLOTPROGRAM);    }
  strcat(plotcmd," ");    ungetc(c,ficpar);
  strcat(plotcmd,optionfilegnuplot);    
  system(plotcmd);    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);
 #ifdef windows    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
   while (z[0] != 'q') {    printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     /* chdir(path); */    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);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");     
     scanf("%s",z);    while((c=getc(ficpar))=='#' && c!= EOF){
     if (z[0] == 'c') system("./imach");      ungetc(c,ficpar);
     else if (z[0] == 'e') system(optionfilehtm);      fgets(line, MAXLINE, ficpar);
     else if (z[0] == 'g') system(plotcmd);      puts(line);
     else if (z[0] == 'q') exit(0);      fputs(line,ficparo);
   }    }
 #endif    ungetc(c,ficpar);
 }   
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

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changed lines
  Added in v.1.78


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