Diff for /imach/src/imach.c between versions 1.5 and 1.74

version 1.5, 2001/05/02 17:42:45 version 1.74, 2003/05/02 18:51:41
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************             Interpolated Markov Chain
   This program computes Healthy Life Expectancies from cross-longitudinal  
   data. Cross-longitudinal consist in a first survey ("cross") where    Short summary of the programme:
   individuals from different ages are interviewed on their health status    
   or degree of  disability. At least a second wave of interviews    This program computes Healthy Life Expectancies from
   ("longitudinal") should  measure each new individual health status.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   Health expectancies are computed from the transistions observed between    first survey ("cross") where individuals from different ages are
   waves and are computed for each degree of severity of disability (number    interviewed on their health status or degree of disability (in the
   of life states). More degrees you consider, more time is necessary to    case of a health survey which is our main interest) -2- at least a
   reach the Maximum Likelihood of the parameters involved in the model.    second wave of interviews ("longitudinal") which measure each change
   The simplest model is the multinomial logistic model where pij is    (if any) in individual health status.  Health expectancies are
   the probabibility to be observed in state j at the second wave conditional    computed from the time spent in each health state according to a
   to be observed in state i at the first wave. Therefore the model is:    model. More health states you consider, more time is necessary to reach the
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Maximum Likelihood of the parameters involved in the model.  The
   is a covariate. If you want to have a more complex model than "constant and    simplest model is the multinomial logistic model where pij is the
   age", you should modify the program where the markup    probability to be observed in state j at the second wave
     *Covariates have to be included here again* invites you to do it.    conditional to be observed in state i at the first wave. Therefore
   More covariates you add, less is the speed of the convergence.    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
   The advantage that this computer programme claims, comes from that if the    complex model than "constant and age", you should modify the program
   delay between waves is not identical for each individual, or if some    where the markup *Covariates have to be included here again* invites
   individual missed an interview, the information is not rounded or lost, but    you to do it.  More covariates you add, slower the
   taken into account using an interpolation or extrapolation.    convergence.
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    The advantage of this computer programme, compared to a simple
   x. The delay 'h' can be split into an exact number (nh*stepm) of    multinomial logistic model, is clear when the delay between waves is not
   unobserved intermediate  states. This elementary transition (by month or    identical for each individual. Also, if a individual missed an
   quarter trimester, semester or year) is model as a multinomial logistic.    intermediate interview, the information is lost, but taken into
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    account using an interpolation or extrapolation.  
   and the contribution of each individual to the likelihood is simply hPijx.  
     hPijx is the probability to be observed in state i at age x+h
   Also this programme outputs the covariance matrix of the parameters but also    conditional to the observed state i at age x. The delay 'h' can be
   of the life expectancies. It also computes the prevalence limits.    split into an exact number (nh*stepm) of unobserved intermediate
      states. This elementary transition (by month, quarter,
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    semester or year) is modelled as a multinomial logistic.  The hPx
            Institut national d'études démographiques, Paris.    matrix is simply the matrix product of nh*stepm elementary matrices
   This software have been partly granted by Euro-REVES, a concerted action    and the contribution of each individual to the likelihood is simply
   from the European Union.    hPijx.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Also this programme outputs the covariance matrix of the parameters but also
   can be accessed at http://euroreves.ined.fr/imach .    of the life expectancies. It also computes the stable prevalence. 
   **********************************************************************/    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #include <math.h>             Institut national d'études démographiques, Paris.
 #include <stdio.h>    This software have been partly granted by Euro-REVES, a concerted action
 #include <stdlib.h>    from the European Union.
 #include <unistd.h>    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define MAXLINE 256    can be accessed at http://euroreves.ined.fr/imach .
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define windows    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    **********************************************************************/
   /*
     main
     read parameterfile
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    read datafile
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    concatwav
     if (mle >= 1)
 #define NINTERVMAX 8      mlikeli
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    print results files
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    if mle==1 
 #define NCOVMAX 8 /* Maximum number of covariates */       computes hessian
 #define MAXN 20000    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define YEARM 12. /* Number of months per year */        begin-prev-date,...
 #define AGESUP 130    open gnuplot file
 #define AGEBASE 40    open html file
     stable prevalence
      for age prevalim()
 int nvar;    h Pij x
 static int cptcov;    variance of p varprob
 int cptcovn;    forecasting if prevfcast==1 prevforecast call prevalence()
 int npar=NPARMAX;    health expectancies
 int nlstate=2; /* Number of live states */    Variance-covariance of DFLE
 int ndeath=1; /* Number of dead states */    prevalence()
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */     movingaverage()
     varevsij() 
 int *wav; /* Number of waves for this individuual 0 is possible */    if popbased==1 varevsij(,popbased)
 int maxwav; /* Maxim number of waves */    total life expectancies
 int mle, weightopt;    Variance of stable prevalence
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */   end
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  
 FILE *ficgp, *fichtm;   
 FILE *ficreseij;  #include <math.h>
   char filerese[FILENAMELENGTH];  #include <stdio.h>
  FILE  *ficresvij;  #include <stdlib.h>
   char fileresv[FILENAMELENGTH];  #include <unistd.h>
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 80
   /*#define DEBUG*/
 #define NR_END 1  #define windows
 #define FREE_ARG char*  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define FTOL 1.0e-10  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define NRANSI  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define ITMAX 200  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define TOL 2.0e-4  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define CGOLD 0.3819660  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define ZEPS 1.0e-10  #define NCOVMAX 8 /* Maximum number of covariates */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 #define GOLD 1.618034  #define AGESUP 130
 #define GLIMIT 100.0  #define AGEBASE 40
 #define TINY 1.0e-20  #ifdef windows
   #define DIRSEPARATOR '\\'
 static double maxarg1,maxarg2;  #define ODIRSEPARATOR '/'
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #else
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define DIRSEPARATOR '/'
    #define ODIRSEPARATOR '\\'
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #endif
 #define rint(a) floor(a+0.5)  
   char version[80]="Imach version 0.95, February 2003, INED-EUROREVES ";
 static double sqrarg;  int erreur; /* Error number */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  int nvar;
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
 int imx;  int nlstate=2; /* Number of live states */
 int stepm;  int ndeath=1; /* Number of dead states */
 /* Stepm, step in month: minimum step interpolation*/  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;  int *wav; /* Number of waves for this individuual 0 is possible */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  int maxwav; /* Maxim number of waves */
 double **pmmij;  int jmin, jmax; /* min, max spacing between 2 waves */
   int mle, weightopt;
 double *weight;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int **s; /* Status */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 double *agedc, **covar, idx;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 int **nbcode, *Tcode, *Tvar, **codtab;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double ftolhess; /* Tolerance for computing hessian */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog;
 static  int split( char *path, char *dirc, char *name )  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 {  FILE *ficresprobmorprev;
    char *s;                             /* pointer */  FILE *fichtm; /* Html File */
    int  l1, l2;                         /* length counters */  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
    l1 = strlen( path );                 /* length of path */  FILE  *ficresvij;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  char fileresv[FILENAMELENGTH];
    s = strrchr( path, '\\' );           /* find last / */  FILE  *ficresvpl;
    if ( s == NULL ) {                   /* no directory, so use current */  char fileresvpl[FILENAMELENGTH];
 #if     defined(__bsd__)                /* get current working directory */  char title[MAXLINE];
       extern char       *getwd( );  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
       if ( getwd( dirc ) == NULL ) {  
 #else  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       extern char       *getcwd( );  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  char fileregp[FILENAMELENGTH];
 #endif  char popfile[FILENAMELENGTH];
          return( GLOCK_ERROR_GETCWD );  
       }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  #define NR_END 1
       s++;                              /* after this, the filename */  #define FREE_ARG char*
       l2 = strlen( s );                 /* length of filename */  #define FTOL 1.0e-10
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */  #define NRANSI 
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define ITMAX 200 
       dirc[l1-l2] = 0;                  /* add zero */  
    }  #define TOL 2.0e-4 
    l1 = strlen( dirc );                 /* length of directory */  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define CGOLD 0.3819660 
    return( 0 );                         /* we're done */  #define ZEPS 1.0e-10 
 }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
   #define GOLD 1.618034 
 /******************************************/  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
 void replace(char *s, char*t)  
 {  static double maxarg1,maxarg2;
   int i;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   int lg=20;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   i=0;    
   lg=strlen(t);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   for(i=0; i<= lg; i++) {  #define rint(a) floor(a+0.5)
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';  static double sqrarg;
   }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
 int nbocc(char *s, char occ)  int imx; 
 {  int stepm;
   int i,j=0;  /* Stepm, step in month: minimum step interpolation*/
   int lg=20;  
   i=0;  int estepm;
   lg=strlen(s);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  int m,nb;
   }  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   return j;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 }  double **pmmij, ***probs;
   double dateintmean=0;
 void cutv(char *u,char *v, char*t, char occ)  
 {  double *weight;
   int i,lg,j,p;  int **s; /* Status */
   i=0;  double *agedc, **covar, idx;
   for(j=0; j<=strlen(t)-1; j++) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
   lg=strlen(t);  
   for(j=0; j<p; j++) {  /**************** split *************************/
     (u[j] = t[j]);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     u[p]='\0';  {
   }    char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    l1 = strlen(path );                   /* length of path */
   }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
 /********************** nrerror ********************/      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 void nrerror(char error_text[])      /* get current working directory */
 {      /*    extern  char* getcwd ( char *buf , int len);*/
   fprintf(stderr,"ERREUR ...\n");      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   fprintf(stderr,"%s\n",error_text);        return( GLOCK_ERROR_GETCWD );
   exit(1);      }
 }      strcpy( name, path );               /* we've got it */
 /*********************** vector *******************/    } else {                              /* strip direcotry from path */
 double *vector(int nl, int nh)      ss++;                               /* after this, the filename */
 {      l2 = strlen( ss );                  /* length of filename */
   double *v;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));      strcpy( name, ss );         /* save file name */
   if (!v) nrerror("allocation failure in vector");      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   return v-nl+NR_END;      dirc[l1-l2] = 0;                    /* add zero */
 }    }
     l1 = strlen( dirc );                  /* length of directory */
 /************************ free vector ******************/  #ifdef windows
 void free_vector(double*v, int nl, int nh)    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 {  #else
   free((FREE_ARG)(v+nl-NR_END));    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 }  #endif
     ss = strrchr( name, '.' );            /* find last / */
 /************************ivector *******************************/    ss++;
 int *ivector(long nl,long nh)    strcpy(ext,ss);                       /* save extension */
 {    l1= strlen( name);
   int *v;    l2= strlen(ss)+1;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    strncpy( finame, name, l1-l2);
   if (!v) nrerror("allocation failure in ivector");    finame[l1-l2]= 0;
   return v-nl+NR_END;    return( 0 );                          /* we're done */
 }  }
   
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  /******************************************/
 {  
   free((FREE_ARG)(v+nl-NR_END));  void replace(char *s, char*t)
 }  {
     int i;
 /******************* imatrix *******************************/    int lg=20;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    i=0;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;      (s[i] = t[i]);
   int **m;      if (t[i]== '\\') s[i]='/';
      }
   /* allocate pointers to rows */  }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  int nbocc(char *s, char occ)
   m += NR_END;  {
   m -= nrl;    int i,j=0;
      int lg=20;
      i=0;
   /* allocate rows and set pointers to them */    lg=strlen(s);
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    for(i=0; i<= lg; i++) {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if  (s[i] == occ ) j++;
   m[nrl] += NR_END;    }
   m[nrl] -= ncl;    return j;
    }
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    void cutv(char *u,char *v, char*t, char occ)
   /* return pointer to array of pointers to rows */  {
   return m;    /* cuts string t into u and v where u is ended by char occ excluding it
 }       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
        gives u="abcedf" and v="ghi2j" */
 /****************** free_imatrix *************************/    int i,lg,j,p=0;
 void free_imatrix(m,nrl,nrh,ncl,nch)    i=0;
       int **m;    for(j=0; j<=strlen(t)-1; j++) {
       long nch,ncl,nrh,nrl;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
      /* free an int matrix allocated by imatrix() */    }
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    lg=strlen(t);
   free((FREE_ARG) (m+nrl-NR_END));    for(j=0; j<p; j++) {
 }      (u[j] = t[j]);
     }
 /******************* matrix *******************************/       u[p]='\0';
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {     for(j=0; j<= lg; j++) {
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;      if (j>=(p+1))(v[j-p-1] = t[j]);
   double **m;    }
   }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /********************** nrerror ********************/
   m += NR_END;  
   m -= nrl;  void nrerror(char error_text[])
   {
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    fprintf(stderr,"ERREUR ...\n");
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    fprintf(stderr,"%s\n",error_text);
   m[nrl] += NR_END;    exit(EXIT_FAILURE);
   m[nrl] -= ncl;  }
   /*********************** vector *******************/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  double *vector(int nl, int nh)
   return m;  {
 }    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 /*************************free matrix ************************/    if (!v) nrerror("allocation failure in vector");
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    return v-nl+NR_END;
 {  }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /******************* ma3x *******************************/    free((FREE_ARG)(v+nl-NR_END));
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  }
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  /************************ivector *******************************/
   double ***m;  int *ivector(long nl,long nh)
   {
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    int *v;
   if (!m) nrerror("allocation failure 1 in matrix()");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m += NR_END;    if (!v) nrerror("allocation failure in ivector");
   m -= nrl;    return v-nl+NR_END;
   }
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /******************free ivector **************************/
   m[nrl] += NR_END;  void free_ivector(int *v, long nl, long nh)
   m[nrl] -= ncl;  {
     free((FREE_ARG)(v+nl-NR_END));
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  /******************* imatrix *******************************/
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   m[nrl][ncl] += NR_END;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   m[nrl][ncl] -= nll;  { 
   for (j=ncl+1; j<=nch; j++)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     m[nrl][j]=m[nrl][j-1]+nlay;    int **m; 
      
   for (i=nrl+1; i<=nrh; i++) {    /* allocate pointers to rows */ 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     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;    
 }    
     /* allocate rows and set pointers to them */ 
 /*************************free ma3x ************************/    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 {    m[nrl] += NR_END; 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m[nrl] -= ncl; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    
   free((FREE_ARG)(m+nrl-NR_END));    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 }    
     /* return pointer to array of pointers to rows */ 
 /***************** f1dim *************************/    return m; 
 extern int ncom;  } 
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  /****************** free_imatrix *************************/
    void free_imatrix(m,nrl,nrh,ncl,nch)
 double f1dim(double x)        int **m;
 {        long nch,ncl,nrh,nrl; 
   int j;       /* free an int matrix allocated by imatrix() */ 
   double f;  { 
   double *xt;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      free((FREE_ARG) (m+nrl-NR_END)); 
   xt=vector(1,ncom);  } 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  /******************* matrix *******************************/
   free_vector(xt,1,ncom);  double **matrix(long nrl, long nrh, long ncl, long nch)
   return f;  {
 }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   int iter;    m += NR_END;
   double a,b,d,etemp;    m -= nrl;
   double fu,fv,fw,fx;  
   double ftemp;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double p,q,r,tol1,tol2,u,v,w,x,xm;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double e=0.0;    m[nrl] += NR_END;
      m[nrl] -= ncl;
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   x=w=v=bx;    return m;
   fw=fv=fx=(*f)(x);    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
   for (iter=1;iter<=ITMAX;iter++) {     */
     xm=0.5*(a+b);  }
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  /*************************free matrix ************************/
     printf(".");fflush(stdout);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 #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);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    free((FREE_ARG)(m+nrl-NR_END));
 #endif  }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /******************* ma3x *******************************/
       return fx;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     }  {
     ftemp=fu;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     if (fabs(e) > tol1) {    double ***m;
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       p=(x-v)*q-(x-w)*r;    if (!m) nrerror("allocation failure 1 in matrix()");
       q=2.0*(q-r);    m += NR_END;
       if (q > 0.0) p = -p;    m -= nrl;
       q=fabs(q);  
       etemp=e;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       e=d;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m[nrl] += NR_END;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl] -= ncl;
       else {  
         d=p/q;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
           d=SIGN(tol1,xm-x);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       }    m[nrl][ncl] += NR_END;
     } else {    m[nrl][ncl] -= nll;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    for (j=ncl+1; j<=nch; j++) 
     }      m[nrl][j]=m[nrl][j-1]+nlay;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    
     fu=(*f)(u);    for (i=nrl+1; i<=nrh; i++) {
     if (fu <= fx) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       if (u >= x) a=x; else b=x;      for (j=ncl+1; j<=nch; j++) 
       SHFT(v,w,x,u)        m[i][j]=m[i][j-1]+nlay;
         SHFT(fv,fw,fx,fu)    }
         } else {    return m; 
           if (u < x) a=u; else b=u;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
           if (fu <= fw || w == x) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
             v=w;    */
             w=u;  }
             fv=fw;  
             fw=fu;  /*************************free ma3x ************************/
           } else if (fu <= fv || v == x || v == w) {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
             v=u;  {
             fv=fu;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
           }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         }    free((FREE_ARG)(m+nrl-NR_END));
   }  }
   nrerror("Too many iterations in brent");  
   *xmin=x;  /***************** f1dim *************************/
   return fx;  extern int ncom; 
 }  extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
 /****************** mnbrak ***********************/   
   double f1dim(double x) 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  { 
             double (*func)(double))    int j; 
 {    double f;
   double ulim,u,r,q, dum;    double *xt; 
   double fu;   
      xt=vector(1,ncom); 
   *fa=(*func)(*ax);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   *fb=(*func)(*bx);    f=(*nrfunc)(xt); 
   if (*fb > *fa) {    free_vector(xt,1,ncom); 
     SHFT(dum,*ax,*bx,dum)    return f; 
       SHFT(dum,*fb,*fa,dum)  } 
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  /*****************brent *************************/
   *fc=(*func)(*cx);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   while (*fb > *fc) {  { 
     r=(*bx-*ax)*(*fb-*fc);    int iter; 
     q=(*bx-*cx)*(*fb-*fa);    double a,b,d,etemp;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    double fu,fv,fw,fx;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    double ftemp;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     if ((*bx-u)*(u-*cx) > 0.0) {    double e=0.0; 
       fu=(*func)(u);   
     } else if ((*cx-u)*(u-ulim) > 0.0) {    a=(ax < cx ? ax : cx); 
       fu=(*func)(u);    b=(ax > cx ? ax : cx); 
       if (fu < *fc) {    x=w=v=bx; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    fw=fv=fx=(*f)(x); 
           SHFT(*fb,*fc,fu,(*func)(u))    for (iter=1;iter<=ITMAX;iter++) { 
           }      xm=0.5*(a+b); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       u=ulim;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       fu=(*func)(u);      printf(".");fflush(stdout);
     } else {      fprintf(ficlog,".");fflush(ficlog);
       u=(*cx)+GOLD*(*cx-*bx);  #ifdef DEBUG
       fu=(*func)(u);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     }      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     SHFT(*ax,*bx,*cx,u)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       SHFT(*fa,*fb,*fc,fu)  #endif
       }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 }        *xmin=x; 
         return fx; 
 /*************** linmin ************************/      } 
       ftemp=fu;
 int ncom;      if (fabs(e) > tol1) { 
 double *pcom,*xicom;        r=(x-w)*(fx-fv); 
 double (*nrfunc)(double []);        q=(x-v)*(fx-fw); 
          p=(x-v)*q-(x-w)*r; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        q=2.0*(q-r); 
 {        if (q > 0.0) p = -p; 
   double brent(double ax, double bx, double cx,        q=fabs(q); 
                double (*f)(double), double tol, double *xmin);        etemp=e; 
   double f1dim(double x);        e=d; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
               double *fc, double (*func)(double));          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int j;        else { 
   double xx,xmin,bx,ax;          d=p/q; 
   double fx,fb,fa;          u=x+d; 
            if (u-a < tol2 || b-u < tol2) 
   ncom=n;            d=SIGN(tol1,xm-x); 
   pcom=vector(1,n);        } 
   xicom=vector(1,n);      } else { 
   nrfunc=func;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (j=1;j<=n;j++) {      } 
     pcom[j]=p[j];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     xicom[j]=xi[j];      fu=(*f)(u); 
   }      if (fu <= fx) { 
   ax=0.0;        if (u >= x) a=x; else b=x; 
   xx=1.0;        SHFT(v,w,x,u) 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);          SHFT(fv,fw,fx,fu) 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);          } else { 
 #ifdef DEBUG            if (u < x) a=u; else b=u; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);            if (fu <= fw || w == x) { 
 #endif              v=w; 
   for (j=1;j<=n;j++) {              w=u; 
     xi[j] *= xmin;              fv=fw; 
     p[j] += xi[j];              fw=fu; 
   }            } else if (fu <= fv || v == x || v == w) { 
   free_vector(xicom,1,n);              v=u; 
   free_vector(pcom,1,n);              fv=fu; 
 }            } 
           } 
 /*************** powell ************************/    } 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    nrerror("Too many iterations in brent"); 
             double (*func)(double []))    *xmin=x; 
 {    return fx; 
   void linmin(double p[], double xi[], int n, double *fret,  } 
               double (*func)(double []));  
   int i,ibig,j;  /****************** mnbrak ***********************/
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double *xits;              double (*func)(double)) 
   pt=vector(1,n);  { 
   ptt=vector(1,n);    double ulim,u,r,q, dum;
   xit=vector(1,n);    double fu; 
   xits=vector(1,n);   
   *fret=(*func)(p);    *fa=(*func)(*ax); 
   for (j=1;j<=n;j++) pt[j]=p[j];    *fb=(*func)(*bx); 
   for (*iter=1;;++(*iter)) {    if (*fb > *fa) { 
     fp=(*fret);      SHFT(dum,*ax,*bx,dum) 
     ibig=0;        SHFT(dum,*fb,*fa,dum) 
     del=0.0;        } 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    *cx=(*bx)+GOLD*(*bx-*ax); 
     for (i=1;i<=n;i++)    *fc=(*func)(*cx); 
       printf(" %d %.12f",i, p[i]);    while (*fb > *fc) { 
     printf("\n");      r=(*bx-*ax)*(*fb-*fc); 
     for (i=1;i<=n;i++) {      q=(*bx-*cx)*(*fb-*fa); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       fptt=(*fret);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 #ifdef DEBUG      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       printf("fret=%lf \n",*fret);      if ((*bx-u)*(u-*cx) > 0.0) { 
 #endif        fu=(*func)(u); 
       printf("%d",i);fflush(stdout);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       linmin(p,xit,n,fret,func);        fu=(*func)(u); 
       if (fabs(fptt-(*fret)) > del) {        if (fu < *fc) { 
         del=fabs(fptt-(*fret));          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         ibig=i;            SHFT(*fb,*fc,fu,(*func)(u)) 
       }            } 
 #ifdef DEBUG      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       printf("%d %.12e",i,(*fret));        u=ulim; 
       for (j=1;j<=n;j++) {        fu=(*func)(u); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      } else { 
         printf(" x(%d)=%.12e",j,xit[j]);        u=(*cx)+GOLD*(*cx-*bx); 
       }        fu=(*func)(u); 
       for(j=1;j<=n;j++)      } 
         printf(" p=%.12e",p[j]);      SHFT(*ax,*bx,*cx,u) 
       printf("\n");        SHFT(*fa,*fb,*fc,fu) 
 #endif        } 
     }  } 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  /*************** linmin ************************/
       int k[2],l;  
       k[0]=1;  int ncom; 
       k[1]=-1;  double *pcom,*xicom;
       printf("Max: %.12e",(*func)(p));  double (*nrfunc)(double []); 
       for (j=1;j<=n;j++)   
         printf(" %.12e",p[j]);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       printf("\n");  { 
       for(l=0;l<=1;l++) {    double brent(double ax, double bx, double cx, 
         for (j=1;j<=n;j++) {                 double (*f)(double), double tol, double *xmin); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    double f1dim(double x); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         }                double *fc, double (*func)(double)); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    int j; 
       }    double xx,xmin,bx,ax; 
 #endif    double fx,fb,fa;
    
     ncom=n; 
       free_vector(xit,1,n);    pcom=vector(1,n); 
       free_vector(xits,1,n);    xicom=vector(1,n); 
       free_vector(ptt,1,n);    nrfunc=func; 
       free_vector(pt,1,n);    for (j=1;j<=n;j++) { 
       return;      pcom[j]=p[j]; 
     }      xicom[j]=xi[j]; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    } 
     for (j=1;j<=n;j++) {    ax=0.0; 
       ptt[j]=2.0*p[j]-pt[j];    xx=1.0; 
       xit[j]=p[j]-pt[j];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       pt[j]=p[j];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
     fptt=(*func)(ptt);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if (fptt < fp) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #endif
       if (t < 0.0) {    for (j=1;j<=n;j++) { 
         linmin(p,xit,n,fret,func);      xi[j] *= xmin; 
         for (j=1;j<=n;j++) {      p[j] += xi[j]; 
           xi[j][ibig]=xi[j][n];    } 
           xi[j][n]=xit[j];    free_vector(xicom,1,n); 
         }    free_vector(pcom,1,n); 
 #ifdef DEBUG  } 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)  /*************** powell ************************/
           printf(" %.12e",xit[j]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         printf("\n");              double (*func)(double [])) 
 #endif  { 
       }    void linmin(double p[], double xi[], int n, double *fret, 
     }                double (*func)(double [])); 
   }    int i,ibig,j; 
 }    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
 /**** Prevalence limit ****************/    double *xits;
     pt=vector(1,n); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    ptt=vector(1,n); 
 {    xit=vector(1,n); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    xits=vector(1,n); 
      matrix by transitions matrix until convergence is reached */    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
   int i, ii,j,k;    for (*iter=1;;++(*iter)) { 
   double min, max, maxmin, maxmax,sumnew=0.;      fp=(*fret); 
   double **matprod2();      ibig=0; 
   double **out, cov[NCOVMAX], **pmij();      del=0.0; 
   double **newm;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   double agefin, delaymax=50 ; /* Max number of years to converge */      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       for (i=1;i<=n;i++) 
   for (ii=1;ii<=nlstate+ndeath;ii++)        printf(" %d %.12f",i, p[i]);
     for (j=1;j<=nlstate+ndeath;j++){      fprintf(ficlog," %d %.12f",i, p[i]);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf("\n");
     }      fprintf(ficlog,"\n");
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      for (i=1;i<=n;i++) { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     newm=savm;        fptt=(*fret); 
     /* Covariates have to be included here again */  #ifdef DEBUG
     cov[1]=1.;        printf("fret=%lf \n",*fret);
     cov[2]=agefin;        fprintf(ficlog,"fret=%lf \n",*fret);
     if (cptcovn>0){  #endif
       for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}        printf("%d",i);fflush(stdout);
     }        fprintf(ficlog,"%d",i);fflush(ficlog);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
     savm=oldm;          del=fabs(fptt-(*fret)); 
     oldm=newm;          ibig=i; 
     maxmax=0.;        } 
     for(j=1;j<=nlstate;j++){  #ifdef DEBUG
       min=1.;        printf("%d %.12e",i,(*fret));
       max=0.;        fprintf(ficlog,"%d %.12e",i,(*fret));
       for(i=1; i<=nlstate; i++) {        for (j=1;j<=n;j++) {
         sumnew=0;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          printf(" x(%d)=%.12e",j,xit[j]);
         prlim[i][j]= newm[i][j]/(1-sumnew);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         max=FMAX(max,prlim[i][j]);        }
         min=FMIN(min,prlim[i][j]);        for(j=1;j<=n;j++) {
       }          printf(" p=%.12e",p[j]);
       maxmin=max-min;          fprintf(ficlog," p=%.12e",p[j]);
       maxmax=FMAX(maxmax,maxmin);        }
     }        printf("\n");
     if(maxmax < ftolpl){        fprintf(ficlog,"\n");
       return prlim;  #endif
     }      } 
   }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 }  #ifdef DEBUG
         int k[2],l;
 /*************** transition probabilities **********/        k[0]=1;
         k[1]=-1;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        printf("Max: %.12e",(*func)(p));
 {        fprintf(ficlog,"Max: %.12e",(*func)(p));
   double s1, s2;        for (j=1;j<=n;j++) {
   /*double t34;*/          printf(" %.12e",p[j]);
   int i,j,j1, nc, ii, jj;          fprintf(ficlog," %.12e",p[j]);
         }
     for(i=1; i<= nlstate; i++){        printf("\n");
     for(j=1; j<i;j++){        fprintf(ficlog,"\n");
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        for(l=0;l<=1;l++) {
         /*s2 += param[i][j][nc]*cov[nc];*/          for (j=1;j<=n;j++) {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       ps[i][j]=s2;          }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(j=i+1; j<=nlstate+ndeath;j++){        }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #endif
         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);*/  
       }        free_vector(xit,1,n); 
       ps[i][j]=s2;        free_vector(xits,1,n); 
     }        free_vector(ptt,1,n); 
   }        free_vector(pt,1,n); 
   for(i=1; i<= nlstate; i++){        return; 
      s1=0;      } 
     for(j=1; j<i; j++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       s1+=exp(ps[i][j]);      for (j=1;j<=n;j++) { 
     for(j=i+1; j<=nlstate+ndeath; j++)        ptt[j]=2.0*p[j]-pt[j]; 
       s1+=exp(ps[i][j]);        xit[j]=p[j]-pt[j]; 
     ps[i][i]=1./(s1+1.);        pt[j]=p[j]; 
     for(j=1; j<i; j++)      } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      fptt=(*func)(ptt); 
     for(j=i+1; j<=nlstate+ndeath; j++)      if (fptt < fp) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        if (t < 0.0) { 
   } /* end i */          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){            xi[j][ibig]=xi[j][n]; 
     for(jj=1; jj<= nlstate+ndeath; jj++){            xi[j][n]=xit[j]; 
       ps[ii][jj]=0;          }
       ps[ii][ii]=1;  #ifdef DEBUG
     }          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(ii=1; ii<= nlstate+ndeath; ii++){            printf(" %.12e",xit[j]);
     for(jj=1; jj<= nlstate+ndeath; jj++){            fprintf(ficlog," %.12e",xit[j]);
      printf("%lf ",ps[ii][jj]);          }
    }          printf("\n");
     printf("\n ");          fprintf(ficlog,"\n");
     }  #endif
     printf("\n ");printf("%lf ",cov[2]);*/        }
 /*      } 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    } 
   goto end;*/  } 
     return ps;  
 }  /**** Prevalence limit (stable prevalence)  ****************/
   
 /**************** Product of 2 matrices ******************/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 {       matrix by transitions matrix until convergence is reached */
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    int i, ii,j,k;
   /* in, b, out are matrice of pointers which should have been initialized    double min, max, maxmin, maxmax,sumnew=0.;
      before: only the contents of out is modified. The function returns    double **matprod2();
      a pointer to pointers identical to out */    double **out, cov[NCOVMAX], **pmij();
   long i, j, k;    double **newm;
   for(i=nrl; i<= nrh; i++)    double agefin, delaymax=50 ; /* Max number of years to converge */
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    for (ii=1;ii<=nlstate+ndeath;ii++)
         out[i][k] +=in[i][j]*b[j][k];      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   return out;      }
 }  
      cov[1]=1.;
    
 /************* Higher Matrix Product ***************/   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      newm=savm;
 {      /* Covariates have to be included here again */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month       cov[2]=agefin;
      duration (i.e. until    
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        for (k=1; k<=cptcovn;k++) {
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      (typically every 2 years instead of every month which is too big).          /*      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]]);*/
      Model is determined by parameters x and covariates have to be        }
      included manually here.        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
      */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   int i, j, d, h, k;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   double **out, cov[NCOVMAX];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   double **newm;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)      savm=oldm;
     for (j=1;j<=nlstate+ndeath;j++){      oldm=newm;
       oldm[i][j]=(i==j ? 1.0 : 0.0);      maxmax=0.;
       po[i][j][0]=(i==j ? 1.0 : 0.0);      for(j=1;j<=nlstate;j++){
     }        min=1.;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        max=0.;
   for(h=1; h <=nhstepm; h++){        for(i=1; i<=nlstate; i++) {
     for(d=1; d <=hstepm; d++){          sumnew=0;
       newm=savm;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       /* Covariates have to be included here again */          prlim[i][j]= newm[i][j]/(1-sumnew);
       cov[1]=1.;          max=FMAX(max,prlim[i][j]);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          min=FMIN(min,prlim[i][j]);
       if (cptcovn>0){        }
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];        maxmin=max-min;
     }        maxmax=FMAX(maxmax,maxmin);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      if(maxmax < ftolpl){
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        return prlim;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      }
       savm=oldm;    }
       oldm=newm;  }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  /*************** transition probabilities ***************/ 
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  {
          */    double s1, s2;
       }    /*double t34;*/
   } /* end h */    int i,j,j1, nc, ii, jj;
   return po;  
 }      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 /*************** log-likelihood *************/          /*s2 += param[i][j][nc]*cov[nc];*/
 double func( double *x)          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);*/
   int i, ii, j, k, mi, d;        }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        ps[i][j]=s2;
   double **out;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   double sw; /* Sum of weights */      }
   double lli; /* Individual log likelihood */      for(j=i+1; j<=nlstate+ndeath;j++){
   long ipmx;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /*extern weight */          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   /* We are differentiating ll according to initial status */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        }
   /*for(i=1;i<imx;i++)        ps[i][j]=s2;
 printf(" %d\n",s[4][i]);      }
   */    }
       /*ps[3][2]=1;*/
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for(i=1; i<= nlstate; i++){
        for(mi=1; mi<= wav[i]-1; mi++){       s1=0;
       for (ii=1;ii<=nlstate+ndeath;ii++)      for(j=1; j<i; j++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        s1+=exp(ps[i][j]);
             for(d=0; d<dh[mi][i]; d++){      for(j=i+1; j<=nlstate+ndeath; j++)
         newm=savm;        s1+=exp(ps[i][j]);
           cov[1]=1.;      ps[i][i]=1./(s1+1.);
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      for(j=1; j<i; j++)
           if (cptcovn>0){        ps[i][j]= exp(ps[i][j])*ps[i][i];
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];      for(j=i+1; j<=nlstate+ndeath; j++)
             }        ps[i][j]= exp(ps[i][j])*ps[i][i];
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    } /* end i */
           savm=oldm;  
           oldm=newm;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
         ps[ii][jj]=0;
       } /* end mult */        ps[ii][ii]=1;
          }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;  
       sw += weight[i];    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      for(jj=1; jj<= nlstate+ndeath; jj++){
     } /* end of wave */       printf("%lf ",ps[ii][jj]);
   } /* end of individual */     }
       printf("\n ");
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      printf("\n ");printf("%lf ",cov[2]);*/
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  /*
   return -l;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
 }    goto end;*/
       return ps;
   }
 /*********** Maximum Likelihood Estimation ***************/  
   /**************** Product of 2 matrices ******************/
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   int i,j, iter;  {
   double **xi,*delti;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double fret;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   xi=matrix(1,npar,1,npar);    /* in, b, out are matrice of pointers which should have been initialized 
   for (i=1;i<=npar;i++)       before: only the contents of out is modified. The function returns
     for (j=1;j<=npar;j++)       a pointer to pointers identical to out */
       xi[i][j]=(i==j ? 1.0 : 0.0);    long i, j, k;
   printf("Powell\n");    for(i=nrl; i<= nrh; i++)
   powell(p,xi,npar,ftol,&iter,&fret,func);      for(k=ncolol; k<=ncoloh; k++)
         for(j=ncl,out[i][k]=0.; j<=nch; j++)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          out[i][k] +=in[i][j]*b[j][k];
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  
     return out;
 }  }
   
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /************* Higher Matrix Product ***************/
 {  
   double  **a,**y,*x,pd;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   double **hess;  {
   int i, j,jk;    /* Computes the transition matrix starting at age 'age' over 
   int *indx;       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   double hessii(double p[], double delta, int theta, double delti[]);       nhstepm*hstepm matrices. 
   double hessij(double p[], double delti[], int i, int j);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   void lubksb(double **a, int npar, int *indx, double b[]) ;       (typically every 2 years instead of every month which is too big 
   void ludcmp(double **a, int npar, int *indx, double *d) ;       for the memory).
        Model is determined by parameters x and covariates have to be 
        included manually here. 
   hess=matrix(1,npar,1,npar);  
        */
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){    int i, j, d, h, k;
     printf("%d",i);fflush(stdout);    double **out, cov[NCOVMAX];
     hess[i][i]=hessii(p,ftolhess,i,delti);    double **newm;
     /*printf(" %f ",p[i]);*/  
   }    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
   for (i=1;i<=npar;i++) {      for (j=1;j<=nlstate+ndeath;j++){
     for (j=1;j<=npar;j++)  {        oldm[i][j]=(i==j ? 1.0 : 0.0);
       if (j>i) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
         printf(".%d%d",i,j);fflush(stdout);      }
         hess[i][j]=hessij(p,delti,i,j);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         hess[j][i]=hess[i][j];    for(h=1; h <=nhstepm; h++){
       }      for(d=1; d <=hstepm; d++){
     }        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("\nInverting the hessian to get the covariance matrix. Wait...\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
          for (k=1; k<=cptcovage;k++)
   a=matrix(1,npar,1,npar);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   y=matrix(1,npar,1,npar);        for (k=1; k<=cptcovprod;k++)
   x=vector(1,npar);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   ludcmp(a,npar,indx,&pd);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   for (j=1;j<=npar;j++) {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=1;i<=npar;i++) x[i]=0;        savm=oldm;
     x[j]=1;        oldm=newm;
     lubksb(a,npar,indx,x);      }
     for (i=1;i<=npar;i++){      for(i=1; i<=nlstate+ndeath; i++)
       matcov[i][j]=x[i];        for(j=1;j<=nlstate+ndeath;j++) {
     }          po[i][j][h]=newm[i][j];
   }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
            */
   printf("\n#Hessian matrix#\n");        }
   for (i=1;i<=npar;i++) {    } /* end h */
     for (j=1;j<=npar;j++) {    return po;
       printf("%.3e ",hess[i][j]);  }
     }  
     printf("\n");  
   }  /*************** log-likelihood *************/
   double func( double *x)
   /* Recompute Inverse */  {
   for (i=1;i<=npar;i++)    int i, ii, j, k, mi, d, kk;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   ludcmp(a,npar,indx,&pd);    double **out;
     double sw; /* Sum of weights */
   /*  printf("\n#Hessian matrix recomputed#\n");    double lli; /* Individual log likelihood */
     int s1, s2;
   for (j=1;j<=npar;j++) {    double bbh, survp;
     for (i=1;i<=npar;i++) x[i]=0;    long ipmx;
     x[j]=1;    /*extern weight */
     lubksb(a,npar,indx,x);    /* We are differentiating ll according to initial status */
     for (i=1;i<=npar;i++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       y[i][j]=x[i];    /*for(i=1;i<imx;i++) 
       printf("%.3e ",y[i][j]);      printf(" %d\n",s[4][i]);
     }    */
     printf("\n");    cov[1]=1.;
   }  
   */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   free_matrix(a,1,npar,1,npar);    if(mle==1){
   free_matrix(y,1,npar,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_vector(x,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_ivector(indx,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   free_matrix(hess,1,npar,1,npar);          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);
             }
 /*************** hessian matrix ****************/          for(d=0; d<dh[mi][i]; d++){
 double hessii( double x[], double delta, int theta, double delti[])            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i;            for (kk=1; kk<=cptcovage;kk++) {
   int l=1, lmax=20;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double k1,k2;            }
   double p2[NPARMAX+1];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double res;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            savm=oldm;
   double fx;            oldm=newm;
   int k=0,kmax=10;          } /* end mult */
   double l1;        
           /*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 (i=1;i<=npar;i++) p2[i]=x[i];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   for(l=0 ; l <=lmax; l++){           * (in months) between two waves is not a multiple of stepm, we rounded to 
     l1=pow(10,l);           * the nearest (and in case of equal distance, to the lowest) interval but now
     delts=delt;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for(k=1 ; k <kmax; k=k+1){           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       delt = delta*(l1*k);           * probability in order to take into account the bias as a fraction of the way
       p2[theta]=x[theta] +delt;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       k1=func(p2)-fx;           * -stepm/2 to stepm/2 .
       p2[theta]=x[theta]-delt;           * For stepm=1 the results are the same as for previous versions of Imach.
       k2=func(p2)-fx;           * For stepm > 1 the results are less biased than in previous versions. 
       /*res= (k1-2.0*fx+k2)/delt/delt; */           */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          s1=s[mw[mi][i]][i];
                s2=s[mw[mi+1][i]][i];
 #ifdef DEBUG          bbh=(double)bh[mi][i]/(double)stepm; 
       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);          /* bias is positive if real duration
 #endif           * is higher than the multiple of stepm and negative otherwise.
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */           */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         k=kmax;          if( s2 > nlstate){ 
       }            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */               to the likelihood is the probability to die between last step unit time and current 
         k=kmax; l=lmax*10.;               step unit time, which is also the differences between probability to die before dh 
       }               and probability to die before dh-stepm . 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){               In version up to 0.92 likelihood was computed
         delts=delt;          as if date of death was unknown. Death was treated as any other
       }          health state: the date of the interview describes the actual state
     }          and not the date of a change in health state. The former idea was
   }          to consider that at each interview the state was recorded
   delti[theta]=delts;          (healthy, disable or death) and IMaCh was corrected; but when we
   return res;          introduced the exact date of death then we should have modified
            the contribution of an exact death to the likelihood. This new
 }          contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
 double hessij( double x[], double delti[], int thetai,int thetaj)          and month of death but the probability to survive from last
 {          interview up to one month before death multiplied by the
   int i;          probability to die within a month. Thanks to Chris
   int l=1, l1, lmax=20;          Jackson for correcting this bug.  Former versions increased
   double k1,k2,k3,k4,res,fx;          mortality artificially. The bad side is that we add another loop
   double p2[NPARMAX+1];          which slows down the processing. The difference can be up to 10%
   int k;          lower mortality.
             */
   fx=func(x);            lli=log(out[s1][s2] - savm[s1][s2]);
   for (k=1; k<=2; k++) {          }else{
     for (i=1;i<=npar;i++) p2[i]=x[i];            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     p2[thetai]=x[thetai]+delti[thetai]/k;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          } 
     k1=func(p2)-fx;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            /*if(lli ==000.0)*/
     p2[thetai]=x[thetai]+delti[thetai]/k;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          ipmx +=1;
     k2=func(p2)-fx;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     p2[thetai]=x[thetai]-delti[thetai]/k;        } /* end of wave */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      } /* end of individual */
     k3=func(p2)-fx;    }  else if(mle==2){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     p2[thetai]=x[thetai]-delti[thetai]/k;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     k4=func(p2)-fx;          for (ii=1;ii<=nlstate+ndeath;ii++)
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            for (j=1;j<=nlstate+ndeath;j++){
 #ifdef DEBUG              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 #endif            }
   }          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++) {
 /************** Inverse of matrix **************/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 void ludcmp(double **a, int n, int *indx, double *d)            }
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i,imax,j,k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double big,dum,sum,temp;            savm=oldm;
   double *vv;            oldm=newm;
            } /* end mult */
   vv=vector(1,n);        
   *d=1.0;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   for (i=1;i<=n;i++) {          /* But now since version 0.9 we anticipate for bias and large stepm.
     big=0.0;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (j=1;j<=n;j++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
       if ((temp=fabs(a[i][j])) > big) big=temp;           * the nearest (and in case of equal distance, to the lowest) interval but now
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     vv[i]=1.0/big;           * (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
   for (j=1;j<=n;j++) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     for (i=1;i<j;i++) {           * -stepm/2 to stepm/2 .
       sum=a[i][j];           * For stepm=1 the results are the same as for previous versions of Imach.
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];           * For stepm > 1 the results are less biased than in previous versions. 
       a[i][j]=sum;           */
     }          s1=s[mw[mi][i]][i];
     big=0.0;          s2=s[mw[mi+1][i]][i];
     for (i=j;i<=n;i++) {          bbh=(double)bh[mi][i]/(double)stepm; 
       sum=a[i][j];          /* bias is positive if real duration
       for (k=1;k<j;k++)           * is higher than the multiple of stepm and negative otherwise.
         sum -= a[i][k]*a[k][j];           */
       a[i][j]=sum;          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 */
       if ( (dum=vv[i]*fabs(sum)) >= big) {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         big=dum;          /*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 */
         imax=i;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       }          /*if(lli ==000.0)*/
     }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     if (j != imax) {          ipmx +=1;
       for (k=1;k<=n;k++) {          sw += weight[i];
         dum=a[imax][k];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         a[imax][k]=a[j][k];        } /* end of wave */
         a[j][k]=dum;      } /* end of individual */
       }    }  else if(mle==3){  /* exponential inter-extrapolation */
       *d = -(*d);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       vv[imax]=vv[j];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
     indx[j]=imax;          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (a[j][j] == 0.0) a[j][j]=TINY;            for (j=1;j<=nlstate+ndeath;j++){
     if (j != n) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       dum=1.0/(a[j][j]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            }
     }          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
   free_vector(vv,1,n);  /* Doesn't work */            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];
             }
 void lubksb(double **a, int n, int *indx, double b[])            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i,ii=0,ip,j;            savm=oldm;
   double sum;            oldm=newm;
            } /* end mult */
   for (i=1;i<=n;i++) {        
     ip=indx[i];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     sum=b[ip];          /* But now since version 0.9 we anticipate for bias and large stepm.
     b[ip]=b[i];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     if (ii)           * (in months) between two waves is not a multiple of stepm, we rounded to 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];           * the nearest (and in case of equal distance, to the lowest) interval but now
     else if (sum) ii=i;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     b[i]=sum;           * (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
   for (i=n;i>=1;i--) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     sum=b[i];           * -stepm/2 to stepm/2 .
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];           * For stepm=1 the results are the same as for previous versions of Imach.
     b[i]=sum/a[i][i];           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
 }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 /************ Frequencies ********************/          bbh=(double)bh[mi][i]/(double)stepm; 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)          /* bias is positive if real duration
 {  /* Some frequencies */           * is higher than the multiple of stepm and negative otherwise.
             */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
   double ***freq; /* Frequencies */          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   double *pp;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double pos;          /*if(lli ==000.0)*/
   FILE *ficresp;          /*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); */
   char fileresp[FILENAMELENGTH];          ipmx +=1;
           sw += weight[i];
   pp=vector(1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
   strcpy(fileresp,"p");      } /* end of individual */
   strcat(fileresp,fileres);    }else{  /* ml=4 no inter-extrapolation */
   if((ficresp=fopen(fileresp,"w"))==NULL) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     exit(0);        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            for (j=1;j<=nlstate+ndeath;j++){
   j1=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   j=cptcovn;            }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   for(k1=1; k1<=j;k1++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
    for(i1=1; i1<=ncodemax[k1];i1++){            for (kk=1; kk<=cptcovage;kk++) {
        j1++;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
         for (i=-1; i<=nlstate+ndeath; i++)            
          for (jk=-1; jk<=nlstate+ndeath; jk++)              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
            for(m=agemin; m <= agemax+3; m++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              freq[i][jk][m]=0;            savm=oldm;
                    oldm=newm;
        for (i=1; i<=imx; i++) {          } /* end mult */
          bool=1;        
          if  (cptcovn>0) {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            for (z1=1; z1<=cptcovn; z1++)          ipmx +=1;
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;          sw += weight[i];
          }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if (bool==1) {        } /* end of wave */
            for(m=firstpass; m<=lastpass-1; m++){      } /* end of individual */
              if(agev[m][i]==0) agev[m][i]=agemax+1;    } /* End of if */
              if(agev[m][i]==1) agev[m][i]=agemax+2;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
            }    return -l;
          }  }
        }  
         if  (cptcovn>0) {  
          fprintf(ficresp, "\n#Variable");  /*********** Maximum Likelihood Estimation ***************/
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);  
        }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
        fprintf(ficresp, "\n#");  {
        for(i=1; i<=nlstate;i++)    int i,j, iter;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double **xi;
        fprintf(ficresp, "\n");    double fret;
            xi=matrix(1,npar,1,npar);
   for(i=(int)agemin; i <= (int)agemax+3; i++){    for (i=1;i<=npar;i++)
     if(i==(int)agemax+3)      for (j=1;j<=npar;j++)
       printf("Total");        xi[i][j]=(i==j ? 1.0 : 0.0);
     else    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       printf("Age %d", i);    powell(p,xi,npar,ftol,&iter,&fret,func);
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         pp[jk] += freq[jk][m][i];    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)  }
         pos += freq[jk][m][i];  
       if(pp[jk]>=1.e-10)  /**** Computes Hessian and covariance matrix ***/
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       else  {
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    double  **a,**y,*x,pd;
     }    double **hess;
     for(jk=1; jk <=nlstate ; jk++){    int i, j,jk;
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)    int *indx;
         pp[jk] += freq[jk][m][i];  
     }    double hessii(double p[], double delta, int theta, double delti[]);
     for(jk=1,pos=0; jk <=nlstate ; jk++)    double hessij(double p[], double delti[], int i, int j);
       pos += pp[jk];    void lubksb(double **a, int npar, int *indx, double b[]) ;
     for(jk=1; jk <=nlstate ; jk++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
       if(pos>=1.e-5)  
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    hess=matrix(1,npar,1,npar);
       else  
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    printf("\nCalculation of the hessian matrix. Wait...\n");
       if( i <= (int) agemax){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         if(pos>=1.e-5)    for (i=1;i<=npar;i++){
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      printf("%d",i);fflush(stdout);
       else      fprintf(ficlog,"%d",i);fflush(ficlog);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      hess[i][i]=hessii(p,ftolhess,i,delti);
       }      /*printf(" %f ",p[i]);*/
     }      /*printf(" %lf ",hess[i][i]);*/
     for(jk=-1; jk <=nlstate+ndeath; jk++)    }
       for(m=-1; m <=nlstate+ndeath; m++)    
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    for (i=1;i<=npar;i++) {
     if(i <= (int) agemax)      for (j=1;j<=npar;j++)  {
       fprintf(ficresp,"\n");        if (j>i) { 
     printf("\n");          printf(".%d%d",i,j);fflush(stdout);
     }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     }          hess[i][j]=hessij(p,delti,i,j);
  }          hess[j][i]=hess[i][j];    
            /*printf(" %lf ",hess[i][j]);*/
   fclose(ficresp);        }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      }
   free_vector(pp,1,nlstate);    }
     printf("\n");
 }  /* End of Freq */    fprintf(ficlog,"\n");
   
 /************* Waves Concatenation ***************/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    
 {    a=matrix(1,npar,1,npar);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    y=matrix(1,npar,1,npar);
      Death is a valid wave (if date is known).    x=vector(1,npar);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    indx=ivector(1,npar);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    for (i=1;i<=npar;i++)
      and mw[mi+1][i]. dh depends on stepm.      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
      */    ludcmp(a,npar,indx,&pd);
   
   int i, mi, m;    for (j=1;j<=npar;j++) {
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      for (i=1;i<=npar;i++) x[i]=0;
 float sum=0.;      x[j]=1;
       lubksb(a,npar,indx,x);
   for(i=1; i<=imx; i++){      for (i=1;i<=npar;i++){ 
     mi=0;        matcov[i][j]=x[i];
     m=firstpass;      }
     while(s[m][i] <= nlstate){    }
       if(s[m][i]>=1)  
         mw[++mi][i]=m;    printf("\n#Hessian matrix#\n");
       if(m >=lastpass)    fprintf(ficlog,"\n#Hessian matrix#\n");
         break;    for (i=1;i<=npar;i++) { 
       else      for (j=1;j<=npar;j++) { 
         m++;        printf("%.3e ",hess[i][j]);
     }/* end while */        fprintf(ficlog,"%.3e ",hess[i][j]);
     if (s[m][i] > nlstate){      }
       mi++;     /* Death is another wave */      printf("\n");
       /* if(mi==0)  never been interviewed correctly before death */      fprintf(ficlog,"\n");
          /* Only death is a correct wave */    }
       mw[mi][i]=m;  
     }    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
     wav[i]=mi;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     if(mi==0)    ludcmp(a,npar,indx,&pd);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  
   }    /*  printf("\n#Hessian matrix recomputed#\n");
   
   for(i=1; i<=imx; i++){    for (j=1;j<=npar;j++) {
     for(mi=1; mi<wav[i];mi++){      for (i=1;i<=npar;i++) x[i]=0;
       if (stepm <=0)      x[j]=1;
         dh[mi][i]=1;      lubksb(a,npar,indx,x);
       else{      for (i=1;i<=npar;i++){ 
         if (s[mw[mi+1][i]][i] > nlstate) {        y[i][j]=x[i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        printf("%.3e ",y[i][j]);
           if(j=0) j=1;  /* Survives at least one month after exam */        fprintf(ficlog,"%.3e ",y[i][j]);
         }      }
         else{      printf("\n");
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      fprintf(ficlog,"\n");
           k=k+1;    }
           if (j >= jmax) jmax=j;    */
           else if (j <= jmin)jmin=j;  
           sum=sum+j;    free_matrix(a,1,npar,1,npar);
         }    free_matrix(y,1,npar,1,npar);
         jk= j/stepm;    free_vector(x,1,npar);
         jl= j -jk*stepm;    free_ivector(indx,1,npar);
         ju= j -(jk+1)*stepm;    free_matrix(hess,1,npar,1,npar);
         if(jl <= -ju)  
           dh[mi][i]=jk;  
         else  }
           dh[mi][i]=jk+1;  
         if(dh[mi][i]==0)  /*************** hessian matrix ****************/
           dh[mi][i]=1; /* At least one step */  double hessii( double x[], double delta, int theta, double delti[])
       }  {
     }    int i;
   }    int l=1, lmax=20;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);    double k1,k2;
 }    double p2[NPARMAX+1];
 /*********** Tricode ****************************/    double res;
 void tricode(int *Tvar, int **nbcode, int imx)    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 {    double fx;
   int Ndum[80],ij, k, j, i;    int k=0,kmax=10;
   int cptcode=0;    double l1;
   for (k=0; k<79; k++) Ndum[k]=0;  
   for (k=1; k<=7; k++) ncodemax[k]=0;    fx=func(x);
      for (i=1;i<=npar;i++) p2[i]=x[i];
   for (j=1; j<=cptcovn; j++) {    for(l=0 ; l <=lmax; l++){
     for (i=1; i<=imx; i++) {      l1=pow(10,l);
       ij=(int)(covar[Tvar[j]][i]);      delts=delt;
       Ndum[ij]++;      for(k=1 ; k <kmax; k=k+1){
       if (ij > cptcode) cptcode=ij;        delt = delta*(l1*k);
     }        p2[theta]=x[theta] +delt;
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/        k1=func(p2)-fx;
     for (i=0; i<=cptcode; i++) {        p2[theta]=x[theta]-delt;
       if(Ndum[i]!=0) ncodemax[j]++;        k2=func(p2)-fx;
     }        /*res= (k1-2.0*fx+k2)/delt/delt; */
          res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     ij=1;        
     for (i=1; i<=ncodemax[j]; i++) {  #ifdef DEBUG
       for (k=0; k<=79; k++) {        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 (Ndum[k] != 0) {        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);
           nbcode[Tvar[j]][ij]=k;  #endif
           ij++;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         if (ij > ncodemax[j]) break;          k=kmax;
       }          }
     }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   }            k=kmax; l=lmax*10.;
         }
   }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
 /*********** Health Expectancies ****************/        }
       }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    }
 {    delti[theta]=delts;
   /* Health expectancies */    return res; 
   int i, j, nhstepm, hstepm, h;    
   double age, agelim,hf;  }
   double ***p3mat;  
    double hessij( double x[], double delti[], int thetai,int thetaj)
   fprintf(ficreseij,"# Health expectancies\n");  {
   fprintf(ficreseij,"# Age");    int i;
   for(i=1; i<=nlstate;i++)    int l=1, l1, lmax=20;
     for(j=1; j<=nlstate;j++)    double k1,k2,k3,k4,res,fx;
       fprintf(ficreseij," %1d-%1d",i,j);    double p2[NPARMAX+1];
   fprintf(ficreseij,"\n");    int k;
   
   hstepm=1*YEARM; /*  Every j years of age (in month) */    fx=func(x);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
   agelim=AGESUP;      p2[thetai]=x[thetai]+delti[thetai]/k;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     /* nhstepm age range expressed in number of stepm */      k1=func(p2)-fx;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    
     /* Typically if 20 years = 20*12/6=40 stepm */      p2[thetai]=x[thetai]+delti[thetai]/k;
     if (stepm >= YEARM) hstepm=1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      k2=func(p2)-fx;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      p2[thetai]=x[thetai]-delti[thetai]/k;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        k3=func(p2)-fx;
     
       p2[thetai]=x[thetai]-delti[thetai]/k;
     for(i=1; i<=nlstate;i++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(j=1; j<=nlstate;j++)      k4=func(p2)-fx;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           eij[i][j][(int)age] +=p3mat[i][j][h];  #ifdef DEBUG
         }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
          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);
     hf=1;  #endif
     if (stepm >= YEARM) hf=stepm/YEARM;    }
     fprintf(ficreseij,"%.0f",age );    return res;
     for(i=1; i<=nlstate;i++)  }
       for(j=1; j<=nlstate;j++){  
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);  /************** Inverse of matrix **************/
       }  void ludcmp(double **a, int n, int *indx, double *d) 
     fprintf(ficreseij,"\n");  { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i,imax,j,k; 
   }    double big,dum,sum,temp; 
 }    double *vv; 
    
 /************ Variance ******************/    vv=vector(1,n); 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    *d=1.0; 
 {    for (i=1;i<=n;i++) { 
   /* Variance of health expectancies */      big=0.0; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      for (j=1;j<=n;j++) 
   double **newm;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   double **dnewm,**doldm;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   int i, j, nhstepm, hstepm, h;      vv[i]=1.0/big; 
   int k, cptcode;    } 
    double *xp;    for (j=1;j<=n;j++) { 
   double **gp, **gm;      for (i=1;i<j;i++) { 
   double ***gradg, ***trgradg;        sum=a[i][j]; 
   double ***p3mat;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   double age,agelim;        a[i][j]=sum; 
   int theta;      } 
       big=0.0; 
    fprintf(ficresvij,"# Covariances of life expectancies\n");      for (i=j;i<=n;i++) { 
   fprintf(ficresvij,"# Age");        sum=a[i][j]; 
   for(i=1; i<=nlstate;i++)        for (k=1;k<j;k++) 
     for(j=1; j<=nlstate;j++)          sum -= a[i][k]*a[k][j]; 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        a[i][j]=sum; 
   fprintf(ficresvij,"\n");        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
   xp=vector(1,npar);          imax=i; 
   dnewm=matrix(1,nlstate,1,npar);        } 
   doldm=matrix(1,nlstate,1,nlstate);      } 
        if (j != imax) { 
   hstepm=1*YEARM; /* Every year of age */        for (k=1;k<=n;k++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          dum=a[imax][k]; 
   agelim = AGESUP;          a[imax][k]=a[j][k]; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          a[j][k]=dum; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        } 
     if (stepm >= YEARM) hstepm=1;        *d = -(*d); 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        vv[imax]=vv[j]; 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      indx[j]=imax; 
     gp=matrix(0,nhstepm,1,nlstate);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     gm=matrix(0,nhstepm,1,nlstate);      if (j != n) { 
         dum=1.0/(a[j][j]); 
     for(theta=1; theta <=npar; theta++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       for(i=1; i<=npar; i++){ /* Computes gradient */      } 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    } 
       }    free_vector(vv,1,n);  /* Doesn't work */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    ;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  } 
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  void lubksb(double **a, int n, int *indx, double b[]) 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  { 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    int i,ii=0,ip,j; 
         }    double sum; 
       }   
        for (i=1;i<=n;i++) { 
       for(i=1; i<=npar; i++) /* Computes gradient */      ip=indx[i]; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      sum=b[ip]; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        b[ip]=b[i]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if (ii) 
       for(j=1; j<= nlstate; j++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         for(h=0; h<=nhstepm; h++){      else if (sum) ii=i; 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      b[i]=sum; 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    } 
         }    for (i=n;i>=1;i--) { 
       }      sum=b[i]; 
       for(j=1; j<= nlstate; j++)      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         for(h=0; h<=nhstepm; h++){      b[i]=sum/a[i][i]; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    } 
         }  } 
     } /* End theta */  
   /************ Frequencies ********************/
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  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 */
     for(h=0; h<=nhstepm; h++)    
       for(j=1; j<=nlstate;j++)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         for(theta=1; theta <=npar; theta++)    int first;
           trgradg[h][j][theta]=gradg[h][theta][j];    double ***freq; /* Frequencies */
     double *pp, **prop;
     for(i=1;i<=nlstate;i++)    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       for(j=1;j<=nlstate;j++)    FILE *ficresp;
         vareij[i][j][(int)age] =0.;    char fileresp[FILENAMELENGTH];
     for(h=0;h<=nhstepm;h++){    
       for(k=0;k<=nhstepm;k++){    pp=vector(1,nlstate);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    prop=matrix(1,nlstate,iagemin,iagemax+3);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    strcpy(fileresp,"p");
         for(i=1;i<=nlstate;i++)    strcat(fileresp,fileres);
           for(j=1;j<=nlstate;j++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
             vareij[i][j][(int)age] += doldm[i][j];      printf("Problem with prevalence resultfile: %s\n", fileresp);
       }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     }      exit(0);
     h=1;    }
     if (stepm >= YEARM) h=stepm/YEARM;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     fprintf(ficresvij,"%.0f ",age );    j1=0;
     for(i=1; i<=nlstate;i++)    
       for(j=1; j<=nlstate;j++){    j=cptcoveff;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       }  
     fprintf(ficresvij,"\n");    first=1;
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);    for(k1=1; k1<=j;k1++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      for(i1=1; i1<=ncodemax[k1];i1++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        j1++;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   } /* End age */          scanf("%d", i);*/
          for (i=-1; i<=nlstate+ndeath; i++)  
   free_vector(xp,1,npar);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   free_matrix(doldm,1,nlstate,1,npar);            for(m=iagemin; m <= iagemax+3; m++)
   free_matrix(dnewm,1,nlstate,1,nlstate);              freq[i][jk][m]=0;
   
 }      for (i=1; i<=nlstate; i++)  
         for(m=iagemin; m <= iagemax+3; m++)
 /************ Variance of prevlim ******************/          prop[i][m]=0;
 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)        
 {        dateintsum=0;
   /* Variance of prevalence limit */        k2cpt=0;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for (i=1; i<=imx; i++) {
   double **newm;          bool=1;
   double **dnewm,**doldm;          if  (cptcovn>0) {
   int i, j, nhstepm, hstepm;            for (z1=1; z1<=cptcoveff; z1++) 
   int k, cptcode;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double *xp;                bool=0;
   double *gp, *gm;          }
   double **gradg, **trgradg;          if (bool==1){
   double age,agelim;            for(m=firstpass; m<=lastpass; m++){
   int theta;              k2=anint[m][i]+(mint[m][i]/12.);
                  if ((k2>=dateprev1) && (k2<=dateprev2)) {
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fprintf(ficresvpl,"# Age");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   for(i=1; i<=nlstate;i++)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficresvpl," %1d-%1d",i,i);                if (m<lastpass) {
   fprintf(ficresvpl,"\n");                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   xp=vector(1,npar);                }
   dnewm=matrix(1,nlstate,1,npar);                
   doldm=matrix(1,nlstate,1,nlstate);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                    dateintsum=dateintsum+k2;
   hstepm=1*YEARM; /* Every year of age */                  k2cpt++;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                }
   agelim = AGESUP;              }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          }
     if (stepm >= YEARM) hstepm=1;        }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */         
     gradg=matrix(1,npar,1,nlstate);        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
     for(theta=1; theta <=npar; theta++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for(i=1; i<=npar; i++){ /* Computes gradient */          fprintf(ficresp, "**********\n#");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        }
       }        for(i=1; i<=nlstate;i++) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       for(i=1;i<=nlstate;i++)        fprintf(ficresp, "\n");
         gp[i] = prlim[i][i];        
            for(i=iagemin; i <= iagemax+3; i++){
       for(i=1; i<=npar; i++) /* Computes gradient */          if(i==iagemax+3){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            fprintf(ficlog,"Total");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }else{
       for(i=1;i<=nlstate;i++)            if(first==1){
         gm[i] = prlim[i][i];              first=0;
               printf("See log file for details...\n");
       for(i=1;i<=nlstate;i++)            }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            fprintf(ficlog,"Age %d", i);
     } /* End theta */          }
           for(jk=1; jk <=nlstate ; jk++){
     trgradg =matrix(1,nlstate,1,npar);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
     for(j=1; j<=nlstate;j++)          }
       for(theta=1; theta <=npar; theta++)          for(jk=1; jk <=nlstate ; jk++){
         trgradg[j][theta]=gradg[theta][j];            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
     for(i=1;i<=nlstate;i++)            if(pp[jk]>=1.e-10){
       varpl[i][(int)age] =0.;              if(first==1){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);              }
     for(i=1;i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            }else{
               if(first==1)
     fprintf(ficresvpl,"%.0f ",age );                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            }
     fprintf(ficresvpl,"\n");          }
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
     free_matrix(gradg,1,npar,1,nlstate);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     free_matrix(trgradg,1,nlstate,1,npar);              pp[jk] += freq[jk][m][i];
   } /* End age */          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   free_vector(xp,1,npar);            pos += pp[jk];
   free_matrix(doldm,1,nlstate,1,npar);            posprop += prop[jk][i];
   free_matrix(dnewm,1,nlstate,1,nlstate);          }
           for(jk=1; jk <=nlstate ; jk++){
 }            if(pos>=1.e-5){
               if(first==1)
                 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{
 /**************** Main Program *****************/              if(first==1)
 /***********************************************/                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 /*int main(int argc, char *argv[])*/            }
 int main()            if( i <= iagemax){
 {              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;                probs[i][jk][j1]= pp[jk]/pos;
   double agedeb, agefin,hf;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   double agemin=1.e20, agemax=-1.e20;              }
               else
   double fret;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   double **xi,tmp,delta;            }
           }
   double dum; /* Dummy variable */          
   double ***p3mat;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   int *indx;            for(m=-1; m <=nlstate+ndeath; m++)
   char line[MAXLINE], linepar[MAXLINE];              if(freq[jk][m][i] !=0 ) {
   char title[MAXLINE];              if(first==1)
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   char filerest[FILENAMELENGTH];              }
   char fileregp[FILENAMELENGTH];          if(i <= iagemax)
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            fprintf(ficresp,"\n");
   int firstobs=1, lastobs=10;          if(first==1)
   int sdeb, sfin; /* Status at beginning and end */            printf("Others in log...\n");
   int c,  h , cpt,l;          fprintf(ficlog,"\n");
   int ju,jl, mi;        }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize;      }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    }
      dateintmean=dateintsum/k2cpt; 
   int hstepm, nhstepm;   
   double bage, fage, age, agelim, agebase;    fclose(ficresp);
   double ftolpl=FTOL;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   double **prlim;    free_vector(pp,1,nlstate);
   double *severity;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   double ***param; /* Matrix of parameters */    /* End of Freq */
   double  *p;  }
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */  /************ Prevalence ********************/
   double *delti; /* Scale */  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)
   double ***eij, ***vareij;  {  
   double **varpl; /* Variances of prevalence limits by age */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   double *epj, vepp;       in each health status at the date of interview (if between dateprev1 and dateprev2).
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";       We still use firstpass and lastpass as another selection.
   char *alph[]={"a","a","b","c","d","e"}, str[4];    */
    
   char z[1]="c", occ;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
 #include <sys/time.h>    double ***freq; /* Frequencies */
 #include <time.h>    double *pp, **prop;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    double pos,posprop; 
   /* long total_usecs;    double  y2; /* in fractional years */
   struct timeval start_time, end_time;    int iagemin, iagemax;
    
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    iagemin= (int) agemin;
     iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
   printf("\nIMACH, Version 0.64a");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   printf("\nEnter the parameter file name: ");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
 #ifdef windows    
   scanf("%s",pathtot);    j=cptcoveff;
   getcwd(pathcd, size);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   /*cygwin_split_path(pathtot,path,optionfile);    
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    for(k1=1; k1<=j;k1++){
   /* cutv(path,optionfile,pathtot,'\\');*/      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
 split(pathtot, path,optionfile);        
   chdir(path);        for (i=1; i<=nlstate; i++)  
   replace(pathc,path);          for(m=iagemin; m <= iagemax+3; m++)
 #endif            prop[i][m]=0.0;
 #ifdef unix       
   scanf("%s",optionfile);        for (i=1; i<=imx; i++) { /* Each individual */
 #endif          bool=1;
           if  (cptcovn>0) {
 /*-------- arguments in the command line --------*/            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   strcpy(fileres,"r");                bool=0;
   strcat(fileres, optionfile);          } 
           if (bool==1) { 
   /*---------arguments file --------*/            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     printf("Problem with optionfile %s\n",optionfile);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     goto end;                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); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
   strcpy(filereso,"o");                  /*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]]);*/
   strcat(filereso,fileres);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   if((ficparo=fopen(filereso,"w"))==NULL) {                  prop[s[m][i]][iagemax+3] += weight[i]; 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                } 
   }              }
             } /* end selection of waves */
   /* Reads comments: lines beginning with '#' */          }
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);        for(i=iagemin; i <= iagemax+3; i++){  
     fgets(line, MAXLINE, ficpar);          
     puts(line);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     fputs(line,ficparo);            posprop += prop[jk][i]; 
   }          } 
   ungetc(c,ficpar);  
           for(jk=1; jk <=nlstate ; jk++){     
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);            if( i <=  iagemax){ 
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);              if(posprop>=1.e-5){ 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);                probs[i][jk][j1]= prop[jk][i]/posprop;
               } 
   covar=matrix(1,NCOVMAX,1,n);                } 
   if (strlen(model)<=1) cptcovn=0;          }/* end jk */ 
   else {        }/* end i */ 
     j=0;      } /* end i1 */
     j=nbocc(model,'+');    } /* end k1 */
     cptcovn=j+1;    
   }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
   ncovmodel=2+cptcovn;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  }  /* End of prevalence */
    
   /* Read guess parameters */  /************* Waves Concatenation ***************/
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  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)
     ungetc(c,ficpar);  {
     fgets(line, MAXLINE, ficpar);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     puts(line);       Death is a valid wave (if date is known).
     fputs(line,ficparo);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   ungetc(c,ficpar);       and mw[mi+1][i]. dh depends on stepm.
         */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)    int i, mi, m;
     for(j=1; j <=nlstate+ndeath-1; j++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);       double sum=0., jmean=0.;*/
       fprintf(ficparo,"%1d%1d",i1,j1);    int first;
       printf("%1d%1d",i,j);    int j, k=0,jk, ju, jl;
       for(k=1; k<=ncovmodel;k++){    double sum=0.;
         fscanf(ficpar," %lf",&param[i][j][k]);    first=0;
         printf(" %lf",param[i][j][k]);    jmin=1e+5;
         fprintf(ficparo," %lf",param[i][j][k]);    jmax=-1;
       }    jmean=0.;
       fscanf(ficpar,"\n");    for(i=1; i<=imx; i++){
       printf("\n");      mi=0;
       fprintf(ficparo,"\n");      m=firstpass;
     }      while(s[m][i] <= nlstate){
          if(s[m][i]>=1)
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          mw[++mi][i]=m;
   p=param[1][1];        if(m >=lastpass)
            break;
   /* Reads comments: lines beginning with '#' */        else
   while((c=getc(ficpar))=='#' && c!= EOF){          m++;
     ungetc(c,ficpar);      }/* end while */
     fgets(line, MAXLINE, ficpar);      if (s[m][i] > nlstate){
     puts(line);        mi++;     /* Death is another wave */
     fputs(line,ficparo);        /* if(mi==0)  never been interviewed correctly before death */
   }           /* Only death is a correct wave */
   ungetc(c,ficpar);        mw[mi][i]=m;
       }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      wav[i]=mi;
   for(i=1; i <=nlstate; i++){      if(mi==0){
     for(j=1; j <=nlstate+ndeath-1; j++){        if(first==0){
       fscanf(ficpar,"%1d%1d",&i1,&j1);          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
       printf("%1d%1d",i,j);          first=1;
       fprintf(ficparo,"%1d%1d",i1,j1);        }
       for(k=1; k<=ncovmodel;k++){        if(first==1){
         fscanf(ficpar,"%le",&delti3[i][j][k]);          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
         printf(" %le",delti3[i][j][k]);        }
         fprintf(ficparo," %le",delti3[i][j][k]);      } /* end mi==0 */
       }    }
       fscanf(ficpar,"\n");  
       printf("\n");    for(i=1; i<=imx; i++){
       fprintf(ficparo,"\n");      for(mi=1; mi<wav[i];mi++){
     }        if (stepm <=0)
   }          dh[mi][i]=1;
   delti=delti3[1][1];        else{
            if (s[mw[mi+1][i]][i] > nlstate) {
   /* Reads comments: lines beginning with '#' */            if (agedc[i] < 2*AGESUP) {
   while((c=getc(ficpar))=='#' && c!= EOF){            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     ungetc(c,ficpar);            if(j==0) j=1;  /* Survives at least one month after exam */
     fgets(line, MAXLINE, ficpar);            k=k+1;
     puts(line);            if (j >= jmax) jmax=j;
     fputs(line,ficparo);            if (j <= jmin) jmin=j;
   }            sum=sum+j;
   ungetc(c,ficpar);            /*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);*/
   matcov=matrix(1,npar,1,npar);            /*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]);*/
   for(i=1; i <=npar; i++){            }
     fscanf(ficpar,"%s",&str);          }
     printf("%s",str);          else{
     fprintf(ficparo,"%s",str);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     for(j=1; j <=i; j++){            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       fscanf(ficpar," %le",&matcov[i][j]);            k=k+1;
       printf(" %.5le",matcov[i][j]);            if (j >= jmax) jmax=j;
       fprintf(ficparo," %.5le",matcov[i][j]);            else if (j <= jmin)jmin=j;
     }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     fscanf(ficpar,"\n");            /*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]);*/
     printf("\n");            sum=sum+j;
     fprintf(ficparo,"\n");          }
   }          jk= j/stepm;
   for(i=1; i <=npar; i++)          jl= j -jk*stepm;
     for(j=i+1;j<=npar;j++)          ju= j -(jk+1)*stepm;
       matcov[i][j]=matcov[j][i];          if(mle <=1){ 
                if(jl==0){
   printf("\n");              dh[mi][i]=jk;
               bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
    if(mle==1){                    * at the price of an extra matrix product in likelihood */
     /*-------- data file ----------*/              dh[mi][i]=jk+1;
     if((ficres =fopen(fileres,"w"))==NULL) {              bh[mi][i]=ju;
       printf("Problem with resultfile: %s\n", fileres);goto end;            }
     }          }else{
     fprintf(ficres,"#%s\n",version);            if(jl <= -ju){
                  dh[mi][i]=jk;
     if((fic=fopen(datafile,"r"))==NULL)    {              bh[mi][i]=jl;       /* bias is positive if real duration
       printf("Problem with datafile: %s\n", datafile);goto end;                                   * is higher than the multiple of stepm and negative otherwise.
     }                                   */
             }
     n= lastobs;            else{
     severity = vector(1,maxwav);              dh[mi][i]=jk+1;
     outcome=imatrix(1,maxwav+1,1,n);              bh[mi][i]=ju;
     num=ivector(1,n);            }
     moisnais=vector(1,n);            if(dh[mi][i]==0){
     annais=vector(1,n);              dh[mi][i]=1; /* At least one step */
     moisdc=vector(1,n);              bh[mi][i]=ju; /* At least one step */
     andc=vector(1,n);              /*  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);*/
     agedc=vector(1,n);            }
     cod=ivector(1,n);          }
     weight=vector(1,n);        } /* end if mle */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      } /* end wave */
     mint=matrix(1,maxwav,1,n);    }
     anint=matrix(1,maxwav,1,n);    jmean=sum/k;
     s=imatrix(1,maxwav+1,1,n);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     adl=imatrix(1,maxwav+1,1,n);        fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     tab=ivector(1,NCOVMAX);   }
     ncodemax=ivector(1,8);  
   /*********** Tricode ****************************/
     i=1;  void tricode(int *Tvar, int **nbcode, int imx)
     while (fgets(line, MAXLINE, fic) != NULL)    {  {
       if ((i >= firstobs) && (i <=lastobs)) {    
            int Ndum[20],ij=1, k, j, i, maxncov=19;
         for (j=maxwav;j>=1;j--){    int cptcode=0;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    cptcoveff=0; 
           strcpy(line,stra);   
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for (k=0; k<maxncov; k++) Ndum[k]=0;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for (k=1; k<=7; k++) ncodemax[k]=0;
         }  
            for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                                 modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        Ndum[ij]++; /*store the modality */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                                         Tvar[j]. If V=sex and male is 0 and 
         for (j=ncov;j>=1;j--){                                         female is 1, then  cptcode=1.*/
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      }
         }  
         num[i]=atol(stra);      for (i=0; i<=cptcode; i++) {
         if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
         /*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]));*/      }
   
         i=i+1;      ij=1; 
       }      for (i=1; i<=ncodemax[j]; i++) {
     }        for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
     /*scanf("%d",i);*/            nbcode[Tvar[j]][ij]=k; 
   imx=i-1; /* Number of individuals */            /* 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; */
             
   /* Calculation of the number of parameter from char model*/            ij++;
   Tvar=ivector(1,8);              }
              if (ij > ncodemax[j]) break; 
   if (strlen(model) >1){        }  
     j=0;      } 
     j=nbocc(model,'+');    }  
     cptcovn=j+1;  
       for (k=0; k< maxncov; k++) Ndum[k]=0;
     strcpy(modelsav,model);  
     if (j==0) {   for (i=1; i<=ncovmodel-2; i++) { 
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     }     ij=Tvar[i];
     else {     Ndum[ij]++;
       for(i=j; i>=1;i--){   }
         cutv(stra,strb,modelsav,'+');  
         if (strchr(strb,'*')) {   ij=1;
           cutv(strd,strc,strb,'*');   for (i=1; i<= maxncov; i++) {
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;     if((Ndum[i]!=0) && (i<=ncovcol)){
           cutv(strb,strc,strd,'V');       Tvaraff[ij]=i; /*For printing */
           for (k=1; k<=lastobs;k++)       ij++;
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];     }
         }   }
         else {cutv(strd,strc,strb,'V');   
         Tvar[i+1]=atoi(strc);   cptcoveff=ij-1; /*Number of simple covariates*/
         }  }
         strcpy(modelsav,stra);    
       }  /*********** Health Expectancies ****************/
       cutv(strd,strc,stra,'V');  
       Tvar[1]=atoi(strc);  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 )
     }  
   }  {
   /*printf("tvar=%d ",Tvar[1]);    /* Health expectancies */
   scanf("%d ",i);*/    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     fclose(fic);    double age, agelim, hf;
     double ***p3mat,***varhe;
     if (weightopt != 1) { /* Maximisation without weights*/    double **dnewm,**doldm;
       for(i=1;i<=n;i++) weight[i]=1.0;    double *xp;
     }    double **gp, **gm;
     /*-calculation of age at interview from date of interview and age at death -*/    double ***gradg, ***trgradg;
     agev=matrix(1,maxwav,1,imx);    int theta;
      
     for (i=1; i<=imx; i++)  {    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    xp=vector(1,npar);
       for(m=1; (m<= maxwav); m++){    dnewm=matrix(1,nlstate*nlstate,1,npar);
         if(s[m][i] >0){    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
           if (s[m][i] == nlstate+1) {    
             if(agedc[i]>0)    fprintf(ficreseij,"# Health expectancies\n");
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(ficreseij,"# Age");
               agev[m][i]=agedc[i];    for(i=1; i<=nlstate;i++)
             else{      for(j=1; j<=nlstate;j++)
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
               agev[m][i]=-1;    fprintf(ficreseij,"\n");
             }  
           }    if(estepm < stepm){
           else if(s[m][i] !=9){ /* Should no more exist */      printf ("Problem %d lower than %d\n",estepm, stepm);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    }
             if(mint[m][i]==99 || anint[m][i]==9999)    else  hstepm=estepm;   
               agev[m][i]=1;    /* We compute the life expectancy from trapezoids spaced every estepm months
             else if(agev[m][i] <agemin){     * This is mainly to measure the difference between two models: for example
               agemin=agev[m][i];     * if stepm=24 months pijx are given only every 2 years and by summing them
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/     * we are calculating an estimate of the Life Expectancy assuming a linear 
             }     * progression in between and thus overestimating or underestimating according
             else if(agev[m][i] >agemax){     * to the curvature of the survival function. If, for the same date, we 
               agemax=agev[m][i];     * estimate the model with stepm=1 month, we can keep estepm to 24 months
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/     * to compare the new estimate of Life expectancy with the same linear 
             }     * hypothesis. A more precise result, taking into account a more precise
             /*agev[m][i]=anint[m][i]-annais[i];*/     * curvature will be obtained if estepm is as small as stepm. */
             /*   agev[m][i] = age[i]+2*m;*/  
           }    /* For example we decided to compute the life expectancy with the smallest unit */
           else { /* =9 */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             agev[m][i]=1;       nhstepm is the number of hstepm from age to agelim 
             s[m][i]=-1;       nstepm is the number of stepm from age to agelin. 
           }       Look at hpijx to understand the reason of that which relies in memory size
         }       and note for a fixed period like estepm months */
         else /*= 0 Unknown */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           agev[m][i]=1;       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
           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.
     for (i=1; i<=imx; i++)  {    */
       for(m=1; (m<= maxwav); m++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         if (s[m][i] > (nlstate+ndeath)) {  
           printf("Error: Wrong value in nlstate or ndeath\n");      agelim=AGESUP;
           goto end;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         }      /* nhstepm age range expressed in number of stepm */
       }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_vector(severity,1,maxwav);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     free_imatrix(outcome,1,maxwav+1,1,n);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     free_vector(moisnais,1,n);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     free_vector(annais,1,n);  
     free_matrix(mint,1,maxwav,1,n);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     free_matrix(anint,1,maxwav,1,n);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     free_vector(moisdc,1,n);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     free_vector(andc,1,n);   
   
          hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      /* Computing Variances of health expectancies */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
           for(theta=1; theta <=npar; theta++){
     /* Concatenates waves */        for(i=1; i<=npar; i++){ 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 Tcode=ivector(1,100);    
    nbcode=imatrix(1,nvar,1,8);          cptj=0;
    ncodemax[1]=1;        for(j=1; j<= nlstate; j++){
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);          for(i=1; i<=nlstate; i++){
              cptj=cptj+1;
    codtab=imatrix(1,100,1,10);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
    h=0;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
    m=pow(2,cptcovn);            }
            }
    for(k=1;k<=cptcovn; k++){        }
      for(i=1; i <=(m/pow(2,k));i++){       
        for(j=1; j <= ncodemax[k]; j++){       
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){        for(i=1; i<=npar; i++) 
            h++;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            if (h>m) h=1;codtab[h][k]=j;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          }        
        }        cptj=0;
      }        for(j=1; j<= nlstate; j++){
    }          for(i=1;i<=nlstate;i++){
             cptj=cptj+1;
    /*for(i=1; i <=m ;i++){            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
      for(k=1; k <=cptcovn; k++){              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);            }
      }          }
      printf("\n");        }
    }*/        for(j=1; j<= nlstate*nlstate; j++)
    /*scanf("%d",i);*/          for(h=0; h<=nhstepm-1; h++){
                gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
    /* Calculates basic frequencies. Computes observed prevalence at single age          }
        and prints on file fileres'p'. */       } 
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);     
   /* End theta */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       for(h=0; h<=nhstepm-1; h++)
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        for(j=1; j<=nlstate*nlstate;j++)
              for(theta=1; theta <=npar; theta++)
     /* For Powell, parameters are in a vector p[] starting at p[1]            trgradg[h][j][theta]=gradg[h][theta][j];
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
           for(i=1;i<=nlstate*nlstate;i++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
      
     /*--------- results files --------------*/       printf("%d|",(int)age);fflush(stdout);
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           for(h=0;h<=nhstepm-1;h++){
    jk=1;        for(k=0;k<=nhstepm-1;k++){
    fprintf(ficres,"# Parameters\n");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
    printf("# Parameters\n");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
    for(i=1,jk=1; i <=nlstate; i++){          for(i=1;i<=nlstate*nlstate;i++)
      for(k=1; k <=(nlstate+ndeath); k++){            for(j=1;j<=nlstate*nlstate;j++)
        if (k != i)              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
          {        }
            printf("%d%d ",i,k);      }
            fprintf(ficres,"%1d%1d ",i,k);      /* Computing expectancies */
            for(j=1; j <=ncovmodel; j++){      for(i=1; i<=nlstate;i++)
              printf("%f ",p[jk]);        for(j=1; j<=nlstate;j++)
              fprintf(ficres,"%f ",p[jk]);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
              jk++;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
            }            
            printf("\n");  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
            fprintf(ficres,"\n");  
          }          }
      }  
    }      fprintf(ficreseij,"%3.0f",age );
       cptj=0;
     /* Computing hessian and covariance matrix */      for(i=1; i<=nlstate;i++)
     ftolhess=ftol; /* Usually correct */        for(j=1; j<=nlstate;j++){
     hesscov(matcov, p, npar, delti, ftolhess, func);          cptj++;
     fprintf(ficres,"# Scales\n");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     printf("# Scales\n");        }
      for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficreseij,"\n");
       for(j=1; j <=nlstate+ndeath; j++){     
         if (j!=i) {      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           fprintf(ficres,"%1d%1d",i,j);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           printf("%1d%1d",i,j);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           for(k=1; k<=ncovmodel;k++){      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
             printf(" %.5e",delti[jk]);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficres," %.5e",delti[jk]);    }
             jk++;    printf("\n");
           }    fprintf(ficlog,"\n");
           printf("\n");  
           fprintf(ficres,"\n");    free_vector(xp,1,npar);
         }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
      }
     k=1;  
     fprintf(ficres,"# Covariance\n");  /************ Variance ******************/
     printf("# Covariance\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)
     for(i=1;i<=npar;i++){  {
       /*  if (k>nlstate) k=1;    /* Variance of health expectancies */
       i1=(i-1)/(ncovmodel*nlstate)+1;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    /* double **newm;*/
       printf("%s%d%d",alph[k],i1,tab[i]);*/    double **dnewm,**doldm;
       fprintf(ficres,"%3d",i);    double **dnewmp,**doldmp;
       printf("%3d",i);    int i, j, nhstepm, hstepm, h, nstepm ;
       for(j=1; j<=i;j++){    int k, cptcode;
         fprintf(ficres," %.5e",matcov[i][j]);    double *xp;
         printf(" %.5e",matcov[i][j]);    double **gp, **gm;  /* for var eij */
       }    double ***gradg, ***trgradg; /*for var eij */
       fprintf(ficres,"\n");    double **gradgp, **trgradgp; /* for var p point j */
       printf("\n");    double *gpp, *gmp; /* for var p point j */
       k++;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     }    double ***p3mat;
        double age,agelim, hf;
     while((c=getc(ficpar))=='#' && c!= EOF){    double ***mobaverage;
       ungetc(c,ficpar);    int theta;
       fgets(line, MAXLINE, ficpar);    char digit[4];
       puts(line);    char digitp[25];
       fputs(line,ficparo);  
     }    char fileresprobmorprev[FILENAMELENGTH];
     ungetc(c,ficpar);  
      if(popbased==1){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      if(mobilav!=0)
            strcpy(digitp,"-populbased-mobilav-");
     if (fage <= 2) {      else strcpy(digitp,"-populbased-nomobil-");
       bage = agemin;    }
       fage = agemax;    else 
     }      strcpy(digitp,"-stablbased-");
   
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    if (mobilav!=0) {
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 /*------------ gnuplot -------------*/      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 chdir(pathcd);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   if((ficgp=fopen("graph.plt","w"))==NULL) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     printf("Problem with file graph.gp");goto end;      }
   }    }
 #ifdef windows  
   fprintf(ficgp,"cd \"%s\" \n",pathc);    strcpy(fileresprobmorprev,"prmorprev"); 
 #endif    sprintf(digit,"%-d",ij);
 m=pow(2,cptcovn);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      strcat(fileresprobmorprev,digit); /* Tvar to be done */
  /* 1eme*/    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   for (cpt=1; cpt<= nlstate ; cpt ++) {    strcat(fileresprobmorprev,fileres);
    for (k1=1; k1<= m ; k1 ++) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
 #ifdef windows      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);    }
 #endif    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 #ifdef unix    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    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);
 #endif    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 for (i=1; i<= nlstate ; i ++) {      fprintf(ficresprobmorprev," p.%-d SE",j);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for(i=1; i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 }    }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficresprobmorprev,"\n");
     for (i=1; i<= nlstate ; i ++) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
 }      exit(0);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    }
      for (i=1; i<= nlstate ; i ++) {    else{
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficgp,"\n# Routine varevsij");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }      if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      printf("Problem with html file: %s\n", optionfilehtm);
 #ifdef unix      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
 fprintf(ficgp,"\nset ter gif small size 400,300");      exit(0);
 #endif    }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    else{
    }      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");
   }      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*2 eme*/    }
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
        fprintf(ficresvij,"# Age");
     for (i=1; i<= nlstate+1 ; i ++) {    for(i=1; i<=nlstate;i++)
       k=2*i;      for(j=1; j<=nlstate;j++)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
       for (j=1; j<= nlstate+1 ; j ++) {    fprintf(ficresvij,"\n");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    xp=vector(1,npar);
 }      dnewm=matrix(1,nlstate,1,npar);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    doldm=matrix(1,nlstate,1,nlstate);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         else fprintf(ficgp," \%%*lf (\%%*lf)");    gpp=vector(nlstate+1,nlstate+ndeath);
 }      gmp=vector(nlstate+1,nlstate+ndeath);
       fprintf(ficgp,"\" t\"\" w l 0,");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point 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(estepm < stepm){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      printf ("Problem %d lower than %d\n",estepm, stepm);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }      else  hstepm=estepm;   
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    /* For example we decided to compute the life expectancy with the smallest unit */
       else fprintf(ficgp,"\" t\"\" w l 0,");    /* 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 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);       nstepm is the number of stepm from age to agelin. 
   }       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like k years */
   /*3eme*/    /* 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 (k1=1; k1<= m ; k1 ++) {       means that if the survival funtion is printed every two years of age and if
     for (cpt=1; cpt<= nlstate ; cpt ++) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       k=2+nlstate*(cpt-1);       results. So we changed our mind and took the option of the best precision.
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);    */
       for (i=1; i< nlstate ; i ++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    agelim = AGESUP;
       }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      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);
   /* CV preval stat */      gp=matrix(0,nhstepm,1,nlstate);
   for (k1=1; k1<= m ; k1 ++) {      gm=matrix(0,nhstepm,1,nlstate);
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      for(theta=1; theta <=npar; theta++){
       for (i=1; i< nlstate ; i ++)        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
         fprintf(ficgp,"+$%d",k+i+1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        }
              hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       l=3+(nlstate+ndeath)*cpt;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {        if (popbased==1) {
         l=3+(nlstate+ndeath)*cpt;          if(mobilav ==0){
         fprintf(ficgp,"+$%d",l+i+1);            for(i=1; i<=nlstate;i++)
       }              prlim[i][i]=probs[(int)age][i][ij];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            }else{ /* mobilav */ 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
         }
   /* proba elementaires */    
    for(i=1,jk=1; i <=nlstate; i++){        for(j=1; j<= nlstate; j++){
     for(k=1; k <=(nlstate+ndeath); k++){          for(h=0; h<=nhstepm; h++){
       if (k != i) {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         for(j=1; j <=ncovmodel; j++){              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/          }
           /*fprintf(ficgp,"%s",alph[1]);*/        }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        /* This for computing probability of death (h=1 means
           jk++;           computed over hstepm matrices product = hstepm*stepm months) 
           fprintf(ficgp,"\n");           as a weighted average of prlim.
         }        */
       }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   for(jk=1; jk <=m; jk++) {        /* end probability of death */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);  
    i=1;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
    for(k2=1; k2<=nlstate; k2++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      k3=i;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      for(k=1; k<=(nlstate+ndeath); k++) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        if (k != k2){   
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        if (popbased==1) {
           if(mobilav ==0){
         for(j=3; j <=ncovmodel; j++)            for(i=1; i<=nlstate;i++)
           fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              prlim[i][i]=probs[(int)age][i][ij];
         fprintf(ficgp,")/(1");          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
         for(k1=1; k1 <=nlstate+1; k1=k1+2){                prlim[i][i]=mobaverage[(int)age][i][ij];
             fprintf(ficgp,"+exp(p%d+p%d*x",k1+k3-1,k1+k3);          }
         }
             for(j=3; j <=ncovmodel; j++)  
               fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for(j=1; j<= nlstate; j++){
             fprintf(ficgp,")");          for(h=0; h<=nhstepm; h++){
         }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          }
     i=i+ncovmodel;        }
        }        /* This for computing probability of death (h=1 means
      }           computed over hstepm matrices product = hstepm*stepm months) 
    }           as a weighted average of prlim.
   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        */
    }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              for(i=1,gmp[j]=0.; i<= nlstate; i++)
   fclose(ficgp);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
            }    
 chdir(path);        /* end probability of death */
     free_matrix(agev,1,maxwav,1,imx);  
     free_ivector(wav,1,imx);        for(j=1; j<= nlstate; j++) /* vareij */
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          for(h=0; h<=nhstepm; h++){
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
              }
     free_imatrix(s,1,maxwav+1,1,n);  
            for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
              gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     free_ivector(num,1,n);        }
     free_vector(agedc,1,n);  
     free_vector(weight,1,n);      } /* End theta */
     /*free_matrix(covar,1,NCOVMAX,1,n);*/  
     fclose(ficparo);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     fclose(ficres);  
    }      for(h=0; h<=nhstepm; h++) /* veij */
            for(j=1; j<=nlstate;j++)
    /*________fin mle=1_________*/          for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
   
        for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     /* No more information from the sample is required now */        for(theta=1; theta <=npar; theta++)
   /* Reads comments: lines beginning with '#' */          trgradgp[j][theta]=gradgp[theta][j];
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     puts(line);      for(i=1;i<=nlstate;i++)
     fputs(line,ficparo);        for(j=1;j<=nlstate;j++)
   }          vareij[i][j][(int)age] =0.;
   ungetc(c,ficpar);  
        for(h=0;h<=nhstepm;h++){
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        for(k=0;k<=nhstepm;k++){
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 /*--------- index.htm --------*/          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
   if((fichtm=fopen("index.htm","w"))==NULL)    {              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     printf("Problem with index.htm \n");goto end;        }
   }      }
     
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n      /* pptj */
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          varppt[j][i]=doldmp[j][i];
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      /* end ppptj */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>      /*  x centered again */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
  fprintf(fichtm," <li>Graphs</li>\n<p>");      if (popbased==1) {
         if(mobilav ==0){
  m=cptcovn;          for(i=1; i<=nlstate;i++)
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
  j1=0;          for(i=1; i<=nlstate;i++)
  for(k1=1; k1<=m;k1++){            prlim[i][i]=mobaverage[(int)age][i][ij];
    for(i1=1; i1<=ncodemax[k1];i1++){        }
        j1++;      }
        if (cptcovn > 0) {               
          fprintf(fichtm,"<hr>************ Results for covariates");      /* This for computing probability of death (h=1 means
          for (cpt=1; cpt<=cptcovn;cpt++)         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);         as a weighted average of prlim.
          fprintf(fichtm," ************\n<hr>");      */
        }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        for(cpt=1; cpt<nlstate;cpt++){      }    
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      /* end probability of death */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
        }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     for(cpt=1; cpt<=nlstate;cpt++) {      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
 interval) in state (%d): v%s%d%d.gif <br>        for(i=1; i<=nlstate;i++){
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
      }        }
      for(cpt=1; cpt<=nlstate;cpt++) {      } 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      fprintf(ficresprobmorprev,"\n");
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
      }      fprintf(ficresvij,"%.0f ",age );
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      for(i=1; i<=nlstate;i++)
 health expectancies in states (1) and (2): e%s%d.gif<br>        for(j=1; j<=nlstate;j++){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
 fprintf(fichtm,"\n</body>");        }
    }      fprintf(ficresvij,"\n");
  }      free_matrix(gp,0,nhstepm,1,nlstate);
 fclose(fichtm);      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   /*--------------- Prevalence limit --------------*/      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcpy(filerespl,"pl");    } /* End age */
   strcat(filerespl,fileres);    free_vector(gpp,nlstate+1,nlstate+ndeath);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    free_vector(gmp,nlstate+1,nlstate+ndeath);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   fprintf(ficrespl,"#Prevalence limit\n");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   fprintf(ficrespl,"#Age ");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficrespl,"\n");  /*   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); */
   prlim=matrix(1,nlstate,1,nlstate);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    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);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   k=0;  */
   agebase=agemin;    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   agelim=agemax;  
   ftolpl=1.e-10;    free_vector(xp,1,npar);
   i1=cptcovn;    free_matrix(doldm,1,nlstate,1,nlstate);
   if (cptcovn < 1){i1=1;}    free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         k=k+1;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    fclose(ficresprobmorprev);
         fprintf(ficrespl,"\n#****** ");    fclose(ficgp);
         for(j=1;j<=cptcovn;j++)    fclose(fichtm);
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);  }  
         fprintf(ficrespl,"******\n");  
          /************ Variance of prevlim ******************/
         for (age=agebase; age<=agelim; age++){  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)
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  {
           fprintf(ficrespl,"%.0f",age );    /* Variance of prevalence limit */
           for(i=1; i<=nlstate;i++)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           fprintf(ficrespl," %.5f", prlim[i][i]);    double **newm;
           fprintf(ficrespl,"\n");    double **dnewm,**doldm;
         }    int i, j, nhstepm, hstepm;
       }    int k, cptcode;
     }    double *xp;
   fclose(ficrespl);    double *gp, *gm;
   /*------------- h Pij x at various ages ------------*/    double **gradg, **trgradg;
      double age,agelim;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    int theta;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {     
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   }    fprintf(ficresvpl,"# Age");
   printf("Computing pij: result on file '%s' \n", filerespij);    for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %1d-%1d",i,i);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficresvpl,"\n");
   if (stepm<=24) stepsize=2;  
     xp=vector(1,npar);
   agelim=AGESUP;    dnewm=matrix(1,nlstate,1,npar);
   hstepm=stepsize*YEARM; /* Every year of age */    doldm=matrix(1,nlstate,1,nlstate);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    
      hstepm=1*YEARM; /* Every year of age */
   k=0;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   for(cptcov=1;cptcov<=i1;cptcov++){    agelim = AGESUP;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       k=k+1;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         fprintf(ficrespij,"\n#****** ");      if (stepm >= YEARM) hstepm=1;
         for(j=1;j<=cptcovn;j++)      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);      gradg=matrix(1,npar,1,nlstate);
         fprintf(ficrespij,"******\n");      gp=vector(1,nlstate);
              gm=vector(1,nlstate);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      for(theta=1; theta <=npar; theta++){
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for(i=1; i<=npar; i++){ /* Computes gradient */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           oldm=oldms;savm=savms;        }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           fprintf(ficrespij,"# Age");        for(i=1;i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)          gp[i] = prlim[i][i];
             for(j=1; j<=nlstate+ndeath;j++)      
               fprintf(ficrespij," %1d-%1d",i,j);        for(i=1; i<=npar; i++) /* Computes gradient */
           fprintf(ficrespij,"\n");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           for (h=0; h<=nhstepm; h++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        for(i=1;i<=nlstate;i++)
             for(i=1; i<=nlstate;i++)          gm[i] = prlim[i][i];
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        for(i=1;i<=nlstate;i++)
             fprintf(ficrespij,"\n");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
           }      } /* End theta */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");      trgradg =matrix(1,nlstate,1,npar);
         }  
     }      for(j=1; j<=nlstate;j++)
   }        for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   fclose(ficrespij);  
       for(i=1;i<=nlstate;i++)
   /*---------- Health expectancies and variances ------------*/        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   strcpy(filerest,"t");      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   strcat(filerest,fileres);      for(i=1;i<=nlstate;i++)
   if((ficrest=fopen(filerest,"w"))==NULL) {        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }      fprintf(ficresvpl,"%.0f ",age );
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
   strcpy(filerese,"e");      free_vector(gp,1,nlstate);
   strcat(filerese,fileres);      free_vector(gm,1,nlstate);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      free_matrix(gradg,1,npar,1,nlstate);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      free_matrix(trgradg,1,nlstate,1,npar);
   }    } /* End age */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
     free_vector(xp,1,npar);
  strcpy(fileresv,"v");    free_matrix(doldm,1,nlstate,1,npar);
   strcat(fileresv,fileres);    free_matrix(dnewm,1,nlstate,1,nlstate);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  }
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  /************ 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)
   k=0;  {
   for(cptcov=1;cptcov<=i1;cptcov++){    int i, j=0,  i1, k1, l1, t, tj;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int k2, l2, j1,  z1;
       k=k+1;    int k=0,l, cptcode;
       fprintf(ficrest,"\n#****** ");    int first=1, first1;
       for(j=1;j<=cptcovn;j++)    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);    double **dnewm,**doldm;
       fprintf(ficrest,"******\n");    double *xp;
     double *gp, *gm;
       fprintf(ficreseij,"\n#****** ");    double **gradg, **trgradg;
       for(j=1;j<=cptcovn;j++)    double **mu;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    double age,agelim, cov[NCOVMAX];
       fprintf(ficreseij,"******\n");    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
       fprintf(ficresvij,"\n#****** ");    char fileresprob[FILENAMELENGTH];
       for(j=1;j<=cptcovn;j++)    char fileresprobcov[FILENAMELENGTH];
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    char fileresprobcor[FILENAMELENGTH];
       fprintf(ficresvij,"******\n");  
     double ***varpij;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    strcpy(fileresprob,"prob"); 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      strcat(fileresprob,fileres);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       oldm=oldms;savm=savms;      printf("Problem with resultfile: %s\n", fileresprob);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
          }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    strcpy(fileresprobcov,"probcov"); 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    strcat(fileresprobcov,fileres);
       fprintf(ficrest,"\n");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
              printf("Problem with resultfile: %s\n", fileresprobcov);
       hf=1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       if (stepm >= YEARM) hf=stepm/YEARM;    }
       epj=vector(1,nlstate+1);    strcpy(fileresprobcor,"probcor"); 
       for(age=bage; age <=fage ;age++){    strcat(fileresprobcor,fileres);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         fprintf(ficrest," %.0f",age);      printf("Problem with resultfile: %s\n", fileresprobcor);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    }
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           epj[nlstate+1] +=epj[j];    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);
         for(i=1, vepp=0.;i <=nlstate;i++)    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           for(j=1;j <=nlstate;j++)    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
             vepp += vareij[i][j][(int)age];    
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         for(j=1;j <=nlstate;j++){    fprintf(ficresprob,"# Age");
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
         }    fprintf(ficresprobcov,"# Age");
         fprintf(ficrest,"\n");    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       }    fprintf(ficresprobcov,"# Age");
     }  
   }  
            for(i=1; i<=nlstate;i++)
  fclose(ficreseij);      for(j=1; j<=(nlstate+ndeath);j++){
  fclose(ficresvij);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   fclose(ficrest);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   fclose(ficpar);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   free_vector(epj,1,nlstate+1);      }  
   /*  scanf("%d ",i); */   /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
   /*------- Variance limit prevalence------*/      fprintf(ficresprobcor,"\n");
    */
 strcpy(fileresvpl,"vpl");   xp=vector(1,npar);
   strcat(fileresvpl,fileres);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     exit(0);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   }    first=1;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
  k=0;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
  for(cptcov=1;cptcov<=i1;cptcov++){      exit(0);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
      k=k+1;    else{
      fprintf(ficresvpl,"\n#****** ");      fprintf(ficgp,"\n# Routine varprob");
      for(j=1;j<=cptcovn;j++)    }
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
      fprintf(ficresvpl,"******\n");      printf("Problem with html file: %s\n", optionfilehtm);
            fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);      exit(0);
      oldm=oldms;savm=savms;    }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    else{
    }      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
  }      fprintf(fichtm,"\n");
   
   fclose(ficresvpl);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       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");
   /*---------- End : free ----------------*/      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");
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
      }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    cov[1]=1;
      tj=cptcoveff;
      if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    j1=0;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    for(t=1; t<=tj;t++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      for(i1=1; i1<=ncodemax[t];i1++){ 
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        j1++;
          if  (cptcovn>0) {
   free_matrix(matcov,1,npar,1,npar);          fprintf(ficresprob, "\n#********** Variable "); 
   free_vector(delti,1,npar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprob, "**********\n#\n");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   printf("End of Imach\n");          fprintf(ficresprobcov, "**********\n#\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          
            fprintf(ficgp, "\n#********** Variable "); 
   /* 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);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /*printf("Total time was %d uSec.\n", total_usecs);*/          fprintf(ficgp, "**********\n#\n");
   /*------ End -----------*/          
           
  end:          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
 #ifdef windows          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  chdir(pathcd);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
 #endif          
  system("wgnuplot graph.plt");          fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 #ifdef windows          fprintf(ficresprobcor, "**********\n#");    
   while (z[0] != 'q') {        }
     chdir(pathcd);        
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        for (age=bage; age<=fage; age ++){ 
     scanf("%s",z);          cov[2]=age;
     if (z[0] == 'c') system("./imach");          for (k=1; k<=cptcovn;k++) {
     else if (z[0] == 'e') {            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       chdir(path);          }
       system("index.htm");          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }          for (k=1; k<=cptcovprod;k++)
     else if (z[0] == 'q') exit(0);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   }          
 #endif          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
 }          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           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(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     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 ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       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(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);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       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);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       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;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fclose(ficgp);
     fclose(fichtm);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
     if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     }
   
      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
    - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
    - Life expectancies by age and initial health status (estepm=%2d months): 
      <a href=\"e%s\">e%s</a> <br>\n</li>", \
     jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    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++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
   <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
   <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
    - 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
    - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
    - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
    - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   
    if(popforecast==1) fprintf(fichtm,"\n
    - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
    - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
           <br>",fileres,fileres,fileres,fileres);
    else 
      fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    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++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   interval) in state (%d): v%s%d%d.png <br>
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   fclose(fichtm);
   }
   
   /******************* Gnuplot file **************/
   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;
     int ng;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   
     /*#ifdef windows */
       fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   m=pow(2,cptcoveff);
     
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      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);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       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 (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         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);
           
         } 
       }
     }
     
     /* CV preval stat */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
         
         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;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      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");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  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;
                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]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fclose(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (YEARM*yearp)) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h==(int)(YEARM*yearp))
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                 }
                 if (h==(int)(YEARM*yearp)){
                   fprintf(ficresf," %.3f", ppij);
                 }
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
       }
     }
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(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: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.5  
changed lines
  Added in v.1.74


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