Diff for /imach/src/imach.c between versions 1.20 and 1.67

version 1.20, 2002/02/20 17:22:01 version 1.67, 2003/01/28 17:41:19
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*/   
 #define windows  #include <math.h>
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #include <stdio.h>
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #include <stdlib.h>
   #include <unistd.h>
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 #define NINTERVMAX 8  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define FILENAMELENGTH 80
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  /*#define DEBUG*/
 #define NCOVMAX 8 /* Maximum number of covariates */  #define windows
 #define MAXN 20000  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define YEARM 12. /* Number of months per year */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #define AGESUP 130  
 #define AGEBASE 40  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 int nvar;  #define NINTERVMAX 8
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 int npar=NPARMAX;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 int nlstate=2; /* Number of live states */  #define NCOVMAX 8 /* Maximum number of covariates */
 int ndeath=1; /* Number of dead states */  #define MAXN 20000
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  #define YEARM 12. /* Number of months per year */
 int popbased=0;  #define AGESUP 130
   #define AGEBASE 40
 int *wav; /* Number of waves for this individuual 0 is possible */  #ifdef windows
 int maxwav; /* Maxim number of waves */  #define DIRSEPARATOR '\\'
 int jmin, jmax; /* min, max spacing between 2 waves */  #define ODIRSEPARATOR '/'
 int mle, weightopt;  #else
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define DIRSEPARATOR '/'
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define ODIRSEPARATOR '\\'
 double jmean; /* Mean space between 2 waves */  #endif
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  char version[80]="Imach version 0.91, November 2002, INED-EUROREVES ";
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  int erreur; /* Error number */
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;  int nvar;
 FILE *ficreseij;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   char filerese[FILENAMELENGTH];  int npar=NPARMAX;
  FILE  *ficresvij;  int nlstate=2; /* Number of live states */
   char fileresv[FILENAMELENGTH];  int ndeath=1; /* Number of dead states */
  FILE  *ficresvpl;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   char fileresvpl[FILENAMELENGTH];  int popbased=0;
   
 #define NR_END 1  int *wav; /* Number of waves for this individuual 0 is possible */
 #define FREE_ARG char*  int maxwav; /* Maxim number of waves */
 #define FTOL 1.0e-10  int jmin, jmax; /* min, max spacing between 2 waves */
   int mle, weightopt;
 #define NRANSI  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #define ITMAX 200  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 #define TOL 2.0e-4             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 #define CGOLD 0.3819660  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #define ZEPS 1.0e-10  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog;
 #define GOLD 1.618034  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define GLIMIT 100.0  FILE *ficresprobmorprev;
 #define TINY 1.0e-20  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 static double maxarg1,maxarg2;  char filerese[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  FILE  *ficresvij;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char fileresv[FILENAMELENGTH];
    FILE  *ficresvpl;
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char fileresvpl[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 static double sqrarg;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 int imx;  char filerest[FILENAMELENGTH];
 int stepm;  char fileregp[FILENAMELENGTH];
 /* Stepm, step in month: minimum step interpolation*/  char popfile[FILENAMELENGTH];
   
 int m,nb;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define NR_END 1
 double **pmmij, ***probs, ***mobaverage;  #define FREE_ARG char*
 double dateintmean=0;  #define FTOL 1.0e-10
   
 double *weight;  #define NRANSI 
 int **s; /* Status */  #define ITMAX 200 
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define TOL 2.0e-4 
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define CGOLD 0.3819660 
 double ftolhess; /* Tolerance for computing hessian */  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name )  #define GOLD 1.618034 
 {  #define GLIMIT 100.0 
    char *s;                             /* pointer */  #define TINY 1.0e-20 
    int  l1, l2;                         /* length counters */  
   static double maxarg1,maxarg2;
    l1 = strlen( path );                 /* length of path */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    s = strrchr( path, '\\' );           /* find last / */    
    if ( s == NULL ) {                   /* no directory, so use current */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #if     defined(__bsd__)                /* get current working directory */  #define rint(a) floor(a+0.5)
       extern char       *getwd( );  
   static double sqrarg;
       if ( getwd( dirc ) == NULL ) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #else  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       extern char       *getcwd( );  
   int imx; 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int stepm;
 #endif  /* Stepm, step in month: minimum step interpolation*/
          return( GLOCK_ERROR_GETCWD );  
       }  int estepm;
       strcpy( name, path );             /* we've got it */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  int m,nb;
       l2 = strlen( s );                 /* length of filename */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       strcpy( name, s );                /* save file name */  double **pmmij, ***probs;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  double dateintmean=0;
       dirc[l1-l2] = 0;                  /* add zero */  
    }  double *weight;
    l1 = strlen( dirc );                 /* length of directory */  int **s; /* Status */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  double *agedc, **covar, idx;
    return( 0 );                         /* we're done */  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 }  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
 /******************************************/  
   /**************** split *************************/
 void replace(char *s, char*t)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
   int i;    char  *ss;                            /* pointer */
   int lg=20;    int   l1, l2;                         /* length counters */
   i=0;  
   lg=strlen(t);    l1 = strlen(path );                   /* length of path */
   for(i=0; i<= lg; i++) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     (s[i] = t[i]);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if (t[i]== '\\') s[i]='/';    if ( ss == NULL ) {                   /* no directory, so use current */
   }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   #if     defined(__bsd__)                /* get current working directory */
 int nbocc(char *s, char occ)      extern char *getwd( );
 {  
   int i,j=0;      if ( getwd( dirc ) == NULL ) {
   int lg=20;  #else
   i=0;      extern char *getcwd( );
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   if  (s[i] == occ ) j++;  #endif
   }        return( GLOCK_ERROR_GETCWD );
   return j;      }
 }      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 void cutv(char *u,char *v, char*t, char occ)      ss++;                               /* after this, the filename */
 {      l2 = strlen( ss );                  /* length of filename */
   int i,lg,j,p=0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   i=0;      strcpy( name, ss );         /* save file name */
   for(j=0; j<=strlen(t)-1; j++) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      dirc[l1-l2] = 0;                    /* add zero */
   }    }
     l1 = strlen( dirc );                  /* length of directory */
   lg=strlen(t);  #ifdef windows
   for(j=0; j<p; j++) {    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
     (u[j] = t[j]);  #else
   }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
      u[p]='\0';  #endif
     ss = strrchr( name, '.' );            /* find last / */
    for(j=0; j<= lg; j++) {    ss++;
     if (j>=(p+1))(v[j-p-1] = t[j]);    strcpy(ext,ss);                       /* save extension */
   }    l1= strlen( name);
 }    l2= strlen(ss)+1;
     strncpy( finame, name, l1-l2);
 /********************** nrerror ********************/    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
 void nrerror(char error_text[])  }
 {  
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  /******************************************/
   exit(1);  
 }  void replace(char *s, char*t)
 /*********************** vector *******************/  {
 double *vector(int nl, int nh)    int i;
 {    int lg=20;
   double *v;    i=0;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    lg=strlen(t);
   if (!v) nrerror("allocation failure in vector");    for(i=0; i<= lg; i++) {
   return v-nl+NR_END;      (s[i] = t[i]);
 }      if (t[i]== '\\') s[i]='/';
     }
 /************************ free vector ******************/  }
 void free_vector(double*v, int nl, int nh)  
 {  int nbocc(char *s, char occ)
   free((FREE_ARG)(v+nl-NR_END));  {
 }    int i,j=0;
     int lg=20;
 /************************ivector *******************************/    i=0;
 int *ivector(long nl,long nh)    lg=strlen(s);
 {    for(i=0; i<= lg; i++) {
   int *v;    if  (s[i] == occ ) j++;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    }
   if (!v) nrerror("allocation failure in ivector");    return j;
   return v-nl+NR_END;  }
 }  
   void cutv(char *u,char *v, char*t, char occ)
 /******************free ivector **************************/  {
 void free_ivector(int *v, long nl, long nh)    /* 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)
   free((FREE_ARG)(v+nl-NR_END));       gives u="abcedf" and v="ghi2j" */
 }    int i,lg,j,p=0;
     i=0;
 /******************* imatrix *******************************/    for(j=0; j<=strlen(t)-1; j++) {
 int **imatrix(long nrl, long nrh, long ncl, long nch)      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    }
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    lg=strlen(t);
   int **m;    for(j=0; j<p; j++) {
        (u[j] = t[j]);
   /* allocate pointers to rows */    }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));       u[p]='\0';
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;     for(j=0; j<= lg; j++) {
   m -= nrl;      if (j>=(p+1))(v[j-p-1] = t[j]);
      }
    }
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  /********************** nrerror ********************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  void nrerror(char error_text[])
   m[nrl] -= ncl;  {
      fprintf(stderr,"ERREUR ...\n");
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    fprintf(stderr,"%s\n",error_text);
      exit(EXIT_FAILURE);
   /* return pointer to array of pointers to rows */  }
   return m;  /*********************** vector *******************/
 }  double *vector(int nl, int nh)
   {
 /****************** free_imatrix *************************/    double *v;
 void free_imatrix(m,nrl,nrh,ncl,nch)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       int **m;    if (!v) nrerror("allocation failure in vector");
       long nch,ncl,nrh,nrl;    return v-nl+NR_END;
      /* free an int matrix allocated by imatrix() */  }
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  /************************ free vector ******************/
   free((FREE_ARG) (m+nrl-NR_END));  void free_vector(double*v, int nl, int nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /******************* matrix *******************************/  }
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  /************************ivector *******************************/
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int *ivector(long nl,long nh)
   double **m;  {
     int *v;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!v) nrerror("allocation failure in ivector");
   m += NR_END;    return v-nl+NR_END;
   m -= nrl;  }
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /******************free ivector **************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  void free_ivector(int *v, long nl, long nh)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    free((FREE_ARG)(v+nl-NR_END));
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  /******************* imatrix *******************************/
 }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 /*************************free matrix ************************/  { 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 {    int **m; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    
   free((FREE_ARG)(m+nrl-NR_END));    /* allocate pointers to rows */ 
 }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 /******************* ma3x *******************************/    m += NR_END; 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    m -= nrl; 
 {    
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    
   double ***m;    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   if (!m) nrerror("allocation failure 1 in matrix()");    m[nrl] += NR_END; 
   m += NR_END;    m[nrl] -= ncl; 
   m -= nrl;    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    /* return pointer to array of pointers to rows */ 
   m[nrl] += NR_END;    return m; 
   m[nrl] -= ncl;  } 
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));        int **m;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");        long nch,ncl,nrh,nrl; 
   m[nrl][ncl] += NR_END;       /* free an int matrix allocated by imatrix() */ 
   m[nrl][ncl] -= nll;  { 
   for (j=ncl+1; j<=nch; j++)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     m[nrl][j]=m[nrl][j-1]+nlay;    free((FREE_ARG) (m+nrl-NR_END)); 
    } 
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /******************* matrix *******************************/
     for (j=ncl+1; j<=nch; j++)  double **matrix(long nrl, long nrh, long ncl, long nch)
       m[i][j]=m[i][j-1]+nlay;  {
   }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   return m;    double **m;
 }  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 /*************************free ma3x ************************/    if (!m) nrerror("allocation failure 1 in matrix()");
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m += NR_END;
 {    m -= nrl;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m+nrl-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
 /***************** f1dim *************************/  
 extern int ncom;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 extern double *pcom,*xicom;    return m;
 extern double (*nrfunc)(double []);  }
    
 double f1dim(double x)  /*************************free matrix ************************/
 {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   int j;  {
   double f;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double *xt;    free((FREE_ARG)(m+nrl-NR_END));
    }
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /******************* ma3x *******************************/
   f=(*nrfunc)(xt);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   free_vector(xt,1,ncom);  {
   return f;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 }    double ***m;
   
 /*****************brent *************************/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   int iter;    m -= nrl;
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double ftemp;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m[nrl] += NR_END;
   double e=0.0;    m[nrl] -= ncl;
    
   a=(ax < cx ? ax : cx);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   fw=fv=fx=(*f)(x);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl][ncl] += NR_END;
     xm=0.5*(a+b);    m[nrl][ncl] -= nll;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    for (j=ncl+1; j<=nch; j++) 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      m[nrl][j]=m[nrl][j-1]+nlay;
     printf(".");fflush(stdout);    
 #ifdef DEBUG    for (i=nrl+1; i<=nrh; i++) {
     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);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      for (j=ncl+1; j<=nch; j++) 
 #endif        m[i][j]=m[i][j-1]+nlay;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    }
       *xmin=x;    return m;
       return fx;  }
     }  
     ftemp=fu;  /*************************free ma3x ************************/
     if (fabs(e) > tol1) {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       r=(x-w)*(fx-fv);  {
       q=(x-v)*(fx-fw);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       p=(x-v)*q-(x-w)*r;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       q=2.0*(q-r);    free((FREE_ARG)(m+nrl-NR_END));
       if (q > 0.0) p = -p;  }
       q=fabs(q);  
       etemp=e;  /***************** f1dim *************************/
       e=d;  extern int ncom; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  extern double *pcom,*xicom;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  extern double (*nrfunc)(double []); 
       else {   
         d=p/q;  double f1dim(double x) 
         u=x+d;  { 
         if (u-a < tol2 || b-u < tol2)    int j; 
           d=SIGN(tol1,xm-x);    double f;
       }    double *xt; 
     } else {   
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    xt=vector(1,ncom); 
     }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    f=(*nrfunc)(xt); 
     fu=(*f)(u);    free_vector(xt,1,ncom); 
     if (fu <= fx) {    return f; 
       if (u >= x) a=x; else b=x;  } 
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  /*****************brent *************************/
         } else {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
           if (u < x) a=u; else b=u;  { 
           if (fu <= fw || w == x) {    int iter; 
             v=w;    double a,b,d,etemp;
             w=u;    double fu,fv,fw,fx;
             fv=fw;    double ftemp;
             fw=fu;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
           } else if (fu <= fv || v == x || v == w) {    double e=0.0; 
             v=u;   
             fv=fu;    a=(ax < cx ? ax : cx); 
           }    b=(ax > cx ? ax : cx); 
         }    x=w=v=bx; 
   }    fw=fv=fx=(*f)(x); 
   nrerror("Too many iterations in brent");    for (iter=1;iter<=ITMAX;iter++) { 
   *xmin=x;      xm=0.5*(a+b); 
   return fx;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
 /****************** mnbrak ***********************/      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      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);
             double (*func)(double))      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   double ulim,u,r,q, dum;  #endif
   double fu;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
          *xmin=x; 
   *fa=(*func)(*ax);        return fx; 
   *fb=(*func)(*bx);      } 
   if (*fb > *fa) {      ftemp=fu;
     SHFT(dum,*ax,*bx,dum)      if (fabs(e) > tol1) { 
       SHFT(dum,*fb,*fa,dum)        r=(x-w)*(fx-fv); 
       }        q=(x-v)*(fx-fw); 
   *cx=(*bx)+GOLD*(*bx-*ax);        p=(x-v)*q-(x-w)*r; 
   *fc=(*func)(*cx);        q=2.0*(q-r); 
   while (*fb > *fc) {        if (q > 0.0) p = -p; 
     r=(*bx-*ax)*(*fb-*fc);        q=fabs(q); 
     q=(*bx-*cx)*(*fb-*fa);        etemp=e; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        e=d; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     ulim=(*bx)+GLIMIT*(*cx-*bx);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     if ((*bx-u)*(u-*cx) > 0.0) {        else { 
       fu=(*func)(u);          d=p/q; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {          u=x+d; 
       fu=(*func)(u);          if (u-a < tol2 || b-u < tol2) 
       if (fu < *fc) {            d=SIGN(tol1,xm-x); 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        } 
           SHFT(*fb,*fc,fu,(*func)(u))      } else { 
           }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      } 
       u=ulim;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*func)(u);      fu=(*f)(u); 
     } else {      if (fu <= fx) { 
       u=(*cx)+GOLD*(*cx-*bx);        if (u >= x) a=x; else b=x; 
       fu=(*func)(u);        SHFT(v,w,x,u) 
     }          SHFT(fv,fw,fx,fu) 
     SHFT(*ax,*bx,*cx,u)          } else { 
       SHFT(*fa,*fb,*fc,fu)            if (u < x) a=u; else b=u; 
       }            if (fu <= fw || w == x) { 
 }              v=w; 
               w=u; 
 /*************** linmin ************************/              fv=fw; 
               fw=fu; 
 int ncom;            } else if (fu <= fv || v == x || v == w) { 
 double *pcom,*xicom;              v=u; 
 double (*nrfunc)(double []);              fv=fu; 
              } 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))          } 
 {    } 
   double brent(double ax, double bx, double cx,    nrerror("Too many iterations in brent"); 
                double (*f)(double), double tol, double *xmin);    *xmin=x; 
   double f1dim(double x);    return fx; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  } 
               double *fc, double (*func)(double));  
   int j;  /****************** mnbrak ***********************/
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                double (*func)(double)) 
   ncom=n;  { 
   pcom=vector(1,n);    double ulim,u,r,q, dum;
   xicom=vector(1,n);    double fu; 
   nrfunc=func;   
   for (j=1;j<=n;j++) {    *fa=(*func)(*ax); 
     pcom[j]=p[j];    *fb=(*func)(*bx); 
     xicom[j]=xi[j];    if (*fb > *fa) { 
   }      SHFT(dum,*ax,*bx,dum) 
   ax=0.0;        SHFT(dum,*fb,*fa,dum) 
   xx=1.0;        } 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    *cx=(*bx)+GOLD*(*bx-*ax); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    *fc=(*func)(*cx); 
 #ifdef DEBUG    while (*fb > *fc) { 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      r=(*bx-*ax)*(*fb-*fc); 
 #endif      q=(*bx-*cx)*(*fb-*fa); 
   for (j=1;j<=n;j++) {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     xi[j] *= xmin;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     p[j] += xi[j];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   }      if ((*bx-u)*(u-*cx) > 0.0) { 
   free_vector(xicom,1,n);        fu=(*func)(u); 
   free_vector(pcom,1,n);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 }        fu=(*func)(u); 
         if (fu < *fc) { 
 /*************** powell ************************/          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,            SHFT(*fb,*fc,fu,(*func)(u)) 
             double (*func)(double []))            } 
 {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   void linmin(double p[], double xi[], int n, double *fret,        u=ulim; 
               double (*func)(double []));        fu=(*func)(u); 
   int i,ibig,j;      } else { 
   double del,t,*pt,*ptt,*xit;        u=(*cx)+GOLD*(*cx-*bx); 
   double fp,fptt;        fu=(*func)(u); 
   double *xits;      } 
   pt=vector(1,n);      SHFT(*ax,*bx,*cx,u) 
   ptt=vector(1,n);        SHFT(*fa,*fb,*fc,fu) 
   xit=vector(1,n);        } 
   xits=vector(1,n);  } 
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  /*************** linmin ************************/
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  int ncom; 
     ibig=0;  double *pcom,*xicom;
     del=0.0;  double (*nrfunc)(double []); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);   
     for (i=1;i<=n;i++)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       printf(" %d %.12f",i, p[i]);  { 
     printf("\n");    double brent(double ax, double bx, double cx, 
     for (i=1;i<=n;i++) {                 double (*f)(double), double tol, double *xmin); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    double f1dim(double x); 
       fptt=(*fret);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 #ifdef DEBUG                double *fc, double (*func)(double)); 
       printf("fret=%lf \n",*fret);    int j; 
 #endif    double xx,xmin,bx,ax; 
       printf("%d",i);fflush(stdout);    double fx,fb,fa;
       linmin(p,xit,n,fret,func);   
       if (fabs(fptt-(*fret)) > del) {    ncom=n; 
         del=fabs(fptt-(*fret));    pcom=vector(1,n); 
         ibig=i;    xicom=vector(1,n); 
       }    nrfunc=func; 
 #ifdef DEBUG    for (j=1;j<=n;j++) { 
       printf("%d %.12e",i,(*fret));      pcom[j]=p[j]; 
       for (j=1;j<=n;j++) {      xicom[j]=xi[j]; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    } 
         printf(" x(%d)=%.12e",j,xit[j]);    ax=0.0; 
       }    xx=1.0; 
       for(j=1;j<=n;j++)    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         printf(" p=%.12e",p[j]);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       printf("\n");  #ifdef DEBUG
 #endif    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #endif
 #ifdef DEBUG    for (j=1;j<=n;j++) { 
       int k[2],l;      xi[j] *= xmin; 
       k[0]=1;      p[j] += xi[j]; 
       k[1]=-1;    } 
       printf("Max: %.12e",(*func)(p));    free_vector(xicom,1,n); 
       for (j=1;j<=n;j++)    free_vector(pcom,1,n); 
         printf(" %.12e",p[j]);  } 
       printf("\n");  
       for(l=0;l<=1;l++) {  /*************** powell ************************/
         for (j=1;j<=n;j++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];              double (*func)(double [])) 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  { 
         }    void linmin(double p[], double xi[], int n, double *fret, 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));                double (*func)(double [])); 
       }    int i,ibig,j; 
 #endif    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
     double *xits;
       free_vector(xit,1,n);    pt=vector(1,n); 
       free_vector(xits,1,n);    ptt=vector(1,n); 
       free_vector(ptt,1,n);    xit=vector(1,n); 
       free_vector(pt,1,n);    xits=vector(1,n); 
       return;    *fret=(*func)(p); 
     }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    for (*iter=1;;++(*iter)) { 
     for (j=1;j<=n;j++) {      fp=(*fret); 
       ptt[j]=2.0*p[j]-pt[j];      ibig=0; 
       xit[j]=p[j]-pt[j];      del=0.0; 
       pt[j]=p[j];      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     fptt=(*func)(ptt);      for (i=1;i<=n;i++) 
     if (fptt < fp) {        printf(" %d %.12f",i, p[i]);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      fprintf(ficlog," %d %.12f",i, p[i]);
       if (t < 0.0) {      printf("\n");
         linmin(p,xit,n,fret,func);      fprintf(ficlog,"\n");
         for (j=1;j<=n;j++) {      for (i=1;i<=n;i++) { 
           xi[j][ibig]=xi[j][n];        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
           xi[j][n]=xit[j];        fptt=(*fret); 
         }  #ifdef DEBUG
 #ifdef DEBUG        printf("fret=%lf \n",*fret);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        fprintf(ficlog,"fret=%lf \n",*fret);
         for(j=1;j<=n;j++)  #endif
           printf(" %.12e",xit[j]);        printf("%d",i);fflush(stdout);
         printf("\n");        fprintf(ficlog,"%d",i);fflush(ficlog);
 #endif        linmin(p,xit,n,fret,func); 
       }        if (fabs(fptt-(*fret)) > del) { 
     }          del=fabs(fptt-(*fret)); 
   }          ibig=i; 
 }        } 
   #ifdef DEBUG
 /**** Prevalence limit ****************/        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        for (j=1;j<=n;j++) {
 {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          printf(" x(%d)=%.12e",j,xit[j]);
      matrix by transitions matrix until convergence is reached */          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
   int i, ii,j,k;        for(j=1;j<=n;j++) {
   double min, max, maxmin, maxmax,sumnew=0.;          printf(" p=%.12e",p[j]);
   double **matprod2();          fprintf(ficlog," p=%.12e",p[j]);
   double **out, cov[NCOVMAX], **pmij();        }
   double **newm;        printf("\n");
   double agefin, delaymax=50 ; /* Max number of years to converge */        fprintf(ficlog,"\n");
   #endif
   for (ii=1;ii<=nlstate+ndeath;ii++)      } 
     for (j=1;j<=nlstate+ndeath;j++){      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #ifdef DEBUG
     }        int k[2],l;
         k[0]=1;
    cov[1]=1.;        k[1]=-1;
          printf("Max: %.12e",(*func)(p));
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        fprintf(ficlog,"Max: %.12e",(*func)(p));
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        for (j=1;j<=n;j++) {
     newm=savm;          printf(" %.12e",p[j]);
     /* Covariates have to be included here again */          fprintf(ficlog," %.12e",p[j]);
      cov[2]=agefin;        }
          printf("\n");
       for (k=1; k<=cptcovn;k++) {        fprintf(ficlog,"\n");
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        for(l=0;l<=1;l++) {
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/          for (j=1;j<=n;j++) {
       }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       for (k=1; k<=cptcovage;k++)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for (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]]];          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)));
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        }
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  #endif
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
         free_vector(xit,1,n); 
     savm=oldm;        free_vector(xits,1,n); 
     oldm=newm;        free_vector(ptt,1,n); 
     maxmax=0.;        free_vector(pt,1,n); 
     for(j=1;j<=nlstate;j++){        return; 
       min=1.;      } 
       max=0.;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for(i=1; i<=nlstate; i++) {      for (j=1;j<=n;j++) { 
         sumnew=0;        ptt[j]=2.0*p[j]-pt[j]; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        xit[j]=p[j]-pt[j]; 
         prlim[i][j]= newm[i][j]/(1-sumnew);        pt[j]=p[j]; 
         max=FMAX(max,prlim[i][j]);      } 
         min=FMIN(min,prlim[i][j]);      fptt=(*func)(ptt); 
       }      if (fptt < fp) { 
       maxmin=max-min;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       maxmax=FMAX(maxmax,maxmin);        if (t < 0.0) { 
     }          linmin(p,xit,n,fret,func); 
     if(maxmax < ftolpl){          for (j=1;j<=n;j++) { 
       return prlim;            xi[j][ibig]=xi[j][n]; 
     }            xi[j][n]=xit[j]; 
   }          }
 }  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 /*************** transition probabilities ***************/          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++){
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )            printf(" %.12e",xit[j]);
 {            fprintf(ficlog," %.12e",xit[j]);
   double s1, s2;          }
   /*double t34;*/          printf("\n");
   int i,j,j1, nc, ii, jj;          fprintf(ficlog,"\n");
   #endif
     for(i=1; i<= nlstate; i++){        }
     for(j=1; j<i;j++){      } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    } 
         /*s2 += param[i][j][nc]*cov[nc];*/  } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /**** Prevalence limit (stable prevalence)  ****************/
       }  
       ps[i][j]=s2;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  {
     }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     for(j=i+1; j<=nlstate+ndeath;j++){       matrix by transitions matrix until convergence is reached */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    int i, ii,j,k;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    double min, max, maxmin, maxmax,sumnew=0.;
       }    double **matprod2();
       ps[i][j]=(s2);    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
     /*ps[3][2]=1;*/  
     for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=1; i<= nlstate; i++){      for (j=1;j<=nlstate+ndeath;j++){
      s1=0;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(j=1; j<i; j++)      }
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)     cov[1]=1.;
       s1+=exp(ps[i][j]);   
     ps[i][i]=1./(s1+1.);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(j=1; j<i; j++)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       ps[i][j]= exp(ps[i][j])*ps[i][i];      newm=savm;
     for(j=i+1; j<=nlstate+ndeath; j++)      /* Covariates have to be included here again */
       ps[i][j]= exp(ps[i][j])*ps[i][i];       cov[2]=agefin;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    
   } /* end i */        for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     for(jj=1; jj<= nlstate+ndeath; jj++){        }
       ps[ii][jj]=0;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       ps[ii][ii]=1;        for (k=1; k<=cptcovprod;k++)
     }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   }  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     for(jj=1; jj<= nlstate+ndeath; jj++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
      printf("%lf ",ps[ii][jj]);  
    }      savm=oldm;
     printf("\n ");      oldm=newm;
     }      maxmax=0.;
     printf("\n ");printf("%lf ",cov[2]);*/      for(j=1;j<=nlstate;j++){
 /*        min=1.;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        max=0.;
   goto end;*/        for(i=1; i<=nlstate; i++) {
     return ps;          sumnew=0;
 }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
 /**************** Product of 2 matrices ******************/          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        }
 {        maxmin=max-min;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        maxmax=FMAX(maxmax,maxmin);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      }
   /* in, b, out are matrice of pointers which should have been initialized      if(maxmax < ftolpl){
      before: only the contents of out is modified. The function returns        return prlim;
      a pointer to pointers identical to out */      }
   long i, j, k;    }
   for(i=nrl; i<= nrh; i++)  }
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /*************** transition probabilities ***************/ 
         out[i][k] +=in[i][j]*b[j][k];  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   return out;  {
 }    double s1, s2;
     /*double t34;*/
     int i,j,j1, nc, ii, jj;
 /************* Higher Matrix Product ***************/  
       for(i=1; i<= nlstate; i++){
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      for(j=1; j<i;j++){
 {        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          /*s2 += param[i][j][nc]*cov[nc];*/
      duration (i.e. until          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        }
      (typically every 2 years instead of every month which is too big).        ps[i][j]=s2;
      Model is determined by parameters x and covariates have to be        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
      included manually here.      }
       for(j=i+1; j<=nlstate+ndeath;j++){
      */        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   int i, j, d, h, k;          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   double **out, cov[NCOVMAX];        }
   double **newm;        ps[i][j]=s2;
       }
   /* Hstepm could be zero and should return the unit matrix */    }
   for (i=1;i<=nlstate+ndeath;i++)      /*ps[3][2]=1;*/
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);    for(i=1; i<= nlstate; i++){
       po[i][j][0]=(i==j ? 1.0 : 0.0);       s1=0;
     }      for(j=1; j<i; j++)
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        s1+=exp(ps[i][j]);
   for(h=1; h <=nhstepm; h++){      for(j=i+1; j<=nlstate+ndeath; j++)
     for(d=1; d <=hstepm; d++){        s1+=exp(ps[i][j]);
       newm=savm;      ps[i][i]=1./(s1+1.);
       /* Covariates have to be included here again */      for(j=1; j<i; j++)
       cov[1]=1.;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      for(j=i+1; j<=nlstate+ndeath; j++)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for (k=1; k<=cptcovage;k++)      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    } /* end i */
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
         ps[ii][jj]=0;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        ps[ii][ii]=1;
       /*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,    }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  
       oldm=newm;    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     }      for(jj=1; jj<= nlstate+ndeath; jj++){
     for(i=1; i<=nlstate+ndeath; i++)       printf("%lf ",ps[ii][jj]);
       for(j=1;j<=nlstate+ndeath;j++) {     }
         po[i][j][h]=newm[i][j];      printf("\n ");
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      }
          */      printf("\n ");printf("%lf ",cov[2]);*/
       }  /*
   } /* end h */    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   return po;    goto end;*/
 }      return ps;
   }
   
 /*************** log-likelihood *************/  /**************** Product of 2 matrices ******************/
 double func( double *x)  
 {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   int i, ii, j, k, mi, d, kk;  {
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double **out;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   double sw; /* Sum of weights */    /* in, b, out are matrice of pointers which should have been initialized 
   double lli; /* Individual log likelihood */       before: only the contents of out is modified. The function returns
   long ipmx;       a pointer to pointers identical to out */
   /*extern weight */    long i, j, k;
   /* We are differentiating ll according to initial status */    for(i=nrl; i<= nrh; i++)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      for(k=ncolol; k<=ncoloh; k++)
   /*for(i=1;i<imx;i++)        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     printf(" %d\n",s[4][i]);          out[i][k] +=in[i][j]*b[j][k];
   */  
   cov[1]=1.;    return out;
   }
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /************* Higher Matrix Product ***************/
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
       for(d=0; d<dh[mi][i]; d++){    /* Computes the transition matrix starting at age 'age' over 
         newm=savm;       'nhstepm*hstepm*stepm' months (i.e. until
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         for (kk=1; kk<=cptcovage;kk++) {       nhstepm*hstepm matrices. 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         }       (typically every 2 years instead of every month which is too big 
               for the memory).
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       Model is determined by parameters x and covariates have to be 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       included manually here. 
         savm=oldm;  
         oldm=newm;       */
          
            int i, j, d, h, k;
       } /* end mult */    double **out, cov[NCOVMAX];
          double **newm;
       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]]);*/    /* Hstepm could be zero and should return the unit matrix */
       ipmx +=1;    for (i=1;i<=nlstate+ndeath;i++)
       sw += weight[i];      for (j=1;j<=nlstate+ndeath;j++){
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        oldm[i][j]=(i==j ? 1.0 : 0.0);
     } /* end of wave */        po[i][j][0]=(i==j ? 1.0 : 0.0);
   } /* end of individual */      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    for(h=1; h <=nhstepm; h++){
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      for(d=1; d <=hstepm; d++){
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        newm=savm;
   return -l;        /* Covariates have to be included here again */
 }        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 /*********** Maximum Likelihood Estimation ***************/        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        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, iter;  
   double **xi,*delti;  
   double fret;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   xi=matrix(1,npar,1,npar);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   for (i=1;i<=npar;i++)        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));
       xi[i][j]=(i==j ? 1.0 : 0.0);        savm=oldm;
   printf("Powell\n");        oldm=newm;
   powell(p,xi,npar,ftol,&iter,&fret,func);      }
       for(i=1; i<=nlstate+ndeath; i++)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        for(j=1;j<=nlstate+ndeath;j++) {
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));          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]);
 }           */
         }
 /**** Computes Hessian and covariance matrix ***/    } /* end h */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    return po;
 {  }
   double  **a,**y,*x,pd;  
   double **hess;  
   int i, j,jk;  /*************** log-likelihood *************/
   int *indx;  double func( double *x)
   {
   double hessii(double p[], double delta, int theta, double delti[]);    int i, ii, j, k, mi, d, kk;
   double hessij(double p[], double delti[], int i, int j);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double **out;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
   hess=matrix(1,npar,1,npar);    int s1, s2;
     double bbh;
   printf("\nCalculation of the hessian matrix. Wait...\n");    long ipmx;
   for (i=1;i<=npar;i++){    /*extern weight */
     printf("%d",i);fflush(stdout);    /* We are differentiating ll according to initial status */
     hess[i][i]=hessii(p,ftolhess,i,delti);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*printf(" %f ",p[i]);*/    /*for(i=1;i<imx;i++) 
     /*printf(" %lf ",hess[i][i]);*/      printf(" %d\n",s[4][i]);
   }    */
      cov[1]=1.;
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {    for(k=1; k<=nlstate; k++) ll[k]=0.;
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);    if(mle==1){
         hess[i][j]=hessij(p,delti,i,j);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         hess[j][i]=hess[i][j];            for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         /*printf(" %lf ",hess[i][j]);*/        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   a=matrix(1,npar,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   y=matrix(1,npar,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
   x=vector(1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   indx=ivector(1,npar);            }
   for (i=1;i<=npar;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   ludcmp(a,npar,indx,&pd);            savm=oldm;
             oldm=newm;
   for (j=1;j<=npar;j++) {          } /* end mult */
     for (i=1;i<=npar;i++) x[i]=0;        
     x[j]=1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     lubksb(a,npar,indx,x);          /* But now since version 0.9 we anticipate for bias and large stepm.
     for (i=1;i<=npar;i++){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       matcov[i][j]=x[i];           * (in months) between two waves is not a multiple of stepm, we rounded to 
     }           * the nearest (and in case of equal distance, to the lowest) interval but now
   }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   printf("\n#Hessian matrix#\n");           * probability in order to take into account the bias as a fraction of the way
   for (i=1;i<=npar;i++) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     for (j=1;j<=npar;j++) {           * -stepm/2 to stepm/2 .
       printf("%.3e ",hess[i][j]);           * For stepm=1 the results are the same as for previous versions of Imach.
     }           * For stepm > 1 the results are less biased than in previous versions. 
     printf("\n");           */
   }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   /* Recompute Inverse */          bbh=(double)bh[mi][i]/(double)stepm; 
   for (i=1;i<=npar;i++)          /* bias is positive if real duration
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];           * is higher than the multiple of stepm and negative otherwise.
   ludcmp(a,npar,indx,&pd);           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   /*  printf("\n#Hessian matrix recomputed#\n");          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 */
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for (j=1;j<=npar;j++) {          /*if(lli ==000.0)*/
     for (i=1;i<=npar;i++) x[i]=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); */
     x[j]=1;          ipmx +=1;
     lubksb(a,npar,indx,x);          sw += weight[i];
     for (i=1;i<=npar;i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       y[i][j]=x[i];        } /* end of wave */
       printf("%.3e ",y[i][j]);      } /* end of individual */
     }    }  else if(mle==2){
     printf("\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   free_matrix(a,1,npar,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   free_matrix(y,1,npar,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(x,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_ivector(indx,1,npar);            }
   free_matrix(hess,1,npar,1,npar);          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /*************** hessian matrix ****************/            }
 double hessii( double x[], double delta, int theta, double delti[])            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i;            savm=oldm;
   int l=1, lmax=20;            oldm=newm;
   double k1,k2;          } /* end mult */
   double p2[NPARMAX+1];        
   double res;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          /* But now since version 0.9 we anticipate for bias and large stepm.
   double fx;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   int k=0,kmax=10;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double l1;           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
   fx=func(x);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   for (i=1;i<=npar;i++) p2[i]=x[i];           * probability in order to take into account the bias as a fraction of the way
   for(l=0 ; l <=lmax; l++){           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     l1=pow(10,l);           * -stepm/2 to stepm/2 .
     delts=delt;           * For stepm=1 the results are the same as for previous versions of Imach.
     for(k=1 ; k <kmax; k=k+1){           * For stepm > 1 the results are less biased than in previous versions. 
       delt = delta*(l1*k);           */
       p2[theta]=x[theta] +delt;          s1=s[mw[mi][i]][i];
       k1=func(p2)-fx;          s2=s[mw[mi+1][i]][i];
       p2[theta]=x[theta]-delt;          bbh=(double)bh[mi][i]/(double)stepm; 
       k2=func(p2)-fx;          /* bias is positive if real duration
       /*res= (k1-2.0*fx+k2)/delt/delt; */           * is higher than the multiple of stepm and negative otherwise.
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */           */
                lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 #ifdef DEBUG          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       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);          /*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 */
 #endif          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /*if(lli ==000.0)*/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /*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); */
         k=kmax;          ipmx +=1;
       }          sw += weight[i];
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         k=kmax; l=lmax*10.;        } /* end of wave */
       }      } /* end of individual */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    }  else if(mle==3){  /* exponential inter-extrapolation */
         delts=delt;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   delti[theta]=delts;            for (j=1;j<=nlstate+ndeath;j++){
   return res;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<dh[mi][i]; d++){
 double hessij( double x[], double delti[], int thetai,int thetaj)            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i;            for (kk=1; kk<=cptcovage;kk++) {
   int l=1, l1, lmax=20;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double k1,k2,k3,k4,res,fx;            }
   double p2[NPARMAX+1];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   fx=func(x);            oldm=newm;
   for (k=1; k<=2; k++) {          } /* end mult */
     for (i=1;i<=npar;i++) p2[i]=x[i];        
     p2[thetai]=x[thetai]+delti[thetai]/k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /* But now since version 0.9 we anticipate for bias and large stepm.
     k1=func(p2)-fx;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             * (in months) between two waves is not a multiple of stepm, we rounded to 
     p2[thetai]=x[thetai]+delti[thetai]/k;           * the nearest (and in case of equal distance, to the lowest) interval but now
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     k2=func(p2)-fx;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
             * probability in order to take into account the bias as a fraction of the way
     p2[thetai]=x[thetai]-delti[thetai]/k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * -stepm/2 to stepm/2 .
     k3=func(p2)-fx;           * For stepm=1 the results are the same as for previous versions of Imach.
             * For stepm > 1 the results are less biased than in previous versions. 
     p2[thetai]=x[thetai]-delti[thetai]/k;           */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          s1=s[mw[mi][i]][i];
     k4=func(p2)-fx;          s2=s[mw[mi+1][i]][i];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          bbh=(double)bh[mi][i]/(double)stepm; 
 #ifdef DEBUG          /* bias is positive if real duration
     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);           * is higher than the multiple of stepm and negative otherwise.
 #endif           */
   }          /* 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 */
   return res;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
 }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
 /************** Inverse of matrix **************/          /*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); */
 void ludcmp(double **a, int n, int *indx, double *d)          ipmx +=1;
 {          sw += weight[i];
   int i,imax,j,k;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double big,dum,sum,temp;        } /* end of wave */
   double *vv;      } /* end of individual */
      }else{  /* ml=4 no inter-extrapolation */
   vv=vector(1,n);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   *d=1.0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (i=1;i<=n;i++) {        for(mi=1; mi<= wav[i]-1; mi++){
     big=0.0;          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=n;j++)            for (j=1;j<=nlstate+ndeath;j++){
       if ((temp=fabs(a[i][j])) > big) big=temp;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     vv[i]=1.0/big;            }
   }          for(d=0; d<dh[mi][i]; d++){
   for (j=1;j<=n;j++) {            newm=savm;
     for (i=1;i<j;i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       sum=a[i][j];            for (kk=1; kk<=cptcovage;kk++) {
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       a[i][j]=sum;            }
     }          
     big=0.0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=j;i<=n;i++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       sum=a[i][j];            savm=oldm;
       for (k=1;k<j;k++)            oldm=newm;
         sum -= a[i][k]*a[k][j];          } /* end mult */
       a[i][j]=sum;        
       if ( (dum=vv[i]*fabs(sum)) >= big) {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         big=dum;          ipmx +=1;
         imax=i;          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     if (j != imax) {      } /* end of individual */
       for (k=1;k<=n;k++) {    } /* End of if */
         dum=a[imax][k];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         a[imax][k]=a[j][k];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         a[j][k]=dum;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       }    return -l;
       *d = -(*d);  }
       vv[imax]=vv[j];  
     }  
     indx[j]=imax;  /*********** Maximum Likelihood Estimation ***************/
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       dum=1.0/(a[j][j]);  {
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    int i,j, iter;
     }    double **xi,*delti;
   }    double fret;
   free_vector(vv,1,n);  /* Doesn't work */    xi=matrix(1,npar,1,npar);
 ;    for (i=1;i<=npar;i++)
 }      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
 void lubksb(double **a, int n, int *indx, double b[])    printf("Powell\n");  fprintf(ficlog,"Powell\n");
 {    powell(p,xi,npar,ftol,&iter,&fret,func);
   int i,ii=0,ip,j;  
   double sum;     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
      fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   for (i=1;i<=n;i++) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     ip=indx[i];  
     sum=b[ip];  }
     b[ip]=b[i];  
     if (ii)  /**** Computes Hessian and covariance matrix ***/
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     else if (sum) ii=i;  {
     b[i]=sum;    double  **a,**y,*x,pd;
   }    double **hess;
   for (i=n;i>=1;i--) {    int i, j,jk;
     sum=b[i];    int *indx;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];    double hessii(double p[], double delta, int theta, double delti[]);
   }    double hessij(double p[], double delti[], int i, int j);
 }    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)    hess=matrix(1,npar,1,npar);
 {  /* Some frequencies */  
      printf("\nCalculation of the hessian matrix. Wait...\n");
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   double ***freq; /* Frequencies */    for (i=1;i<=npar;i++){
   double *pp;      printf("%d",i);fflush(stdout);
   double pos, k2, dateintsum=0,k2cpt=0;      fprintf(ficlog,"%d",i);fflush(ficlog);
   FILE *ficresp;      hess[i][i]=hessii(p,ftolhess,i,delti);
   char fileresp[FILENAMELENGTH];      /*printf(" %f ",p[i]);*/
       /*printf(" %lf ",hess[i][i]);*/
   pp=vector(1,nlstate);    }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    
   strcpy(fileresp,"p");    for (i=1;i<=npar;i++) {
   strcat(fileresp,fileres);      for (j=1;j<=npar;j++)  {
   if((ficresp=fopen(fileresp,"w"))==NULL) {        if (j>i) { 
     printf("Problem with prevalence resultfile: %s\n", fileresp);          printf(".%d%d",i,j);fflush(stdout);
     exit(0);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   }          hess[i][j]=hessij(p,delti,i,j);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          hess[j][i]=hess[i][j];    
   j1=0;          /*printf(" %lf ",hess[i][j]);*/
         }
   j=cptcoveff;      }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    }
     printf("\n");
   for(k1=1; k1<=j;k1++){    fprintf(ficlog,"\n");
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
          scanf("%d", i);*/    
         for (i=-1; i<=nlstate+ndeath; i++)      a=matrix(1,npar,1,npar);
          for (jk=-1; jk<=nlstate+ndeath; jk++)      y=matrix(1,npar,1,npar);
            for(m=agemin; m <= agemax+3; m++)    x=vector(1,npar);
              freq[i][jk][m]=0;    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
         dateintsum=0;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         k2cpt=0;    ludcmp(a,npar,indx,&pd);
        for (i=1; i<=imx; i++) {  
          bool=1;    for (j=1;j<=npar;j++) {
          if  (cptcovn>0) {      for (i=1;i<=npar;i++) x[i]=0;
            for (z1=1; z1<=cptcoveff; z1++)      x[j]=1;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      lubksb(a,npar,indx,x);
                bool=0;      for (i=1;i<=npar;i++){ 
          }        matcov[i][j]=x[i];
          if (bool==1) {      }
            for(m=firstpass; m<=lastpass; m++){    }
              k2=anint[m][i]+(mint[m][i]/12.);  
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    printf("\n#Hessian matrix#\n");
                if(agev[m][i]==0) agev[m][i]=agemax+1;    fprintf(ficlog,"\n#Hessian matrix#\n");
                if(agev[m][i]==1) agev[m][i]=agemax+2;    for (i=1;i<=npar;i++) { 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      for (j=1;j<=npar;j++) { 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        printf("%.3e ",hess[i][j]);
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        fprintf(ficlog,"%.3e ",hess[i][j]);
                  dateintsum=dateintsum+k2;      }
                  k2cpt++;      printf("\n");
                }      fprintf(ficlog,"\n");
     }
              }  
            }    /* Recompute Inverse */
          }    for (i=1;i<=npar;i++)
        }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         if  (cptcovn>0) {    ludcmp(a,npar,indx,&pd);
          fprintf(ficresp, "\n#********** Variable ");  
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /*  printf("\n#Hessian matrix recomputed#\n");
        fprintf(ficresp, "**********\n#");  
         }    for (j=1;j<=npar;j++) {
        for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++) x[i]=0;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      x[j]=1;
        fprintf(ficresp, "\n");      lubksb(a,npar,indx,x);
              for (i=1;i<=npar;i++){ 
   for(i=(int)agemin; i <= (int)agemax+3; i++){        y[i][j]=x[i];
     if(i==(int)agemax+3)        printf("%.3e ",y[i][j]);
       printf("Total");        fprintf(ficlog,"%.3e ",y[i][j]);
     else      }
       printf("Age %d", i);      printf("\n");
     for(jk=1; jk <=nlstate ; jk++){      fprintf(ficlog,"\n");
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    }
         pp[jk] += freq[jk][m][i];    */
     }  
     for(jk=1; jk <=nlstate ; jk++){    free_matrix(a,1,npar,1,npar);
       for(m=-1, pos=0; m <=0 ; m++)    free_matrix(y,1,npar,1,npar);
         pos += freq[jk][m][i];    free_vector(x,1,npar);
       if(pp[jk]>=1.e-10)    free_ivector(indx,1,npar);
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    free_matrix(hess,1,npar,1,npar);
       else  
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
     }  }
   
      for(jk=1; jk <=nlstate ; jk++){  /*************** hessian matrix ****************/
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  double hessii( double x[], double delta, int theta, double delti[])
         pp[jk] += freq[jk][m][i];  {
      }    int i;
     int l=1, lmax=20;
     for(jk=1,pos=0; jk <=nlstate ; jk++)    double k1,k2;
       pos += pp[jk];    double p2[NPARMAX+1];
     for(jk=1; jk <=nlstate ; jk++){    double res;
       if(pos>=1.e-5)    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    double fx;
       else    int k=0,kmax=10;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    double l1;
       if( i <= (int) agemax){  
         if(pos>=1.e-5){    fx=func(x);
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    for (i=1;i<=npar;i++) p2[i]=x[i];
           probs[i][jk][j1]= pp[jk]/pos;    for(l=0 ; l <=lmax; l++){
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      l1=pow(10,l);
         }      delts=delt;
       else      for(k=1 ; k <kmax; k=k+1){
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        delt = delta*(l1*k);
       }        p2[theta]=x[theta] +delt;
     }        k1=func(p2)-fx;
     for(jk=-1; jk <=nlstate+ndeath; jk++)        p2[theta]=x[theta]-delt;
       for(m=-1; m <=nlstate+ndeath; m++)        k2=func(p2)-fx;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     if(i <= (int) agemax)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       fprintf(ficresp,"\n");        
     printf("\n");  #ifdef DEBUG
     }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
  }  #endif
   dateintmean=dateintsum/k2cpt;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
          if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   fclose(ficresp);          k=kmax;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        }
   free_vector(pp,1,nlstate);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
   /* End of Freq */        }
 }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
 /************ Prevalence ********************/        }
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      }
 {  /* Some frequencies */    }
      delti[theta]=delts;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    return res; 
   double ***freq; /* Frequencies */    
   double *pp;  }
   double pos, k2;  
   double hessij( double x[], double delti[], int thetai,int thetaj)
   pp=vector(1,nlstate);  {
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i;
      int l=1, l1, lmax=20;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double k1,k2,k3,k4,res,fx;
   j1=0;    double p2[NPARMAX+1];
      int k;
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    fx=func(x);
      for (k=1; k<=2; k++) {
  for(k1=1; k1<=j;k1++){      for (i=1;i<=npar;i++) p2[i]=x[i];
     for(i1=1; i1<=ncodemax[k1];i1++){      p2[thetai]=x[thetai]+delti[thetai]/k;
       j1++;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k1=func(p2)-fx;
       for (i=-1; i<=nlstate+ndeath; i++)      
         for (jk=-1; jk<=nlstate+ndeath; jk++)        p2[thetai]=x[thetai]+delti[thetai]/k;
           for(m=agemin; m <= agemax+3; m++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             freq[i][jk][m]=0;      k2=func(p2)-fx;
          
       for (i=1; i<=imx; i++) {      p2[thetai]=x[thetai]-delti[thetai]/k;
         bool=1;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         if  (cptcovn>0) {      k3=func(p2)-fx;
           for (z1=1; z1<=cptcoveff; z1++)    
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      p2[thetai]=x[thetai]-delti[thetai]/k;
               bool=0;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         }      k4=func(p2)-fx;
         if (bool==1) {      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           for(m=firstpass; m<=lastpass; m++){  #ifdef DEBUG
             k2=anint[m][i]+(mint[m][i]/12.);      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);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
               if(agev[m][i]==0) agev[m][i]=agemax+1;  #endif
               if(agev[m][i]==1) agev[m][i]=agemax+2;    }
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    return res;
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];    }
             }  
           }  /************** Inverse of matrix **************/
         }  void ludcmp(double **a, int n, int *indx, double *d) 
       }  { 
          int i,imax,j,k; 
         for(i=(int)agemin; i <= (int)agemax+3; i++){    double big,dum,sum,temp; 
           for(jk=1; jk <=nlstate ; jk++){    double *vv; 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)   
               pp[jk] += freq[jk][m][i];    vv=vector(1,n); 
           }    *d=1.0; 
           for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=n;i++) { 
             for(m=-1, pos=0; m <=0 ; m++)      big=0.0; 
             pos += freq[jk][m][i];      for (j=1;j<=n;j++) 
         }        if ((temp=fabs(a[i][j])) > big) big=temp; 
              if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
          for(jk=1; jk <=nlstate ; jk++){      vv[i]=1.0/big; 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    } 
              pp[jk] += freq[jk][m][i];    for (j=1;j<=n;j++) { 
          }      for (i=1;i<j;i++) { 
                  sum=a[i][j]; 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
          for(jk=1; jk <=nlstate ; jk++){                } 
            if( i <= (int) agemax){      big=0.0; 
              if(pos>=1.e-5){      for (i=j;i<=n;i++) { 
                probs[i][jk][j1]= pp[jk]/pos;        sum=a[i][j]; 
              }        for (k=1;k<j;k++) 
            }          sum -= a[i][k]*a[k][j]; 
          }        a[i][j]=sum; 
                  if ( (dum=vv[i]*fabs(sum)) >= big) { 
         }          big=dum; 
     }          imax=i; 
   }        } 
        } 
        if (j != imax) { 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for (k=1;k<=n;k++) { 
   free_vector(pp,1,nlstate);          dum=a[imax][k]; 
            a[imax][k]=a[j][k]; 
 }  /* End of Freq */          a[j][k]=dum; 
         } 
 /************* Waves Concatenation ***************/        *d = -(*d); 
         vv[imax]=vv[j]; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      } 
 {      indx[j]=imax; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      if (a[j][j] == 0.0) a[j][j]=TINY; 
      Death is a valid wave (if date is known).      if (j != n) { 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        dum=1.0/(a[j][j]); 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
      and mw[mi+1][i]. dh depends on stepm.      } 
      */    } 
     free_vector(vv,1,n);  /* Doesn't work */
   int i, mi, m;  ;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  } 
      double sum=0., jmean=0.;*/  
   void lubksb(double **a, int n, int *indx, double b[]) 
   int j, k=0,jk, ju, jl;  { 
   double sum=0.;    int i,ii=0,ip,j; 
   jmin=1e+5;    double sum; 
   jmax=-1;   
   jmean=0.;    for (i=1;i<=n;i++) { 
   for(i=1; i<=imx; i++){      ip=indx[i]; 
     mi=0;      sum=b[ip]; 
     m=firstpass;      b[ip]=b[i]; 
     while(s[m][i] <= nlstate){      if (ii) 
       if(s[m][i]>=1)        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         mw[++mi][i]=m;      else if (sum) ii=i; 
       if(m >=lastpass)      b[i]=sum; 
         break;    } 
       else    for (i=n;i>=1;i--) { 
         m++;      sum=b[i]; 
     }/* end while */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     if (s[m][i] > nlstate){      b[i]=sum/a[i][i]; 
       mi++;     /* Death is another wave */    } 
       /* if(mi==0)  never been interviewed correctly before death */  } 
          /* Only death is a correct wave */  
       mw[mi][i]=m;  /************ Frequencies ********************/
     }  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
   {  /* Some frequencies */
     wav[i]=mi;    
     if(mi==0)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    int first;
   }    double ***freq; /* Frequencies */
     double *pp;
   for(i=1; i<=imx; i++){    double pos, k2, dateintsum=0,k2cpt=0;
     for(mi=1; mi<wav[i];mi++){    FILE *ficresp;
       if (stepm <=0)    char fileresp[FILENAMELENGTH];
         dh[mi][i]=1;    
       else{    pp=vector(1,nlstate);
         if (s[mw[mi+1][i]][i] > nlstate) {    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
           if (agedc[i] < 2*AGESUP) {    strcpy(fileresp,"p");
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    strcat(fileresp,fileres);
           if(j==0) j=1;  /* Survives at least one month after exam */    if((ficresp=fopen(fileresp,"w"))==NULL) {
           k=k+1;      printf("Problem with prevalence resultfile: %s\n", fileresp);
           if (j >= jmax) jmax=j;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           if (j <= jmin) jmin=j;      exit(0);
           sum=sum+j;    }
           /* if (j<10) printf("j=%d num=%d ",j,i); */    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
           }    j1=0;
         }    
         else{    j=cptcoveff;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           k=k+1;  
           if (j >= jmax) jmax=j;    first=1;
           else if (j <= jmin)jmin=j;  
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    for(k1=1; k1<=j;k1++){
           sum=sum+j;      for(i1=1; i1<=ncodemax[k1];i1++){
         }        j1++;
         jk= j/stepm;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         jl= j -jk*stepm;          scanf("%d", i);*/
         ju= j -(jk+1)*stepm;        for (i=-1; i<=nlstate+ndeath; i++)  
         if(jl <= -ju)          for (jk=-1; jk<=nlstate+ndeath; jk++)  
           dh[mi][i]=jk;            for(m=agemin; m <= agemax+3; m++)
         else              freq[i][jk][m]=0;
           dh[mi][i]=jk+1;        
         if(dh[mi][i]==0)        dateintsum=0;
           dh[mi][i]=1; /* At least one step */        k2cpt=0;
       }        for (i=1; i<=imx; i++) {
     }          bool=1;
   }          if  (cptcovn>0) {
   jmean=sum/k;            for (z1=1; z1<=cptcoveff; z1++) 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
  }                bool=0;
 /*********** Tricode ****************************/          }
 void tricode(int *Tvar, int **nbcode, int imx)          if (bool==1){
 {            for(m=firstpass; m<=lastpass; m++){
   int Ndum[20],ij=1, k, j, i;              k2=anint[m][i]+(mint[m][i]/12.);
   int cptcode=0;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
   cptcoveff=0;                if(agev[m][i]==0) agev[m][i]=agemax+1;
                  if(agev[m][i]==1) agev[m][i]=agemax+2;
   for (k=0; k<19; k++) Ndum[k]=0;                if (m<lastpass) {
   for (k=1; k<=7; k++) ncodemax[k]=0;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {                }
     for (i=1; i<=imx; i++) {                
       ij=(int)(covar[Tvar[j]][i]);                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
       Ndum[ij]++;                  dateintsum=dateintsum+k2;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/                  k2cpt++;
       if (ij > cptcode) cptcode=ij;                }
     }              }
             }
     for (i=0; i<=cptcode; i++) {          }
       if(Ndum[i]!=0) ncodemax[j]++;        }
     }         
     ij=1;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
         if  (cptcovn>0) {
     for (i=1; i<=ncodemax[j]; i++) {          fprintf(ficresp, "\n#********** Variable "); 
       for (k=0; k<=19; k++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         if (Ndum[k] != 0) {          fprintf(ficresp, "**********\n#");
           nbcode[Tvar[j]][ij]=k;        }
           ij++;        for(i=1; i<=nlstate;i++) 
         }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         if (ij > ncodemax[j]) break;        fprintf(ficresp, "\n");
       }          
     }        for(i=(int)agemin; i <= (int)agemax+3; i++){
   }            if(i==(int)agemax+3){
             fprintf(ficlog,"Total");
  for (k=0; k<19; k++) Ndum[k]=0;          }else{
             if(first==1){
  for (i=1; i<=ncovmodel-2; i++) {              first=0;
       ij=Tvar[i];              printf("See log file for details...\n");
       Ndum[ij]++;            }
     }            fprintf(ficlog,"Age %d", i);
           }
  ij=1;          for(jk=1; jk <=nlstate ; jk++){
  for (i=1; i<=10; i++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
    if((Ndum[i]!=0) && (i<=ncov)){              pp[jk] += freq[jk][m][i]; 
      Tvaraff[ij]=i;          }
      ij++;          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){
     cptcoveff=ij-1;              if(first==1){
 }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
 /*********** Health Expectancies ****************/              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)              if(first==1)
 {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   /* Health expectancies */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int i, j, nhstepm, hstepm, h;            }
   double age, agelim,hf;          }
   double ***p3mat;  
            for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficreseij,"# Health expectancies\n");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   fprintf(ficreseij,"# Age");              pp[jk] += freq[jk][m][i];
   for(i=1; i<=nlstate;i++)          }
     for(j=1; j<=nlstate;j++)  
       fprintf(ficreseij," %1d-%1d",i,j);          for(jk=1,pos=0; jk <=nlstate ; jk++)
   fprintf(ficreseij,"\n");            pos += pp[jk];
           for(jk=1; jk <=nlstate ; jk++){
   hstepm=1*YEARM; /*  Every j years of age (in month) */            if(pos>=1.e-5){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   agelim=AGESUP;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }else{
     /* nhstepm age range expressed in number of stepm */              if(first==1)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     /* Typically if 20 years = 20*12/6=40 stepm */              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     if (stepm >= YEARM) hstepm=1;            }
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            if( i <= (int) agemax){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if(pos>=1.e-5){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                probs[i][jk][j1]= pp[jk]/pos;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
               else
     for(i=1; i<=nlstate;i++)                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
       for(j=1; j<=nlstate;j++)            }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          }
           eij[i][j][(int)age] +=p3mat[i][j][h];          
         }          for(jk=-1; jk <=nlstate+ndeath; jk++)
                for(m=-1; m <=nlstate+ndeath; m++)
     hf=1;              if(freq[jk][m][i] !=0 ) {
     if (stepm >= YEARM) hf=stepm/YEARM;              if(first==1)
     fprintf(ficreseij,"%.0f",age );                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(i=1; i<=nlstate;i++)                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       for(j=1; j<=nlstate;j++){              }
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          if(i <= (int) agemax)
       }            fprintf(ficresp,"\n");
     fprintf(ficreseij,"\n");          if(first==1)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            printf("Others in log...\n");
   }          fprintf(ficlog,"\n");
 }        }
       }
 /************ Variance ******************/    }
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    dateintmean=dateintsum/k2cpt; 
 {   
   /* Variance of health expectancies */    fclose(ficresp);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   double **newm;    free_vector(pp,1,nlstate);
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm, h;    /* End of Freq */
   int k, cptcode;  }
   double *xp;  
   double **gp, **gm;  /************ Prevalence ********************/
   double ***gradg, ***trgradg;  void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
   double ***p3mat;  {  /* Some frequencies */
   double age,agelim;   
   int theta;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
    fprintf(ficresvij,"# Covariances of life expectancies\n");    double *pp;
   fprintf(ficresvij,"# Age");    double pos, k2;
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)    pp=vector(1,nlstate);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    
   fprintf(ficresvij,"\n");    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
     j1=0;
   xp=vector(1,npar);    
   dnewm=matrix(1,nlstate,1,npar);    j=cptcoveff;
   doldm=matrix(1,nlstate,1,nlstate);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
   hstepm=1*YEARM; /* Every year of age */    for(k1=1; k1<=j;k1++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for(i1=1; i1<=ncodemax[k1];i1++){
   agelim = AGESUP;        j1++;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for (i=-1; i<=nlstate+ndeath; i++)  
     if (stepm >= YEARM) hstepm=1;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for(m=agemin; m <= agemax+3; m++)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              freq[i][jk][m]=0;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);       
     gp=matrix(0,nhstepm,1,nlstate);        for (i=1; i<=imx; i++) {
     gm=matrix(0,nhstepm,1,nlstate);          bool=1;
           if  (cptcovn>0) {
     for(theta=1; theta <=npar; theta++){            for (z1=1; z1<=cptcoveff; z1++) 
       for(i=1; i<=npar; i++){ /* Computes gradient */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                bool=0;
       }          } 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            if (bool==1) { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
       if (popbased==1) {              if ((k2>=dateprev1) && (k2<=dateprev2)) {
         for(i=1; i<=nlstate;i++)                if(agev[m][i]==0) agev[m][i]=agemax+1;
           prlim[i][i]=probs[(int)age][i][ij];                if(agev[m][i]==1) agev[m][i]=agemax+2;
       }                if (m<lastpass) {
                        if (calagedate>0) 
       for(j=1; j<= nlstate; j++){                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
         for(h=0; h<=nhstepm; h++){                  else
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
         }                }
       }              }
                }
       for(i=1; i<=npar; i++) /* Computes gradient */          }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          for(i=(int)agemin; i <= (int)agemax+3; i++){ 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       if (popbased==1) {              pp[jk] += freq[jk][m][i]; 
         for(i=1; i<=nlstate;i++)          }
           prlim[i][i]=probs[(int)age][i][ij];          for(jk=1; jk <=nlstate ; jk++){
       }            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
       for(j=1; j<= nlstate; j++){          }
         for(h=0; h<=nhstepm; h++){          
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         }              pp[jk] += freq[jk][m][i];
       }          }
           
       for(j=1; j<= nlstate; j++)          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
         for(h=0; h<=nhstepm; h++){          
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          for(jk=1; jk <=nlstate ; jk++){    
         }            if( i <= (int) agemax){
     } /* End theta */              if(pos>=1.e-5){
                 probs[i][jk][j1]= pp[jk]/pos;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);              }
             }
     for(h=0; h<=nhstepm; h++)          }/* end jk */
       for(j=1; j<=nlstate;j++)        }/* end i */
         for(theta=1; theta <=npar; theta++)      } /* end i1 */
           trgradg[h][j][theta]=gradg[h][theta][j];    } /* end k1 */
   
     for(i=1;i<=nlstate;i++)    
       for(j=1;j<=nlstate;j++)    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
         vareij[i][j][(int)age] =0.;    free_vector(pp,1,nlstate);
     for(h=0;h<=nhstepm;h++){    
       for(k=0;k<=nhstepm;k++){  }  /* End of Freq */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  /************* Waves Concatenation ***************/
         for(i=1;i<=nlstate;i++)  
           for(j=1;j<=nlstate;j++)  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
             vareij[i][j][(int)age] += doldm[i][j];  {
       }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     }       Death is a valid wave (if date is known).
     h=1;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     if (stepm >= YEARM) h=stepm/YEARM;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     fprintf(ficresvij,"%.0f ",age );       and mw[mi+1][i]. dh depends on stepm.
     for(i=1; i<=nlstate;i++)       */
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    int i, mi, m;
       }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     fprintf(ficresvij,"\n");       double sum=0., jmean=0.;*/
     free_matrix(gp,0,nhstepm,1,nlstate);    int first;
     free_matrix(gm,0,nhstepm,1,nlstate);    int j, k=0,jk, ju, jl;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    double sum=0.;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    first=0;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    jmin=1e+5;
   } /* End age */    jmax=-1;
      jmean=0.;
   free_vector(xp,1,npar);    for(i=1; i<=imx; i++){
   free_matrix(doldm,1,nlstate,1,npar);      mi=0;
   free_matrix(dnewm,1,nlstate,1,nlstate);      m=firstpass;
       while(s[m][i] <= nlstate){
 }        if(s[m][i]>=1)
           mw[++mi][i]=m;
 /************ Variance of prevlim ******************/        if(m >=lastpass)
 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)          break;
 {        else
   /* Variance of prevalence limit */          m++;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      }/* end while */
   double **newm;      if (s[m][i] > nlstate){
   double **dnewm,**doldm;        mi++;     /* Death is another wave */
   int i, j, nhstepm, hstepm;        /* if(mi==0)  never been interviewed correctly before death */
   int k, cptcode;           /* Only death is a correct wave */
   double *xp;        mw[mi][i]=m;
   double *gp, *gm;      }
   double **gradg, **trgradg;  
   double age,agelim;      wav[i]=mi;
   int theta;      if(mi==0){
            if(first==0){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
   fprintf(ficresvpl,"# Age");          first=1;
   for(i=1; i<=nlstate;i++)        }
       fprintf(ficresvpl," %1d-%1d",i,i);        if(first==1){
   fprintf(ficresvpl,"\n");          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
         }
   xp=vector(1,npar);      } /* end mi==0 */
   dnewm=matrix(1,nlstate,1,npar);    }
   doldm=matrix(1,nlstate,1,nlstate);  
      for(i=1; i<=imx; i++){
   hstepm=1*YEARM; /* Every year of age */      for(mi=1; mi<wav[i];mi++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        if (stepm <=0)
   agelim = AGESUP;          dh[mi][i]=1;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        else{
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          if (s[mw[mi+1][i]][i] > nlstate) {
     if (stepm >= YEARM) hstepm=1;            if (agedc[i] < 2*AGESUP) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     gradg=matrix(1,npar,1,nlstate);            if(j==0) j=1;  /* Survives at least one month after exam */
     gp=vector(1,nlstate);            k=k+1;
     gm=vector(1,nlstate);            if (j >= jmax) jmax=j;
             if (j <= jmin) jmin=j;
     for(theta=1; theta <=npar; theta++){            sum=sum+j;
       for(i=1; i<=npar; i++){ /* Computes gradient */            /*if (j<0) printf("j=%d num=%d \n",j,i); */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            }
       }          }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          else{
       for(i=1;i<=nlstate;i++)            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         gp[i] = prlim[i][i];            k=k+1;
                if (j >= jmax) jmax=j;
       for(i=1; i<=npar; i++) /* Computes gradient */            else if (j <= jmin)jmin=j;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            sum=sum+j;
       for(i=1;i<=nlstate;i++)          }
         gm[i] = prlim[i][i];          jk= j/stepm;
           jl= j -jk*stepm;
       for(i=1;i<=nlstate;i++)          ju= j -(jk+1)*stepm;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          if(mle <=1){ 
     } /* End theta */            if(jl==0){
               dh[mi][i]=jk;
     trgradg =matrix(1,nlstate,1,npar);              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
     for(j=1; j<=nlstate;j++)                    * at the price of an extra matrix product in likelihood */
       for(theta=1; theta <=npar; theta++)              dh[mi][i]=jk+1;
         trgradg[j][theta]=gradg[theta][j];              bh[mi][i]=ju;
             }
     for(i=1;i<=nlstate;i++)          }else{
       varpl[i][(int)age] =0.;            if(jl <= -ju){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);              dh[mi][i]=jk;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);              bh[mi][i]=jl;       /* bias is positive if real duration
     for(i=1;i<=nlstate;i++)                                   * is higher than the multiple of stepm and negative otherwise.
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */                                   */
             }
     fprintf(ficresvpl,"%.0f ",age );            else{
     for(i=1; i<=nlstate;i++)              dh[mi][i]=jk+1;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));              bh[mi][i]=ju;
     fprintf(ficresvpl,"\n");            }
     free_vector(gp,1,nlstate);            if(dh[mi][i]==0){
     free_vector(gm,1,nlstate);              dh[mi][i]=1; /* At least one step */
     free_matrix(gradg,1,npar,1,nlstate);              bh[mi][i]=ju; /* At least one step */
     free_matrix(trgradg,1,nlstate,1,npar);              printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
   } /* End age */            }
             if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);
   free_vector(xp,1,npar);          }
   free_matrix(doldm,1,nlstate,1,npar);        } /* end if mle */
   free_matrix(dnewm,1,nlstate,1,nlstate);      } /* end wave */
     }
 }    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 /************ Variance of one-step probabilities  ******************/    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)   }
 {  
   int i, j;  /*********** Tricode ****************************/
   int k=0, cptcode;  void tricode(int *Tvar, int **nbcode, int imx)
   double **dnewm,**doldm;  {
   double *xp;    
   double *gp, *gm;    int Ndum[20],ij=1, k, j, i, maxncov=19;
   double **gradg, **trgradg;    int cptcode=0;
   double age,agelim, cov[NCOVMAX];    cptcoveff=0; 
   int theta;   
   char fileresprob[FILENAMELENGTH];    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     printf("Problem with resultfile: %s\n", fileresprob);                                 modality*/ 
   }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        Ndum[ij]++; /*store the modality */
          /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   xp=vector(1,npar);                                         Tvar[j]. If V=sex and male is 0 and 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                                         female is 1, then  cptcode=1.*/
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      }
    
   cov[1]=1;      for (i=0; i<=cptcode; i++) {
   for (age=bage; age<=fage; age ++){        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 */
     cov[2]=age;      }
     gradg=matrix(1,npar,1,9);  
     trgradg=matrix(1,9,1,npar);      ij=1; 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      for (i=1; i<=ncodemax[j]; i++) {
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        for (k=0; k<= maxncov; k++) {
              if (Ndum[k] != 0) {
     for(theta=1; theta <=npar; theta++){            nbcode[Tvar[j]][ij]=k; 
       for(i=1; i<=npar; i++)            /* 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; */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            
                  ij++;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          }
              if (ij > ncodemax[j]) break; 
       k=0;        }  
       for(i=1; i<= (nlstate+ndeath); i++){      } 
         for(j=1; j<=(nlstate+ndeath);j++){    }  
            k=k+1;  
           gp[k]=pmmij[i][j];   for (k=0; k< maxncov; k++) Ndum[k]=0;
         }  
       }   for (i=1; i<=ncovmodel-2; i++) { 
      /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       for(i=1; i<=npar; i++)     ij=Tvar[i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);     Ndum[ij]++;
       }
   
       pmij(pmmij,cov,ncovmodel,xp,nlstate);   ij=1;
       k=0;   for (i=1; i<= maxncov; i++) {
       for(i=1; i<=(nlstate+ndeath); i++){     if((Ndum[i]!=0) && (i<=ncovcol)){
         for(j=1; j<=(nlstate+ndeath);j++){       Tvaraff[ij]=i; /*For printing */
           k=k+1;       ij++;
           gm[k]=pmmij[i][j];     }
         }   }
       }   
         cptcoveff=ij-1; /*Number of simple covariates*/
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  }
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    
     }  /*********** Health Expectancies ****************/
   
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
       for(theta=1; theta <=npar; theta++)  
       trgradg[j][theta]=gradg[theta][j];  {
      /* Health expectancies */
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    double age, agelim, hf;
     double ***p3mat,***varhe;
      pmij(pmmij,cov,ncovmodel,x,nlstate);    double **dnewm,**doldm;
     double *xp;
      k=0;    double **gp, **gm;
      for(i=1; i<=(nlstate+ndeath); i++){    double ***gradg, ***trgradg;
        for(j=1; j<=(nlstate+ndeath);j++){    int theta;
          k=k+1;  
          gm[k]=pmmij[i][j];    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
         }    xp=vector(1,npar);
      }    dnewm=matrix(1,nlstate*2,1,npar);
          doldm=matrix(1,nlstate*2,1,nlstate*2);
      /*printf("\n%d ",(int)age);    
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    fprintf(ficreseij,"# Health expectancies\n");
            fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      for(j=1; j<=nlstate;j++)
      }*/        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
   fprintf(ficresprob,"\n%d ",(int)age);  
     if(estepm < stepm){
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      printf ("Problem %d lower than %d\n",estepm, stepm);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    else  hstepm=estepm;   
   }    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));     * if stepm=24 months pijx are given only every 2 years and by summing them
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));     * we are calculating an estimate of the Life Expectancy assuming a linear 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);     * progression in between and thus overestimating or underestimating according
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);     * to the curvature of the survival function. If, for the same date, we 
 }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
  free_vector(xp,1,npar);     * to compare the new estimate of Life expectancy with the same linear 
 fclose(ficresprob);     * hypothesis. A more precise result, taking into account a more precise
  exit(0);     * curvature will be obtained if estepm is as small as stepm. */
 }  
     /* For example we decided to compute the life expectancy with the smallest unit */
 /***********************************************/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 /**************** Main Program *****************/       nhstepm is the number of hstepm from age to agelim 
 /***********************************************/       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
 /*int main(int argc, char *argv[])*/       and note for a fixed period like estepm months */
 int main()    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 {       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double agedeb, agefin,hf;       results. So we changed our mind and took the option of the best precision.
   double agemin=1.e20, agemax=-1.e20;    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double fret;  
   double **xi,tmp,delta;    agelim=AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double dum; /* Dummy variable */      /* nhstepm age range expressed in number of stepm */
   double ***p3mat;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   int *indx;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   char line[MAXLINE], linepar[MAXLINE];      /* if (stepm >= YEARM) hstepm=1;*/
   char title[MAXLINE];      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   char filerest[FILENAMELENGTH];      gp=matrix(0,nhstepm,1,nlstate*2);
   char fileregp[FILENAMELENGTH];      gm=matrix(0,nhstepm,1,nlstate*2);
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   int firstobs=1, lastobs=10;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   int sdeb, sfin; /* Status at beginning and end */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   int c,  h , cpt,l;   
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
   int mobilav=0,popforecast=0;      /* Computing Variances of health expectancies */
   int hstepm, nhstepm;  
   int *popage;/*boolprev=0 if date and zero if wave*/       for(theta=1; theta <=npar; theta++){
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   double bage, fage, age, agelim, agebase;        }
   double ftolpl=FTOL;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double **prlim;    
   double *severity;        cptj=0;
   double ***param; /* Matrix of parameters */        for(j=1; j<= nlstate; j++){
   double  *p;          for(i=1; i<=nlstate; i++){
   double **matcov; /* Matrix of covariance */            cptj=cptj+1;
   double ***delti3; /* Scale */            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   double *delti; /* Scale */              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   double ***eij, ***vareij;            }
   double **varpl; /* Variances of prevalence limits by age */          }
   double *epj, vepp;        }
   double kk1, kk2;       
   double *popeffectif,*popcount;       
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;        for(i=1; i<=npar; i++) 
   double yp,yp1,yp2;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";        
   char *alph[]={"a","a","b","c","d","e"}, str[4];        cptj=0;
         for(j=1; j<= nlstate; j++){
           for(i=1;i<=nlstate;i++){
   char z[1]="c", occ;            cptj=cptj+1;
 #include <sys/time.h>            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 #include <time.h>              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            }
            }
   /* long total_usecs;        }
   struct timeval start_time, end_time;        for(j=1; j<= nlstate*2; j++)
            for(h=0; h<=nhstepm-1; h++){
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
        } 
   printf("\nIMACH, Version 0.7");     
   printf("\nEnter the parameter file name: ");  /* End theta */
   
 #ifdef windows       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   scanf("%s",pathtot);  
   getcwd(pathcd, size);       for(h=0; h<=nhstepm-1; h++)
   /*cygwin_split_path(pathtot,path,optionfile);        for(j=1; j<=nlstate*2;j++)
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          for(theta=1; theta <=npar; theta++)
   /* cutv(path,optionfile,pathtot,'\\');*/            trgradg[h][j][theta]=gradg[h][theta][j];
        
 split(pathtot, path,optionfile);  
   chdir(path);       for(i=1;i<=nlstate*2;i++)
   replace(pathc,path);        for(j=1;j<=nlstate*2;j++)
 #endif          varhe[i][j][(int)age] =0.;
 #ifdef unix  
   scanf("%s",optionfile);       printf("%d|",(int)age);fflush(stdout);
 #endif       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
 /*-------- arguments in the command line --------*/        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
   strcpy(fileres,"r");          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
   strcat(fileres, optionfile);          for(i=1;i<=nlstate*2;i++)
             for(j=1;j<=nlstate*2;j++)
   /*---------arguments file --------*/              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      }
     printf("Problem with optionfile %s\n",optionfile);      /* Computing expectancies */
     goto end;      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   strcpy(filereso,"o");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   strcat(filereso,fileres);            
   if((ficparo=fopen(filereso,"w"))==NULL) {  /* 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]);*/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }          }
   
   /* Reads comments: lines beginning with '#' */      fprintf(ficreseij,"%3.0f",age );
   while((c=getc(ficpar))=='#' && c!= EOF){      cptj=0;
     ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);        for(j=1; j<=nlstate;j++){
     puts(line);          cptj++;
     fputs(line,ficparo);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   }        }
   ungetc(c,ficpar);      fprintf(ficreseij,"\n");
      
   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);      free_matrix(gm,0,nhstepm,1,nlstate*2);
   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);      free_matrix(gp,0,nhstepm,1,nlstate*2);
   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);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
 while((c=getc(ficpar))=='#' && c!= EOF){      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
     ungetc(c,ficpar);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    printf("\n");
     fputs(line,ficparo);    fprintf(ficlog,"\n");
   }  
   ungetc(c,ficpar);    free_vector(xp,1,npar);
      free_matrix(dnewm,1,nlstate*2,1,npar);
        free_matrix(doldm,1,nlstate*2,1,nlstate*2);
   covar=matrix(0,NCOVMAX,1,n);    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
   cptcovn=0;  }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
   /************ Variance ******************/
   ncovmodel=2+cptcovn;  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)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  {
      /* Variance of health expectancies */
   /* Read guess parameters */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   /* Reads comments: lines beginning with '#' */    /* double **newm;*/
   while((c=getc(ficpar))=='#' && c!= EOF){    double **dnewm,**doldm;
     ungetc(c,ficpar);    double **dnewmp,**doldmp;
     fgets(line, MAXLINE, ficpar);    int i, j, nhstepm, hstepm, h, nstepm ;
     puts(line);    int k, cptcode;
     fputs(line,ficparo);    double *xp;
   }    double **gp, **gm;  /* for var eij */
   ungetc(c,ficpar);    double ***gradg, ***trgradg; /*for var eij */
      double **gradgp, **trgradgp; /* for var p point j */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double *gpp, *gmp; /* for var p point j */
     for(i=1; i <=nlstate; i++)    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     for(j=1; j <=nlstate+ndeath-1; j++){    double ***p3mat;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    double age,agelim, hf;
       fprintf(ficparo,"%1d%1d",i1,j1);    double ***mobaverage;
       printf("%1d%1d",i,j);    int theta;
       for(k=1; k<=ncovmodel;k++){    char digit[4];
         fscanf(ficpar," %lf",&param[i][j][k]);    char digitp[25];
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);    char fileresprobmorprev[FILENAMELENGTH];
       }  
       fscanf(ficpar,"\n");    if(popbased==1){
       printf("\n");      if(mobilav!=0)
       fprintf(ficparo,"\n");        strcpy(digitp,"-populbased-mobilav-");
     }      else strcpy(digitp,"-populbased-nomobil-");
      }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    else 
       strcpy(digitp,"-stablbased-");
   p=param[1][1];  
      if (mobilav!=0) {
   /* Reads comments: lines beginning with '#' */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   while((c=getc(ficpar))=='#' && c!= EOF){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     ungetc(c,ficpar);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     fgets(line, MAXLINE, ficpar);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     puts(line);      }
     fputs(line,ficparo);    }
   }  
   ungetc(c,ficpar);    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   for(i=1; i <=nlstate; i++){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     for(j=1; j <=nlstate+ndeath-1; j++){    strcat(fileresprobmorprev,fileres);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("%1d%1d",i,j);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficparo,"%1d%1d",i1,j1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       for(k=1; k<=ncovmodel;k++){    }
         fscanf(ficpar,"%le",&delti3[i][j][k]);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         printf(" %le",delti3[i][j][k]);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         fprintf(ficparo," %le",delti3[i][j][k]);    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);
       }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       fscanf(ficpar,"\n");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       printf("\n");      fprintf(ficresprobmorprev," p.%-d SE",j);
       fprintf(ficparo,"\n");      for(i=1; i<=nlstate;i++)
     }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   }    }  
   delti=delti3[1][1];    fprintf(ficresprobmorprev,"\n");
      if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   /* Reads comments: lines beginning with '#' */      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     ungetc(c,ficpar);      exit(0);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    else{
     fputs(line,ficparo);      fprintf(ficgp,"\n# Routine varevsij");
   }    }
   ungetc(c,ficpar);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
        printf("Problem with html file: %s\n", optionfilehtm);
   matcov=matrix(1,npar,1,npar);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   for(i=1; i <=npar; i++){      exit(0);
     fscanf(ficpar,"%s",&str);    }
     printf("%s",str);    else{
     fprintf(ficparo,"%s",str);      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");
     for(j=1; j <=i; j++){      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       fscanf(ficpar," %le",&matcov[i][j]);    }
       printf(" %.5le",matcov[i][j]);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }    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");
     fscanf(ficpar,"\n");    fprintf(ficresvij,"# Age");
     printf("\n");    for(i=1; i<=nlstate;i++)
     fprintf(ficparo,"\n");      for(j=1; j<=nlstate;j++)
   }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   for(i=1; i <=npar; i++)    fprintf(ficresvij,"\n");
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];    xp=vector(1,npar);
        dnewm=matrix(1,nlstate,1,npar);
   printf("\n");    doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     /*-------- data file ----------*/  
     if((ficres =fopen(fileres,"w"))==NULL) {    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       printf("Problem with resultfile: %s\n", fileres);goto end;    gpp=vector(nlstate+1,nlstate+ndeath);
     }    gmp=vector(nlstate+1,nlstate+ndeath);
     fprintf(ficres,"#%s\n",version);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        
     if((fic=fopen(datafile,"r"))==NULL)    {    if(estepm < stepm){
       printf("Problem with datafile: %s\n", datafile);goto end;      printf ("Problem %d lower than %d\n",estepm, stepm);
     }    }
     else  hstepm=estepm;   
     n= lastobs;    /* For example we decided to compute the life expectancy with the smallest unit */
     severity = vector(1,maxwav);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     outcome=imatrix(1,maxwav+1,1,n);       nhstepm is the number of hstepm from age to agelim 
     num=ivector(1,n);       nstepm is the number of stepm from age to agelin. 
     moisnais=vector(1,n);       Look at hpijx to understand the reason of that which relies in memory size
     annais=vector(1,n);       and note for a fixed period like k years */
     moisdc=vector(1,n);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     andc=vector(1,n);       survival function given by stepm (the optimization length). Unfortunately it
     agedc=vector(1,n);       means that if the survival funtion is printed every two years of age and if
     cod=ivector(1,n);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     weight=vector(1,n);       results. So we changed our mind and took the option of the best precision.
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    */
     mint=matrix(1,maxwav,1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     anint=matrix(1,maxwav,1,n);    agelim = AGESUP;
     s=imatrix(1,maxwav+1,1,n);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     adl=imatrix(1,maxwav+1,1,n);          nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     tab=ivector(1,NCOVMAX);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     ncodemax=ivector(1,8);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     i=1;      gp=matrix(0,nhstepm,1,nlstate);
     while (fgets(line, MAXLINE, fic) != NULL)    {      gm=matrix(0,nhstepm,1,nlstate);
       if ((i >= firstobs) && (i <=lastobs)) {  
          
         for (j=maxwav;j>=1;j--){      for(theta=1; theta <=npar; theta++){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           strcpy(line,stra);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           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);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        if (popbased==1) {
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              prlim[i][i]=probs[(int)age][i][ij];
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              prlim[i][i]=mobaverage[(int)age][i][ij];
         for (j=ncov;j>=1;j--){          }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
         }    
         num[i]=atol(stra);        for(j=1; j<= nlstate; j++){
                  for(h=0; h<=nhstepm; h++){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
           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;}*/              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         i=i+1;        }
       }        /* This for computing probability of death (h=1 means
     }           computed over hstepm matrices product = hstepm*stepm months) 
     /* printf("ii=%d", ij);           as a weighted average of prlim.
        scanf("%d",i);*/        */
   imx=i-1; /* Number of individuals */        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
           for(i=1; i<= nlstate; i++)
   /* for (i=1; i<=imx; i++){            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     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;        /* end probability of death */
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  
     }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for (i=1; i<=imx; i++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     if (covar[1][i]==0) 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]));*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   /* Calculation of the number of parameter from char model*/        if (popbased==1) {
   Tvar=ivector(1,15);          if(mobilav ==0){
   Tprod=ivector(1,15);            for(i=1; i<=nlstate;i++)
   Tvaraff=ivector(1,15);              prlim[i][i]=probs[(int)age][i][ij];
   Tvard=imatrix(1,15,1,2);          }else{ /* mobilav */ 
   Tage=ivector(1,15);                  for(i=1; i<=nlstate;i++)
                  prlim[i][i]=mobaverage[(int)age][i][ij];
   if (strlen(model) >1){          }
     j=0, j1=0, k1=1, k2=1;        }
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');        for(j=1; j<= nlstate; j++){
     cptcovn=j+1;          for(h=0; h<=nhstepm; h++){
     cptcovprod=j1;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                  gm[h][j] += prlim[i][i]*p3mat[i][j][h];
              }
     strcpy(modelsav,model);        }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        /* This for computing probability of death (h=1 means
       printf("Error. Non available option model=%s ",model);           computed over hstepm matrices product = hstepm*stepm months) 
       goto end;           as a weighted average of prlim.
     }        */
            for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
     for(i=(j+1); i>=1;i--){          for(i=1; i<= nlstate; i++)
       cutv(stra,strb,modelsav,'+');            gmp[j] += prlim[i][i]*p3mat[i][j][1];
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        }    
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        /* end probability of death */
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {        for(j=1; j<= nlstate; j++) /* vareij */
         cutv(strd,strc,strb,'*');          for(h=0; h<=nhstepm; h++){
         if (strcmp(strc,"age")==0) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           cptcovprod--;          }
           cutv(strb,stre,strd,'V');        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           Tvar[i]=atoi(stre);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
           cptcovage++;        }
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/      } /* End theta */
         }  
         else if (strcmp(strd,"age")==0) {      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
           cptcovprod--;  
           cutv(strb,stre,strc,'V');      for(h=0; h<=nhstepm; h++) /* veij */
           Tvar[i]=atoi(stre);        for(j=1; j<=nlstate;j++)
           cptcovage++;          for(theta=1; theta <=npar; theta++)
           Tage[cptcovage]=i;            trgradg[h][j][theta]=gradg[h][theta][j];
         }  
         else {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
           cutv(strb,stre,strc,'V');        for(theta=1; theta <=npar; theta++)
           Tvar[i]=ncov+k1;          trgradgp[j][theta]=gradgp[theta][j];
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           Tvard[k1][1]=atoi(strc);      for(i=1;i<=nlstate;i++)
           Tvard[k1][2]=atoi(stre);        for(j=1;j<=nlstate;j++)
           Tvar[cptcovn+k2]=Tvard[k1][1];          vareij[i][j][(int)age] =0.;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)      for(h=0;h<=nhstepm;h++){
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        for(k=0;k<=nhstepm;k++){
           k1++;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           k2=k2+2;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         }          for(i=1;i<=nlstate;i++)
       }            for(j=1;j<=nlstate;j++)
       else {              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        }
        /*  scanf("%d",i);*/      }
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);      /* pptj */
       }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       strcpy(modelsav,stra);        matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         scanf("%d",i);*/        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     }          varppt[j][i]=doldmp[j][i];
 }      /* end ppptj */
        /*  x centered again */
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   printf("cptcovprod=%d ", cptcovprod);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   scanf("%d ",i);*/   
     fclose(fic);      if (popbased==1) {
         if(mobilav ==0){
     /*  if(mle==1){*/          for(i=1; i<=nlstate;i++)
     if (weightopt != 1) { /* Maximisation without weights*/            prlim[i][i]=probs[(int)age][i][ij];
       for(i=1;i<=n;i++) weight[i]=1.0;        }else{ /* mobilav */ 
     }          for(i=1; i<=nlstate;i++)
     /*-calculation of age at interview from date of interview and age at death -*/            prlim[i][i]=mobaverage[(int)age][i][ij];
     agev=matrix(1,maxwav,1,imx);        }
       }
    for (i=1; i<=imx; i++)      
      for(m=2; (m<= maxwav); m++)      /* This for computing probability of death (h=1 means
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          anint[m][i]=9999;         as a weighted average of prlim.
          s[m][i]=-1;      */
        }      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
            for(i=1; i<= nlstate; i++)
     for (i=1; i<=imx; i++)  {          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      }    
       for(m=1; (m<= maxwav); m++){      /* end probability of death */
         if(s[m][i] >0){  
           if (s[m][i] == nlstate+1) {      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
             if(agedc[i]>0)      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
               if(moisdc[i]!=99 && andc[i]!=9999)        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
               agev[m][i]=agedc[i];        for(i=1; i<=nlstate;i++){
             else {          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
               if (andc[i]!=9999){        }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      } 
               agev[m][i]=-1;      fprintf(ficresprobmorprev,"\n");
               }  
             }      fprintf(ficresvij,"%.0f ",age );
           }      for(i=1; i<=nlstate;i++)
           else if(s[m][i] !=9){ /* Should no more exist */        for(j=1; j<=nlstate;j++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
             if(mint[m][i]==99 || anint[m][i]==9999)        }
               agev[m][i]=1;      fprintf(ficresvij,"\n");
             else if(agev[m][i] <agemin){      free_matrix(gp,0,nhstepm,1,nlstate);
               agemin=agev[m][i];      free_matrix(gm,0,nhstepm,1,nlstate);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
             }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
             else if(agev[m][i] >agemax){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               agemax=agev[m][i];    } /* End age */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    free_vector(gpp,nlstate+1,nlstate+ndeath);
             }    free_vector(gmp,nlstate+1,nlstate+ndeath);
             /*agev[m][i]=anint[m][i]-annais[i];*/    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
             /*   agev[m][i] = age[i]+2*m;*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           else { /* =9 */    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
             agev[m][i]=1;    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
             s[m][i]=-1;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
         }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         else /*= 0 Unknown */    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
           agev[m][i]=1;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
       }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
        fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,digit);
     for (i=1; i<=imx; i++)  {    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       for(m=1; (m<= maxwav); m++){  */
         if (s[m][i] > (nlstate+ndeath)) {    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;    free_vector(xp,1,npar);
         }    free_matrix(doldm,1,nlstate,1,nlstate);
       }    free_matrix(dnewm,1,nlstate,1,npar);
     }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_vector(severity,1,maxwav);    fclose(ficresprobmorprev);
     free_imatrix(outcome,1,maxwav+1,1,n);    fclose(ficgp);
     free_vector(moisnais,1,n);    fclose(fichtm);
     free_vector(annais,1,n);  }
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/  /************ Variance of prevlim ******************/
     free_vector(moisdc,1,n);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
     free_vector(andc,1,n);  {
     /* Variance of prevalence limit */
        /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     wav=ivector(1,imx);    double **newm;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    double **dnewm,**doldm;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    int i, j, nhstepm, hstepm;
        int k, cptcode;
     /* Concatenates waves */    double *xp;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
       Tcode=ivector(1,100);    int theta;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     
       ncodemax[1]=1;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    fprintf(ficresvpl,"# Age");
          for(i=1; i<=nlstate;i++)
    codtab=imatrix(1,100,1,10);        fprintf(ficresvpl," %1d-%1d",i,i);
    h=0;    fprintf(ficresvpl,"\n");
    m=pow(2,cptcoveff);  
      xp=vector(1,npar);
    for(k=1;k<=cptcoveff; k++){    dnewm=matrix(1,nlstate,1,npar);
      for(i=1; i <=(m/pow(2,k));i++){    doldm=matrix(1,nlstate,1,nlstate);
        for(j=1; j <= ncodemax[k]; j++){    
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    hstepm=1*YEARM; /* Every year of age */
            h++;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
            if (h>m) h=1;codtab[h][k]=j;    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);
    /* Calculates basic frequencies. Computes observed prevalence at single age      gp=vector(1,nlstate);
        and prints on file fileres'p'. */      gm=vector(1,nlstate);
   
          for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(i=1;i<=nlstate;i++)
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          gp[i] = prlim[i][i];
            
     /* For Powell, parameters are in a vector p[] starting at p[1]        for(i=1; i<=npar; i++) /* Computes gradient */
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
     if(mle==1){          gm[i] = prlim[i][i];
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }        for(i=1;i<=nlstate;i++)
              gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     /*--------- results files --------------*/      } /* End theta */
     fprintf(ficres,"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);  
        trgradg =matrix(1,nlstate,1,npar);
   
    jk=1;      for(j=1; j<=nlstate;j++)
    fprintf(ficres,"# Parameters\n");        for(theta=1; theta <=npar; theta++)
    printf("# Parameters\n");          trgradg[j][theta]=gradg[theta][j];
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){      for(i=1;i<=nlstate;i++)
        if (k != i)        varpl[i][(int)age] =0.;
          {      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
            printf("%d%d ",i,k);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
            fprintf(ficres,"%1d%1d ",i,k);      for(i=1;i<=nlstate;i++)
            for(j=1; j <=ncovmodel; j++){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);      fprintf(ficresvpl,"%.0f ",age );
              jk++;      for(i=1; i<=nlstate;i++)
            }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
            printf("\n");      fprintf(ficresvpl,"\n");
            fprintf(ficres,"\n");      free_vector(gp,1,nlstate);
          }      free_vector(gm,1,nlstate);
      }      free_matrix(gradg,1,npar,1,nlstate);
    }      free_matrix(trgradg,1,nlstate,1,npar);
  if(mle==1){    } /* End age */
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */    free_vector(xp,1,npar);
     hesscov(matcov, p, npar, delti, ftolhess, func);    free_matrix(doldm,1,nlstate,1,npar);
  }    free_matrix(dnewm,1,nlstate,1,nlstate);
     fprintf(ficres,"# Scales\n");  
     printf("# Scales\n");  }
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){  /************ Variance of one-step probabilities  ******************/
         if (j!=i) {  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
           fprintf(ficres,"%1d%1d",i,j);  {
           printf("%1d%1d",i,j);    int i, j=0,  i1, k1, l1, t, tj;
           for(k=1; k<=ncovmodel;k++){    int k2, l2, j1,  z1;
             printf(" %.5e",delti[jk]);    int k=0,l, cptcode;
             fprintf(ficres," %.5e",delti[jk]);    int first=1, first1;
             jk++;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           }    double **dnewm,**doldm;
           printf("\n");    double *xp;
           fprintf(ficres,"\n");    double *gp, *gm;
         }    double **gradg, **trgradg;
       }    double **mu;
      }    double age,agelim, cov[NCOVMAX];
        double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     k=1;    int theta;
     fprintf(ficres,"# Covariance\n");    char fileresprob[FILENAMELENGTH];
     printf("# Covariance\n");    char fileresprobcov[FILENAMELENGTH];
     for(i=1;i<=npar;i++){    char fileresprobcor[FILENAMELENGTH];
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;    double ***varpij;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/    strcpy(fileresprob,"prob"); 
       fprintf(ficres,"%3d",i);    strcat(fileresprob,fileres);
       printf("%3d",i);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       for(j=1; j<=i;j++){      printf("Problem with resultfile: %s\n", fileresprob);
         fprintf(ficres," %.5e",matcov[i][j]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
         printf(" %.5e",matcov[i][j]);    }
       }    strcpy(fileresprobcov,"probcov"); 
       fprintf(ficres,"\n");    strcat(fileresprobcov,fileres);
       printf("\n");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       k++;      printf("Problem with resultfile: %s\n", fileresprobcov);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
        }
     while((c=getc(ficpar))=='#' && c!= EOF){    strcpy(fileresprobcor,"probcor"); 
       ungetc(c,ficpar);    strcat(fileresprobcor,fileres);
       fgets(line, MAXLINE, ficpar);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       puts(line);      printf("Problem with resultfile: %s\n", fileresprobcor);
       fputs(line,ficparo);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }    }
     ungetc(c,ficpar);    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);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    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);
     if (fage <= 2) {    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       bage = agemin;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       fage = agemax;    
     }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     fprintf(ficres,"# agemin agemax for life expectancy.\n");    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    fprintf(ficresprobcov,"# Age");
    
     while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);      for(j=1; j<=(nlstate+ndeath);j++){
     puts(line);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     fputs(line,ficparo);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   ungetc(c,ficpar);      }  
      fprintf(ficresprob,"\n");
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);    fprintf(ficresprobcov,"\n");
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    fprintf(ficresprobcor,"\n");
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    xp=vector(1,npar);
          dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     ungetc(c,ficpar);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     fgets(line, MAXLINE, ficpar);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     puts(line);    first=1;
     fputs(line,ficparo);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
        exit(0);
     }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    else{
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      fprintf(ficgp,"\n# Routine varprob");
     }
   fscanf(ficpar,"pop_based=%d\n",&popbased);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
    fprintf(ficparo,"pop_based=%d\n",popbased);        printf("Problem with html file: %s\n", optionfilehtm);
    fprintf(ficres,"pop_based=%d\n",popbased);        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
       exit(0);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    else{
     fgets(line, MAXLINE, ficpar);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     puts(line);      fprintf(fichtm,"\n");
     fputs(line,ficparo);  
   }      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   ungetc(c,ficpar);      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");
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);      fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);  
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    }
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);    cov[1]=1;
     tj=cptcoveff;
  /*------------ gnuplot -------------*/    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
 chdir(pathcd);    j1=0;
   if((ficgp=fopen("graph.plt","w"))==NULL) {    for(t=1; t<=tj;t++){
     printf("Problem with file graph.gp");goto end;      for(i1=1; i1<=ncodemax[t];i1++){ 
   }        j1++;
 #ifdef windows        if  (cptcovn>0) {
   fprintf(ficgp,"cd \"%s\" \n",pathc);          fprintf(ficresprob, "\n#********** Variable "); 
 #endif          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 m=pow(2,cptcoveff);          fprintf(ficresprob, "**********\n#");
            fprintf(ficresprobcov, "\n#********** Variable "); 
  /* 1eme*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for (cpt=1; cpt<= nlstate ; cpt ++) {          fprintf(ficresprobcov, "**********\n#");
    for (k1=1; k1<= m ; k1 ++) {          
           fprintf(ficgp, "\n#********** Variable "); 
 #ifdef windows          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     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);          fprintf(ficgp, "**********\n#");
 #endif          
 #ifdef unix          
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
 #endif          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
 for (i=1; i<= nlstate ; i ++) {          
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficresprobcor, "\n#********** Variable ");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }          fprintf(ficgp, "**********\n#");    
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        }
     for (i=1; i<= nlstate ; i ++) {        
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for (age=bage; age<=fage; age ++){ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          cov[2]=age;
 }          for (k=1; k<=cptcovn;k++) {
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
      for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (k=1; k<=cptcovprod;k++)
 }              cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          
 #ifdef unix          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
 fprintf(ficgp,"\nset ter gif small size 400,300");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 #endif          gp=vector(1,(nlstate)*(nlstate+ndeath));
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          gm=vector(1,(nlstate)*(nlstate+ndeath));
    }      
   }          for(theta=1; theta <=npar; theta++){
   /*2 eme*/            for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:0);
   for (k1=1; k1<= m ; k1 ++) {            
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                
     for (i=1; i<= nlstate+1 ; i ++) {            k=0;
       k=2*i;            for(i=1; i<= (nlstate); i++){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              for(j=1; j<=(nlstate+ndeath);j++){
       for (j=1; j<= nlstate+1 ; j ++) {                k=k+1;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                gp[k]=pmmij[i][j];
   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);            for(i=1; i<=npar; i++)
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              xp[i] = x[i] - (i==theta ?delti[theta]:0);
       for (j=1; j<= nlstate+1 ; j ++) {      
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         else fprintf(ficgp," \%%*lf (\%%*lf)");            k=0;
 }              for(i=1; i<=(nlstate); i++){
       fprintf(ficgp,"\" t\"\" w l 0,");              for(j=1; j<=(nlstate+ndeath);j++){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);                k=k+1;
       for (j=1; j<= nlstate+1 ; j ++) {                gm[k]=pmmij[i][j];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              }
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }         
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       else fprintf(ficgp,"\" t\"\" w l 0,");              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
     }          }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  
   }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
              for(theta=1; theta <=npar; theta++)
   /*3eme*/              trgradg[j][theta]=gradg[theta][j];
           
   for (k1=1; k1<= m ; k1 ++) {          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     for (cpt=1; cpt<= nlstate ; cpt ++) {          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       k=2+nlstate*(cpt-1);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
       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);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       for (i=1; i< nlstate ; i ++) {          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         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);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          pmij(pmmij,cov,ncovmodel,x,nlstate);
     }          
   }          k=0;
            for(i=1; i<=(nlstate); i++){
   /* CV preval stat */            for(j=1; j<=(nlstate+ndeath);j++){
   for (k1=1; k1<= m ; k1 ++) {              k=k+1;
     for (cpt=1; cpt<nlstate ; cpt ++) {              mu[k][(int) age]=pmmij[i][j];
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);          }
       for (i=1; i< nlstate ; i ++)          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         fprintf(ficgp,"+$%d",k+i+1);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              varpij[i][j][(int)age] = doldm[i][j];
        
       l=3+(nlstate+ndeath)*cpt;          /*printf("\n%d ",(int)age);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       for (i=1; i< nlstate ; i ++) {            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         l=3+(nlstate+ndeath)*cpt;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         fprintf(ficgp,"+$%d",l+i+1);            }*/
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            fprintf(ficresprob,"\n%d ",(int)age);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          fprintf(ficresprobcov,"\n%d ",(int)age);
     }          fprintf(ficresprobcor,"\n%d ",(int)age);
   }    
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   /* proba elementaires */            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
    for(i=1,jk=1; i <=nlstate; i++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     for(k=1; k <=(nlstate+ndeath); k++){            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       if (k != i) {            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
         for(j=1; j <=ncovmodel; j++){          }
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/          i=0;
           /*fprintf(ficgp,"%s",alph[1]);*/          for (k=1; k<=(nlstate);k++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            for (l=1; l<=(nlstate+ndeath);l++){ 
           jk++;              i=i++;
           fprintf(ficgp,"\n");              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]));
               }
   for(jk=1; jk <=m; jk++) {            }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);          }/* end of loop for state */
    i=1;        } /* end of loop for age */
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;        /* Confidence intervalle of pij  */
      for(k=1; k<=(nlstate+ndeath); k++) {        /*
        if (k != k2){          fprintf(ficgp,"\nset noparametric;unset label");
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
 ij=1;          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         for(j=3; j <=ncovmodel; j++) {          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);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
             ij++;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           }        */
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         }        first1=1;
           fprintf(ficgp,")/(1");        for (k2=1; k2<=(nlstate);k2++){
                  for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         for(k1=1; k1 <=nlstate; k1++){              if(l2==k2) continue;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            j=(k2-1)*(nlstate+ndeath)+l2;
 ij=1;            for (k1=1; k1<=(nlstate);k1++){
           for(j=3; j <=ncovmodel; j++){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                if(l1==k1) continue;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                i=(k1-1)*(nlstate+ndeath)+l1;
             ij++;                if(i<=j) continue;
           }                for (age=bage; age<=fage; age ++){ 
           else                  if ((int)age %5==0){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
           }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
           fprintf(ficgp,")");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         }                    mu1=mu[i][(int) age]/stepm*YEARM ;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);                    mu2=mu[j][(int) age]/stepm*YEARM;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                    c12=cv12/sqrt(v1*v2);
         i=i+ncovmodel;                    /* 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 */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   }                    /*v21=sqrt(1.-v11*v11); *//* error */
                        v21=(lc1-v1)/cv12*v11;
   fclose(ficgp);                    v12=-v21;
                        v22=v11;
 chdir(path);                    tnalp=v21/v11;
                        if(first1==1){
     free_ivector(wav,1,imx);                      first1=0;
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                      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);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                      }
     free_ivector(num,1,n);                    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);
     free_vector(agedc,1,n);                    /*printf(fignu*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     fclose(ficparo);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     fclose(ficres);                    if(first==1){
     /*  }*/                      first=0;
                          fprintf(ficgp,"\nset parametric;unset label");
    /*________fin mle=1_________*/                      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);
     /* No more information from the sample is required now */                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   /* Reads comments: lines beginning with '#' */                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   while((c=getc(ficpar))=='#' && c!= EOF){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     ungetc(c,ficpar);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     fgets(line, MAXLINE, ficpar);                      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",\
     puts(line);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     fputs(line,ficparo);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   }                    }else{
   ungetc(c,ficpar);                      first=0;
                        fprintf(fichtm," %d (%.3f),",(int) age, c12);
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                      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",\
 /*--------- index.htm --------*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   strcpy(optionfilehtm,optionfile);                    }/* if first */
   strcat(optionfilehtm,".htm");                  } /* age mod 5 */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                } /* end loop age */
     printf("Problem with %s \n",optionfilehtm);goto end;                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   }                first=1;
               } /*l12 */
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">            } /* k12 */
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          } /*l1 */
 Total number of observations=%d <br>        }/* k1 */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>      } /* loop covariates */
 <hr  size=\"2\" color=\"#EC5E5E\">    }
 <li>Outputs files<br><br>\n    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    free_vector(xp,1,npar);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    fclose(ficresprob);
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    fclose(ficresprobcov);
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    fclose(ficresprobcor);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    fclose(ficgp);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    fclose(fichtm);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  }
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>  
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>  
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
  fprintf(fichtm," <li>Graphs</li><p>");                    int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
  m=cptcoveff;                    int popforecast, int estepm ,\
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                    double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
  j1=0;    int jj1, k1, i1, cpt;
  for(k1=1; k1<=m;k1++){    /*char optionfilehtm[FILENAMELENGTH];*/
    for(i1=1; i1<=ncodemax[k1];i1++){    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
        j1++;      printf("Problem with %s \n",optionfilehtm), exit(0);
        if (cptcovn > 0) {      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(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[j1][cpt]]);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");   - 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
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);       - Life expectancies by age and initial health status (estepm=%2d months): 
        for(cpt=1; cpt<nlstate;cpt++){     <a href=\"e%s\">e%s</a> <br>\n</li>", \
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
        }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident   m=cptcoveff;
 interval) in state (%d): v%s%d%d.gif <br>   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    
      }   jj1=0;
      for(cpt=1; cpt<=nlstate;cpt++) {   for(k1=1; k1<=m;k1++){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>     for(i1=1; i1<=ncodemax[k1];i1++){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);       jj1++;
      }       if (cptcovn > 0) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 health expectancies in states (1) and (2): e%s%d.gif<br>         for (cpt=1; cpt<=cptcoveff;cpt++) 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
 fprintf(fichtm,"\n</body>");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
    }       }
  }       /* Pij */
 fclose(fichtm);       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);     
   /*--------------- Prevalence limit --------------*/       /* 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>
   strcpy(filerespl,"pl");  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
   strcat(filerespl,fileres);         /* Stable prevalence in each health state */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {         for(cpt=1; cpt<nlstate;cpt++){
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;           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);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);         }
   fprintf(ficrespl,"#Prevalence limit\n");       for(cpt=1; cpt<=nlstate;cpt++) {
   fprintf(ficrespl,"#Age ");          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   fprintf(ficrespl,"\n");       }
         fprintf(fichtm,"\n<br>- Total life expectancy by age and
   prlim=matrix(1,nlstate,1,nlstate);  health expectancies in states (1) and (2): e%s%d.png<br>
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     } /* end i1 */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   }/* End k1 */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   fprintf(fichtm,"</ul>");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;  
   agebase=agemin;   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   agelim=agemax;   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
   ftolpl=1.e-10;   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
   i1=cptcoveff;   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
   if (cptcovn < 1){i1=1;}   - 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 
   for(cptcov=1;cptcov<=i1;cptcov++){   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/   if(popforecast==1) fprintf(fichtm,"\n
         fprintf(ficrespl,"\n#******");   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
         for(j=1;j<=cptcoveff;j++)   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          <br>",fileres,fileres,fileres,fileres);
         fprintf(ficrespl,"******\n");   else 
             fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
         for (age=agebase; age<=agelim; age++){  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );   m=cptcoveff;
           for(i=1; i<=nlstate;i++)   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");   jj1=0;
         }   for(k1=1; k1<=m;k1++){
       }     for(i1=1; i1<=ncodemax[k1];i1++){
     }       jj1++;
   fclose(ficrespl);       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   /*------------- h Pij x at various ages ------------*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   if((ficrespij=fopen(filerespij,"w"))==NULL) {       }
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;       for(cpt=1; cpt<=nlstate;cpt++) {
   }         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   printf("Computing pij: result on file '%s' \n", filerespij);  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);  
   stepsize=(int) (stepm+YEARM-1)/YEARM;       }
   /*if (stepm<=24) stepsize=2;*/     } /* end i1 */
    }/* End k1 */
   agelim=AGESUP;   fprintf(fichtm,"</ul>");
   hstepm=stepsize*YEARM; /* Every year of age */  fclose(fichtm);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  }
    
   k=0;  /******************* Gnuplot file **************/
   for(cptcov=1;cptcov<=i1;cptcov++){  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         fprintf(ficrespij,"\n#****** ");    int ng;
         for(j=1;j<=cptcoveff;j++)    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with file %s",optionfilegnuplot);
         fprintf(ficrespij,"******\n");      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
            }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /*#ifdef windows */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      fprintf(ficgp,"cd \"%s\" \n",pathc);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /*#endif */
           oldm=oldms;savm=savms;  m=pow(2,cptcoveff);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      
           fprintf(ficrespij,"# Age");   /* 1eme*/
           for(i=1; i<=nlstate;i++)    for (cpt=1; cpt<= nlstate ; cpt ++) {
             for(j=1; j<=nlstate+ndeath;j++)     for (k1=1; k1<= m ; k1 ++) {
               fprintf(ficrespij," %1d-%1d",i,j);       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           fprintf(ficrespij,"\n");       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 (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       for (i=1; i<= nlstate ; i ++) {
             for(i=1; i<=nlstate;i++)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
               for(j=1; j<=nlstate+ndeath;j++)         else fprintf(ficgp," \%%*lf (\%%*lf)");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);       }
             fprintf(ficrespij,"\n");       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
           }       for (i=1; i<= nlstate ; i ++) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           fprintf(ficrespij,"\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
         }       } 
     }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
   }       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
   fclose(ficrespij);       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      }
   /*---------- Forecasting ------------------*/    }
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    /*2 eme*/
     
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    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);
   strcpy(fileresf,"f");      
   strcat(fileresf,fileres);      for (i=1; i<= nlstate+1 ; i ++) {
   if((ficresf=fopen(fileresf,"w"))==NULL) {        k=2*i;
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
   }        for (j=1; j<= nlstate+1 ; j ++) {
   printf("Computing forecasting: result on file '%s' \n", fileresf);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   free_matrix(mint,1,maxwav,1,n);        }   
   free_matrix(anint,1,maxwav,1,n);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   free_matrix(agev,1,maxwav,1,imx);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   /* Mobile average */        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 (cptcoveff==0) ncodemax[cptcoveff]=1;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   if (mobilav==1) {        }   
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficgp,"\" t\"\" w l 0,");
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
       for (i=1; i<=nlstate;i++)        for (j=1; j<= nlstate+1 ; j ++) {
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           mobaverage[(int)agedeb][i][cptcod]=0.;          else fprintf(ficgp," \%%*lf (\%%*lf)");
            }   
     for (agedeb=bage+4; agedeb<=fage; agedeb++){        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       for (i=1; i<=nlstate;i++){        else fprintf(ficgp,"\" t\"\" w l 0,");
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      }
           for (cpt=0;cpt<=4;cpt++){    }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    
           }    /*3eme*/
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    
         }    for (k1=1; k1<= m ; k1 ++) { 
       }      for (cpt=1; cpt<= nlstate ; cpt ++) {
     }          k=2+nlstate*(2*cpt-2);
   }        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
   stepsize=(int) (stepm+YEARM-1)/YEARM;        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   if (stepm<=12) stepsize=1;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   agelim=AGESUP;          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   /*hstepm=stepsize*YEARM; *//* Every year of age */          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   hstepm=1;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */          
   yp1=modf(dateintmean,&yp);        */
   anprojmean=yp;        for (i=1; i< nlstate ; i ++) {
   yp2=modf((yp1*12),&yp);          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);
   mprojmean=yp;          
   yp1=modf((yp2*30.5),&yp);        } 
   jprojmean=yp;      }
   if(jprojmean==0) jprojmean=1;    }
   if(mprojmean==0) jprojmean=1;    
     /* CV preval stat */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<nlstate ; cpt ++) {
   if (popforecast==1) {        k=3;
     if((ficpop=fopen(popfile,"r"))==NULL)    {        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       printf("Problem with population file : %s\n",popfile);goto end;        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
     }        
     popage=ivector(0,AGESUP);        for (i=1; i< nlstate ; i ++)
     popeffectif=vector(0,AGESUP);          fprintf(ficgp,"+$%d",k+i+1);
     popcount=vector(0,AGESUP);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
     i=1;          l=3+(nlstate+ndeath)*cpt;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
       {        for (i=1; i< nlstate ; i ++) {
         i=i+1;          l=3+(nlstate+ndeath)*cpt;
       }          fprintf(ficgp,"+$%d",l+i+1);
     imx=i;        }
            fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      } 
   }    }  
     
   for(cptcov=1;cptcov<=i1;cptcov++){    /* proba elementaires */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    for(i=1,jk=1; i <=nlstate; i++){
       k=k+1;      for(k=1; k <=(nlstate+ndeath); k++){
       fprintf(ficresf,"\n#******");        if (k != i) {
       for(j=1;j<=cptcoveff;j++) {          for(j=1; j <=ncovmodel; j++){
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       }            jk++; 
       fprintf(ficresf,"******\n");            fprintf(ficgp,"\n");
       fprintf(ficresf,"# StartingAge FinalAge");          }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        }
       if (popforecast==1)  fprintf(ficresf," [Population]");      }
       }
       for (cpt=0; cpt<=5;cpt++) {  
         fprintf(ficresf,"\n");     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);         for(jk=1; jk <=m; jk++) {
       for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);         if (ng==2)
         nhstepm = nhstepm/hstepm;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/         else
            fprintf(ficgp,"\nset title \"Probability\"\n");
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
         oldm=oldms;savm=savms;         i=1;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           for(k2=1; k2<=nlstate; k2++) {
                           k3=i;
         for (h=0; h<=nhstepm; h++){           for(k=1; k<=(nlstate+ndeath); k++) {
           if (h==(int) (calagedate+YEARM*cpt)) {             if (k != k2){
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);               if(ng==2)
           }                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
           for(j=1; j<=nlstate+ndeath;j++) {               else
             kk1=0.;kk2=0;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
             for(i=1; i<=nlstate;i++) {                       ij=1;
               if (mobilav==1)               for(j=3; j <=ncovmodel; j++) {
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
               else {                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                   ij++;
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/                 }
               }                 else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];               }
             }               fprintf(ficgp,")/(1");
                         
             if (h==(int)(calagedate+12*cpt)){               for(k1=1; k1 <=nlstate; k1++){   
               fprintf(ficresf," %.3f", kk1);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                               ij=1;
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);                 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++;
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                   }
       }                   else
       }                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     }                 }
   }                 fprintf(ficgp,")");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);               }
   if (popforecast==1) {               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     free_ivector(popage,0,AGESUP);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     free_vector(popeffectif,0,AGESUP);               i=i+ncovmodel;
     free_vector(popcount,0,AGESUP);             }
   }           } /* end k */
   free_imatrix(s,1,maxwav+1,1,n);         } /* end k2 */
   free_vector(weight,1,n);       } /* end jk */
   fclose(ficresf);     } /* end ng */
   /*---------- Health expectancies and variances ------------*/     fclose(ficgp); 
   }  /* end gnuplot */
   strcpy(filerest,"t");  
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {  /*************** Moving average **************/
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
   strcpy(filerese,"e");    double age;
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                             a covariate has 2 modalities */
   }    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
  strcpy(fileresv,"v");      if(mobilav==1) mobilavrange=5; /* default */
   strcat(fileresv,fileres);      else mobilavrange=mobilav;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      for (age=bage; age<=fage; age++)
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        for (i=1; i<=nlstate;i++)
   }          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
   k=0;         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   for(cptcov=1;cptcov<=i1;cptcov++){         we use a 5 terms etc. until the borders are no more concerned. 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      */ 
       k=k+1;      for (mob=3;mob <=mobilavrange;mob=mob+2){
       fprintf(ficrest,"\n#****** ");        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
       for(j=1;j<=cptcoveff;j++)          for (i=1; i<=nlstate;i++){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
       fprintf(ficrest,"******\n");              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
       fprintf(ficreseij,"\n#****** ");                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       for(j=1;j<=cptcoveff;j++)                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                }
       fprintf(ficreseij,"******\n");              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
       fprintf(ficresvij,"\n#****** ");          }
       for(j=1;j<=cptcoveff;j++)        }/* end age */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      }/* end mob */
       fprintf(ficresvij,"******\n");    }else return -1;
     return 0;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  }/* End movingaverage */
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  /************** Forecasting ******************/
       oldm=oldms;savm=savms;  prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    
          int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    int *popage;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
       fprintf(ficrest,"\n");    double *popeffectif,*popcount;
            double ***p3mat;
       hf=1;    double ***mobaverage;
       if (stepm >= YEARM) hf=stepm/YEARM;    char fileresf[FILENAMELENGTH];
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){   agelim=AGESUP;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
         if (popbased==1) {  
           for(i=1; i<=nlstate;i++)    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
             prlim[i][i]=probs[(int)age][i][k];   
         }   
            strcpy(fileresf,"f"); 
         fprintf(ficrest," %.0f",age);    strcat(fileresf,fileres);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    if((ficresf=fopen(fileresf,"w"))==NULL) {
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      printf("Problem with forecast resultfile: %s\n", fileresf);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
           }    }
           epj[nlstate+1] +=epj[j];    printf("Computing forecasting: result on file '%s' \n", fileresf);
         }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
         for(i=1, vepp=0.;i <=nlstate;i++)  
           for(j=1;j <=nlstate;j++)    if (cptcoveff==0) ncodemax[cptcoveff]=1;
             vepp += vareij[i][j][(int)age];  
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    if (mobilav!=0) {
         for(j=1;j <=nlstate;j++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         fprintf(ficrest,"\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }      }
     }    }
   }  
            stepsize=(int) (stepm+YEARM-1)/YEARM;
            if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
  fclose(ficreseij);    
  fclose(ficresvij);    hstepm=1;
   fclose(ficrest);    hstepm=hstepm/stepm; 
   fclose(ficpar);    yp1=modf(dateintmean,&yp);
   free_vector(epj,1,nlstate+1);    anprojmean=yp;
   /*  scanf("%d ",i); */    yp2=modf((yp1*12),&yp);
     mprojmean=yp;
   /*------- Variance limit prevalence------*/      yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
 strcpy(fileresvpl,"vpl");    if(jprojmean==0) jprojmean=1;
   strcat(fileresvpl,fileres);    if(mprojmean==0) jprojmean=1;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
     exit(0);    
   }    for(cptcov=1;cptcov<=i2;cptcov++){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
  k=0;        fprintf(ficresf,"\n#******");
  for(cptcov=1;cptcov<=i1;cptcov++){        for(j=1;j<=cptcoveff;j++) {
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
      k=k+1;        }
      fprintf(ficresvpl,"\n#****** ");        fprintf(ficresf,"******\n");
      for(j=1;j<=cptcoveff;j++)        fprintf(ficresf,"# StartingAge FinalAge");
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
      fprintf(ficresvpl,"******\n");        
              
      varpl=matrix(1,nlstate,(int) bage, (int) fage);        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
      oldm=oldms;savm=savms;          fprintf(ficresf,"\n");
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
    }  
  }          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   fclose(ficresvpl);            nhstepm = nhstepm/hstepm; 
             
   /*---------- End : free ----------------*/            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            oldm=oldms;savm=savms;
              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            for (h=0; h<=nhstepm; h++){
                if (h==(int) (calagedate+YEARM*cpt)) {
                  fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);              } 
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);              for(j=1; j<=nlstate+ndeath;j++) {
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                kk1=0.;kk2=0;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                for(i=1; i<=nlstate;i++) {              
                    if (mobilav==1) 
   free_matrix(matcov,1,npar,1,npar);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   free_vector(delti,1,npar);                  else {
                      kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                  }
                   
   printf("End of Imach\n");                }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                if (h==(int)(calagedate+12*cpt)){
                    fprintf(ficresf," %.3f", kk1);
   /* 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 -----------*/              }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  end:          }
 #ifdef windows        }
  chdir(pathcd);      }
 #endif    }
           
  system("..\\gp37mgw\\wgnuplot graph.plt");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
 #ifdef windows    fclose(ficresf);
   while (z[0] != 'q') {  }
     chdir(pathcd);  /************** Forecasting ******************/
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  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){
     scanf("%s",z);    
     if (z[0] == 'c') system("./imach");    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     else if (z[0] == 'e') {    int *popage;
       chdir(path);    double calagedate, agelim, kk1, kk2;
       system(optionfilehtm);    double *popeffectif,*popcount;
     }    double ***p3mat,***tabpop,***tabpopprev;
     else if (z[0] == 'q') exit(0);    double ***mobaverage;
   }    char filerespop[FILENAMELENGTH];
 #endif  
 }    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     
     
     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;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)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %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) (calagedate+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)(calagedate+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+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedate+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)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %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) (calagedate+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)(calagedate+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,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 mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
   
     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,mproj1,anproj1,jproj2,mproj2,anproj2;
   
     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];
     
     /* 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]));}*/
     
    
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=1; (m<= maxwav); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Should no more exist */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=1; (m<= maxwav); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+mprev1/12.+jprev1/365.;
     dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
     fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
     fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
   
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
     fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f",age );
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Age");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     if((stepm == 1) && (strcmp(model,".")==0)){
       prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
       if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     } 
     else{
       erreur=108;
       printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
       fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     calagedate=-1;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     free_vector(delti,1,npar);
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

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  Added in v.1.67


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