Diff for /imach/src/imach.c between versions 1.20 and 1.57

version 1.20, 2002/02/20 17:22:01 version 1.57, 2002/07/25 07:37:44
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 or quarter trimester,
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    semester or year) is model 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 0.8k, July 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 */
   double jmean; /* Mean space between 2 waves */
 #define TOL 2.0e-4  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define CGOLD 0.3819660  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define ZEPS 1.0e-10  FILE *ficlog;
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 #define GOLD 1.618034  FILE *fichtm; /* Html File */
 #define GLIMIT 100.0  FILE *ficreseij;
 #define TINY 1.0e-20  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 static double maxarg1,maxarg2;  char fileresv[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  FILE  *ficresvpl;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char fileresvpl[FILENAMELENGTH];
    char title[MAXLINE];
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
 static double sqrarg;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  char filelog[FILENAMELENGTH]; /* Log file */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 int imx;  char popfile[FILENAMELENGTH];
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   
 int m,nb;  #define NR_END 1
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define FREE_ARG char*
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define FTOL 1.0e-10
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;  #define NRANSI 
   #define ITMAX 200 
 double *weight;  
 int **s; /* Status */  #define TOL 2.0e-4 
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 double ftolhess; /* Tolerance for computing hessian */  
   #define GOLD 1.618034 
 /**************** split *************************/  #define GLIMIT 100.0 
 static  int split( char *path, char *dirc, char *name )  #define TINY 1.0e-20 
 {  
    char *s;                             /* pointer */  static double maxarg1,maxarg2;
    int  l1, l2;                         /* length counters */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    l1 = strlen( path );                 /* length of path */    
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
    s = strrchr( path, '\\' );           /* find last / */  #define rint(a) floor(a+0.5)
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */  static double sqrarg;
       extern char       *getwd( );  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       if ( getwd( dirc ) == NULL ) {  
 #else  int imx; 
       extern char       *getcwd( );  int stepm;
   /* Stepm, step in month: minimum step interpolation*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  int estepm;
          return( GLOCK_ERROR_GETCWD );  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       }  
       strcpy( name, path );             /* we've got it */  int m,nb;
    } else {                             /* strip direcotry from path */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
       s++;                              /* after this, the filename */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       l2 = strlen( s );                 /* length of filename */  double **pmmij, ***probs;
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  double dateintmean=0;
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  double *weight;
       dirc[l1-l2] = 0;                  /* add zero */  int **s; /* Status */
    }  double *agedc, **covar, idx;
    l1 = strlen( dirc );                 /* length of directory */  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
    return( 0 );                         /* we're done */  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 }  double ftolhess; /* Tolerance for computing hessian */
   
   /**************** split *************************/
 /******************************************/  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 void replace(char *s, char*t)     char *s;                             /* pointer */
 {     int  l1, l2;                         /* length counters */
   int i;  
   int lg=20;     l1 = strlen( path );                 /* length of path */
   i=0;     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   lg=strlen(t);     s= strrchr( path, DIRSEPARATOR );            /* find last / */
   for(i=0; i<= lg; i++) {     if ( s == NULL ) {                   /* no directory, so use current */
     (s[i] = t[i]);       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     if (t[i]== '\\') s[i]='/';         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   }  #if     defined(__bsd__)                /* get current working directory */
 }        extern char       *getwd( );
   
 int nbocc(char *s, char occ)        if ( getwd( dirc ) == NULL ) {
 {  #else
   int i,j=0;        extern char       *getcwd( );
   int lg=20;  
   i=0;        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   lg=strlen(s);  #endif
   for(i=0; i<= lg; i++) {           return( GLOCK_ERROR_GETCWD );
   if  (s[i] == occ ) j++;        }
   }        strcpy( name, path );             /* we've got it */
   return j;     } else {                             /* strip direcotry from path */
 }        s++;                              /* after this, the filename */
         l2 = strlen( s );                 /* length of filename */
 void cutv(char *u,char *v, char*t, char occ)        if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {        strcpy( name, s );                /* save file name */
   int i,lg,j,p=0;        strncpy( dirc, path, l1 - l2 );   /* now the directory */
   i=0;        dirc[l1-l2] = 0;                  /* add zero */
   for(j=0; j<=strlen(t)-1; j++) {     }
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;     l1 = strlen( dirc );                 /* length of directory */
   }  #ifdef windows
      if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   lg=strlen(t);  #else
   for(j=0; j<p; j++) {     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
     (u[j] = t[j]);  #endif
   }     s = strrchr( name, '.' );            /* find last / */
      u[p]='\0';     s++;
      strcpy(ext,s);                       /* save extension */
    for(j=0; j<= lg; j++) {     l1= strlen( name);
     if (j>=(p+1))(v[j-p-1] = t[j]);     l2= strlen( s)+1;
   }     strncpy( finame, name, l1-l2);
 }     finame[l1-l2]= 0;
      return( 0 );                         /* we're done */
 /********************** nrerror ********************/  }
   
 void nrerror(char error_text[])  
 {  /******************************************/
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  void replace(char *s, char*t)
   exit(1);  {
 }    int i;
 /*********************** vector *******************/    int lg=20;
 double *vector(int nl, int nh)    i=0;
 {    lg=strlen(t);
   double *v;    for(i=0; i<= lg; i++) {
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));      (s[i] = t[i]);
   if (!v) nrerror("allocation failure in vector");      if (t[i]== '\\') s[i]='/';
   return v-nl+NR_END;    }
 }  }
   
 /************************ free vector ******************/  int nbocc(char *s, char occ)
 void free_vector(double*v, int nl, int nh)  {
 {    int i,j=0;
   free((FREE_ARG)(v+nl-NR_END));    int lg=20;
 }    i=0;
     lg=strlen(s);
 /************************ivector *******************************/    for(i=0; i<= lg; i++) {
 int *ivector(long nl,long nh)    if  (s[i] == occ ) j++;
 {    }
   int *v;    return j;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  }
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  void cutv(char *u,char *v, char*t, char occ)
 }  {
     /* cuts string t into u and v where u is ended by char occ excluding it
 /******************free ivector **************************/       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 void free_ivector(int *v, long nl, long nh)       gives u="abcedf" and v="ghi2j" */
 {    int i,lg,j,p=0;
   free((FREE_ARG)(v+nl-NR_END));    i=0;
 }    for(j=0; j<=strlen(t)-1; j++) {
       if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 /******************* imatrix *******************************/    }
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    lg=strlen(t);
 {    for(j=0; j<p; j++) {
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;      (u[j] = t[j]);
   int **m;    }
         u[p]='\0';
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));     for(j=0; j<= lg; j++) {
   if (!m) nrerror("allocation failure 1 in matrix()");      if (j>=(p+1))(v[j-p-1] = t[j]);
   m += NR_END;    }
   m -= nrl;  }
    
    /********************** nrerror ********************/
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  void nrerror(char error_text[])
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  {
   m[nrl] += NR_END;    fprintf(stderr,"ERREUR ...\n");
   m[nrl] -= ncl;    fprintf(stderr,"%s\n",error_text);
      exit(1);
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  }
    /*********************** vector *******************/
   /* return pointer to array of pointers to rows */  double *vector(int nl, int nh)
   return m;  {
 }    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 /****************** free_imatrix *************************/    if (!v) nrerror("allocation failure in vector");
 void free_imatrix(m,nrl,nrh,ncl,nch)    return v-nl+NR_END;
       int **m;  }
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  /************************ free vector ******************/
 {  void free_vector(double*v, int nl, int nh)
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  {
   free((FREE_ARG) (m+nrl-NR_END));    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
 /******************* matrix *******************************/  /************************ivector *******************************/
 double **matrix(long nrl, long nrh, long ncl, long nch)  int *ivector(long nl,long nh)
 {  {
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    int *v;
   double **m;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    return v-nl+NR_END;
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   m += NR_END;  
   m -= nrl;  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    free((FREE_ARG)(v+nl-NR_END));
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
   /******************* imatrix *******************************/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   return m;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 }  { 
     long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 /*************************free matrix ************************/    int **m; 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    
 {    /* allocate pointers to rows */ 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   free((FREE_ARG)(m+nrl-NR_END));    if (!m) nrerror("allocation failure 1 in matrix()"); 
 }    m += NR_END; 
     m -= nrl; 
 /******************* ma3x *******************************/    
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    
 {    /* allocate rows and set pointers to them */ 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double ***m;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl] -= ncl; 
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m -= nrl;    
     /* return pointer to array of pointers to rows */ 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    return m; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  } 
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;        int **m;
         long nch,ncl,nrh,nrl; 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));       /* free an int matrix allocated by imatrix() */ 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  { 
   m[nrl][ncl] += NR_END;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   m[nrl][ncl] -= nll;    free((FREE_ARG) (m+nrl-NR_END)); 
   for (j=ncl+1; j<=nch; j++)  } 
     m[nrl][j]=m[nrl][j-1]+nlay;  
    /******************* matrix *******************************/
   for (i=nrl+1; i<=nrh; i++) {  double **matrix(long nrl, long nrh, long ncl, long nch)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  {
     for (j=ncl+1; j<=nch; j++)    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       m[i][j]=m[i][j-1]+nlay;    double **m;
   }  
   return m;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /*************************free ma3x ************************/    m -= nrl;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl] += NR_END;
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /***************** f1dim *************************/    return m;
 extern int ncom;  }
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  /*************************free matrix ************************/
    void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 double f1dim(double x)  {
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int j;    free((FREE_ARG)(m+nrl-NR_END));
   double f;  }
   double *xt;  
    /******************* ma3x *******************************/
   xt=vector(1,ncom);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  {
   f=(*nrfunc)(xt);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   free_vector(xt,1,ncom);    double ***m;
   return f;  
 }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /*****************brent *************************/    m += NR_END;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    m -= nrl;
 {  
   int iter;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double a,b,d,etemp;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double fu,fv,fw,fx;    m[nrl] += NR_END;
   double ftemp;    m[nrl] -= ncl;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    
   a=(ax < cx ? ax : cx);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   b=(ax > cx ? ax : cx);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   x=w=v=bx;    m[nrl][ncl] += NR_END;
   fw=fv=fx=(*f)(x);    m[nrl][ncl] -= nll;
   for (iter=1;iter<=ITMAX;iter++) {    for (j=ncl+1; j<=nch; j++) 
     xm=0.5*(a+b);      m[nrl][j]=m[nrl][j-1]+nlay;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    for (i=nrl+1; i<=nrh; i++) {
     printf(".");fflush(stdout);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 #ifdef DEBUG      for (j=ncl+1; j<=nch; j++) 
     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][j]=m[i][j-1]+nlay;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    }
 #endif    return m;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  }
       *xmin=x;  
       return fx;  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     ftemp=fu;  {
     if (fabs(e) > tol1) {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       r=(x-w)*(fx-fv);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       q=(x-v)*(fx-fw);    free((FREE_ARG)(m+nrl-NR_END));
       p=(x-v)*q-(x-w)*r;  }
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /***************** f1dim *************************/
       q=fabs(q);  extern int ncom; 
       etemp=e;  extern double *pcom,*xicom;
       e=d;  extern double (*nrfunc)(double []); 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))   
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  double f1dim(double x) 
       else {  { 
         d=p/q;    int j; 
         u=x+d;    double f;
         if (u-a < tol2 || b-u < tol2)    double *xt; 
           d=SIGN(tol1,xm-x);   
       }    xt=vector(1,ncom); 
     } else {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    f=(*nrfunc)(xt); 
     }    free_vector(xt,1,ncom); 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    return f; 
     fu=(*f)(u);  } 
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  /*****************brent *************************/
       SHFT(v,w,x,u)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         SHFT(fv,fw,fx,fu)  { 
         } else {    int iter; 
           if (u < x) a=u; else b=u;    double a,b,d,etemp;
           if (fu <= fw || w == x) {    double fu,fv,fw,fx;
             v=w;    double ftemp;
             w=u;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
             fv=fw;    double e=0.0; 
             fw=fu;   
           } else if (fu <= fv || v == x || v == w) {    a=(ax < cx ? ax : cx); 
             v=u;    b=(ax > cx ? ax : cx); 
             fv=fu;    x=w=v=bx; 
           }    fw=fv=fx=(*f)(x); 
         }    for (iter=1;iter<=ITMAX;iter++) { 
   }      xm=0.5*(a+b); 
   nrerror("Too many iterations in brent");      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   *xmin=x;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   return fx;      printf(".");fflush(stdout);
 }      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
 /****************** mnbrak ***********************/      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
             double (*func)(double))  #endif
 {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double ulim,u,r,q, dum;        *xmin=x; 
   double fu;        return fx; 
        } 
   *fa=(*func)(*ax);      ftemp=fu;
   *fb=(*func)(*bx);      if (fabs(e) > tol1) { 
   if (*fb > *fa) {        r=(x-w)*(fx-fv); 
     SHFT(dum,*ax,*bx,dum)        q=(x-v)*(fx-fw); 
       SHFT(dum,*fb,*fa,dum)        p=(x-v)*q-(x-w)*r; 
       }        q=2.0*(q-r); 
   *cx=(*bx)+GOLD*(*bx-*ax);        if (q > 0.0) p = -p; 
   *fc=(*func)(*cx);        q=fabs(q); 
   while (*fb > *fc) {        etemp=e; 
     r=(*bx-*ax)*(*fb-*fc);        e=d; 
     q=(*bx-*cx)*(*fb-*fa);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        else { 
     ulim=(*bx)+GLIMIT*(*cx-*bx);          d=p/q; 
     if ((*bx-u)*(u-*cx) > 0.0) {          u=x+d; 
       fu=(*func)(u);          if (u-a < tol2 || b-u < tol2) 
     } else if ((*cx-u)*(u-ulim) > 0.0) {            d=SIGN(tol1,xm-x); 
       fu=(*func)(u);        } 
       if (fu < *fc) {      } else { 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           SHFT(*fb,*fc,fu,(*func)(u))      } 
           }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      fu=(*f)(u); 
       u=ulim;      if (fu <= fx) { 
       fu=(*func)(u);        if (u >= x) a=x; else b=x; 
     } else {        SHFT(v,w,x,u) 
       u=(*cx)+GOLD*(*cx-*bx);          SHFT(fv,fw,fx,fu) 
       fu=(*func)(u);          } else { 
     }            if (u < x) a=u; else b=u; 
     SHFT(*ax,*bx,*cx,u)            if (fu <= fw || w == x) { 
       SHFT(*fa,*fb,*fc,fu)              v=w; 
       }              w=u; 
 }              fv=fw; 
               fw=fu; 
 /*************** linmin ************************/            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
 int ncom;              fv=fu; 
 double *pcom,*xicom;            } 
 double (*nrfunc)(double []);          } 
      } 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    nrerror("Too many iterations in brent"); 
 {    *xmin=x; 
   double brent(double ax, double bx, double cx,    return fx; 
                double (*f)(double), double tol, double *xmin);  } 
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /****************** mnbrak ***********************/
               double *fc, double (*func)(double));  
   int j;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double xx,xmin,bx,ax;              double (*func)(double)) 
   double fx,fb,fa;  { 
      double ulim,u,r,q, dum;
   ncom=n;    double fu; 
   pcom=vector(1,n);   
   xicom=vector(1,n);    *fa=(*func)(*ax); 
   nrfunc=func;    *fb=(*func)(*bx); 
   for (j=1;j<=n;j++) {    if (*fb > *fa) { 
     pcom[j]=p[j];      SHFT(dum,*ax,*bx,dum) 
     xicom[j]=xi[j];        SHFT(dum,*fb,*fa,dum) 
   }        } 
   ax=0.0;    *cx=(*bx)+GOLD*(*bx-*ax); 
   xx=1.0;    *fc=(*func)(*cx); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    while (*fb > *fc) { 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      r=(*bx-*ax)*(*fb-*fc); 
 #ifdef DEBUG      q=(*bx-*cx)*(*fb-*fa); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 #endif        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   for (j=1;j<=n;j++) {      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     xi[j] *= xmin;      if ((*bx-u)*(u-*cx) > 0.0) { 
     p[j] += xi[j];        fu=(*func)(u); 
   }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   free_vector(xicom,1,n);        fu=(*func)(u); 
   free_vector(pcom,1,n);        if (fu < *fc) { 
 }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
 /*************** powell ************************/            } 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
             double (*func)(double []))        u=ulim; 
 {        fu=(*func)(u); 
   void linmin(double p[], double xi[], int n, double *fret,      } else { 
               double (*func)(double []));        u=(*cx)+GOLD*(*cx-*bx); 
   int i,ibig,j;        fu=(*func)(u); 
   double del,t,*pt,*ptt,*xit;      } 
   double fp,fptt;      SHFT(*ax,*bx,*cx,u) 
   double *xits;        SHFT(*fa,*fb,*fc,fu) 
   pt=vector(1,n);        } 
   ptt=vector(1,n);  } 
   xit=vector(1,n);  
   xits=vector(1,n);  /*************** linmin ************************/
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  int ncom; 
   for (*iter=1;;++(*iter)) {  double *pcom,*xicom;
     fp=(*fret);  double (*nrfunc)(double []); 
     ibig=0;   
     del=0.0;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  { 
     for (i=1;i<=n;i++)    double brent(double ax, double bx, double cx, 
       printf(" %d %.12f",i, p[i]);                 double (*f)(double), double tol, double *xmin); 
     printf("\n");    double f1dim(double x); 
     for (i=1;i<=n;i++) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];                double *fc, double (*func)(double)); 
       fptt=(*fret);    int j; 
 #ifdef DEBUG    double xx,xmin,bx,ax; 
       printf("fret=%lf \n",*fret);    double fx,fb,fa;
 #endif   
       printf("%d",i);fflush(stdout);    ncom=n; 
       linmin(p,xit,n,fret,func);    pcom=vector(1,n); 
       if (fabs(fptt-(*fret)) > del) {    xicom=vector(1,n); 
         del=fabs(fptt-(*fret));    nrfunc=func; 
         ibig=i;    for (j=1;j<=n;j++) { 
       }      pcom[j]=p[j]; 
 #ifdef DEBUG      xicom[j]=xi[j]; 
       printf("%d %.12e",i,(*fret));    } 
       for (j=1;j<=n;j++) {    ax=0.0; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    xx=1.0; 
         printf(" x(%d)=%.12e",j,xit[j]);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       for(j=1;j<=n;j++)  #ifdef DEBUG
         printf(" p=%.12e",p[j]);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       printf("\n");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #endif  #endif
     }    for (j=1;j<=n;j++) { 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      xi[j] *= xmin; 
 #ifdef DEBUG      p[j] += xi[j]; 
       int k[2],l;    } 
       k[0]=1;    free_vector(xicom,1,n); 
       k[1]=-1;    free_vector(pcom,1,n); 
       printf("Max: %.12e",(*func)(p));  } 
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /*************** powell ************************/
       printf("\n");  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for(l=0;l<=1;l++) {              double (*func)(double [])) 
         for (j=1;j<=n;j++) {  { 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    void linmin(double p[], double xi[], int n, double *fret, 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);                double (*func)(double [])); 
         }    int i,ibig,j; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double del,t,*pt,*ptt,*xit;
       }    double fp,fptt;
 #endif    double *xits;
     pt=vector(1,n); 
     ptt=vector(1,n); 
       free_vector(xit,1,n);    xit=vector(1,n); 
       free_vector(xits,1,n);    xits=vector(1,n); 
       free_vector(ptt,1,n);    *fret=(*func)(p); 
       free_vector(pt,1,n);    for (j=1;j<=n;j++) pt[j]=p[j]; 
       return;    for (*iter=1;;++(*iter)) { 
     }      fp=(*fret); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      ibig=0; 
     for (j=1;j<=n;j++) {      del=0.0; 
       ptt[j]=2.0*p[j]-pt[j];      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       xit[j]=p[j]-pt[j];      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       pt[j]=p[j];      for (i=1;i<=n;i++) 
     }        printf(" %d %.12f",i, p[i]);
     fptt=(*func)(ptt);      fprintf(ficlog," %d %.12f",i, p[i]);
     if (fptt < fp) {      printf("\n");
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      fprintf(ficlog,"\n");
       if (t < 0.0) {      for (i=1;i<=n;i++) { 
         linmin(p,xit,n,fret,func);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         for (j=1;j<=n;j++) {        fptt=(*fret); 
           xi[j][ibig]=xi[j][n];  #ifdef DEBUG
           xi[j][n]=xit[j];        printf("fret=%lf \n",*fret);
         }        fprintf(ficlog,"fret=%lf \n",*fret);
 #ifdef DEBUG  #endif
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        printf("%d",i);fflush(stdout);
         for(j=1;j<=n;j++)        fprintf(ficlog,"%d",i);fflush(ficlog);
           printf(" %.12e",xit[j]);        linmin(p,xit,n,fret,func); 
         printf("\n");        if (fabs(fptt-(*fret)) > del) { 
 #endif          del=fabs(fptt-(*fret)); 
       }          ibig=i; 
     }        } 
   }  #ifdef DEBUG
 }        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
 /**** Prevalence limit ****************/        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)          printf(" x(%d)=%.12e",j,xit[j]);
 {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        }
      matrix by transitions matrix until convergence is reached */        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
   int i, ii,j,k;          fprintf(ficlog," p=%.12e",p[j]);
   double min, max, maxmin, maxmax,sumnew=0.;        }
   double **matprod2();        printf("\n");
   double **out, cov[NCOVMAX], **pmij();        fprintf(ficlog,"\n");
   double **newm;  #endif
   double agefin, delaymax=50 ; /* Max number of years to converge */      } 
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   for (ii=1;ii<=nlstate+ndeath;ii++)  #ifdef DEBUG
     for (j=1;j<=nlstate+ndeath;j++){        int k[2],l;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        k[0]=1;
     }        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
    cov[1]=1.;        fprintf(ficlog,"Max: %.12e",(*func)(p));
          for (j=1;j<=n;j++) {
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */          printf(" %.12e",p[j]);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){          fprintf(ficlog," %.12e",p[j]);
     newm=savm;        }
     /* Covariates have to be included here again */        printf("\n");
      cov[2]=agefin;        fprintf(ficlog,"\n");
          for(l=0;l<=1;l++) {
       for (k=1; k<=cptcovn;k++) {          for (j=1;j<=n;j++) {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            ptt[j]=p[j]+(p[j]-pt[j])*k[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]);*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for (k=1; k<=cptcovage;k++)          }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for (k=1; k<=cptcovprod;k++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        }
   #endif
       /*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]);*/  
         free_vector(xit,1,n); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
     savm=oldm;        free_vector(pt,1,n); 
     oldm=newm;        return; 
     maxmax=0.;      } 
     for(j=1;j<=nlstate;j++){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       min=1.;      for (j=1;j<=n;j++) { 
       max=0.;        ptt[j]=2.0*p[j]-pt[j]; 
       for(i=1; i<=nlstate; i++) {        xit[j]=p[j]-pt[j]; 
         sumnew=0;        pt[j]=p[j]; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      } 
         prlim[i][j]= newm[i][j]/(1-sumnew);      fptt=(*func)(ptt); 
         max=FMAX(max,prlim[i][j]);      if (fptt < fp) { 
         min=FMIN(min,prlim[i][j]);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       }        if (t < 0.0) { 
       maxmin=max-min;          linmin(p,xit,n,fret,func); 
       maxmax=FMAX(maxmax,maxmin);          for (j=1;j<=n;j++) { 
     }            xi[j][ibig]=xi[j][n]; 
     if(maxmax < ftolpl){            xi[j][n]=xit[j]; 
       return prlim;          }
     }  #ifdef DEBUG
   }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
 /*************** transition probabilities ***************/            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          }
 {          printf("\n");
   double s1, s2;          fprintf(ficlog,"\n");
   /*double t34;*/  #endif
   int i,j,j1, nc, ii, jj;        }
       } 
     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];*/  /**** Prevalence limit (stable prevalence)  ****************/
         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);*/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       }  {
       ps[i][j]=s2;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/       matrix by transitions matrix until convergence is reached */
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){    int i, ii,j,k;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double min, max, maxmin, maxmax,sumnew=0.;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double **matprod2();
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    double **out, cov[NCOVMAX], **pmij();
       }    double **newm;
       ps[i][j]=(s2);    double agefin, delaymax=50 ; /* Max number of years to converge */
     }  
   }    for (ii=1;ii<=nlstate+ndeath;ii++)
     /*ps[3][2]=1;*/      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<= nlstate; i++){      }
      s1=0;  
     for(j=1; j<i; j++)     cov[1]=1.;
       s1+=exp(ps[i][j]);   
     for(j=i+1; j<=nlstate+ndeath; j++)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       s1+=exp(ps[i][j]);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     ps[i][i]=1./(s1+1.);      newm=savm;
     for(j=1; j<i; j++)      /* Covariates have to be included here again */
       ps[i][j]= exp(ps[i][j])*ps[i][i];       cov[2]=agefin;
     for(j=i+1; j<=nlstate+ndeath; j++)    
       ps[i][j]= exp(ps[i][j])*ps[i][i];        for (k=1; k<=cptcovn;k++) {
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   } /* end i */          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(jj=1; jj<= nlstate+ndeath; jj++){        for (k=1; k<=cptcovprod;k++)
       ps[ii][jj]=0;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       ps[ii][ii]=1;  
     }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){      savm=oldm;
      printf("%lf ",ps[ii][jj]);      oldm=newm;
    }      maxmax=0.;
     printf("\n ");      for(j=1;j<=nlstate;j++){
     }        min=1.;
     printf("\n ");printf("%lf ",cov[2]);*/        max=0.;
 /*        for(i=1; i<=nlstate; i++) {
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          sumnew=0;
   goto end;*/          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     return ps;          prlim[i][j]= newm[i][j]/(1-sumnew);
 }          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
 /**************** Product of 2 matrices ******************/        }
         maxmin=max-min;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        maxmax=FMAX(maxmax,maxmin);
 {      }
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      if(maxmax < ftolpl){
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        return prlim;
   /* in, b, out are matrice of pointers which should have been initialized      }
      before: only the contents of out is modified. The function returns    }
      a pointer to pointers identical to out */  }
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /*************** transition probabilities ***************/ 
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         out[i][k] +=in[i][j]*b[j][k];  {
     double s1, s2;
   return out;    /*double t34;*/
 }    int i,j,j1, nc, ii, jj;
   
       for(i=1; i<= nlstate; i++){
 /************* Higher Matrix Product ***************/      for(j=1; j<i;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )          /*s2 += param[i][j][nc]*cov[nc];*/
 {          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
      duration (i.e. until        }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        ps[i][j]=s2;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
      (typically every 2 years instead of every month which is too big).      }
      Model is determined by parameters x and covariates have to be      for(j=i+1; j<=nlstate+ndeath;j++){
      included manually here.        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];
      */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
         }
   int i, j, d, h, k;        ps[i][j]=s2;
   double **out, cov[NCOVMAX];      }
   double **newm;    }
       /*ps[3][2]=1;*/
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)    for(i=1; i<= nlstate; i++){
     for (j=1;j<=nlstate+ndeath;j++){       s1=0;
       oldm[i][j]=(i==j ? 1.0 : 0.0);      for(j=1; j<i; j++)
       po[i][j][0]=(i==j ? 1.0 : 0.0);        s1+=exp(ps[i][j]);
     }      for(j=i+1; j<=nlstate+ndeath; j++)
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        s1+=exp(ps[i][j]);
   for(h=1; h <=nhstepm; h++){      ps[i][i]=1./(s1+1.);
     for(d=1; d <=hstepm; d++){      for(j=1; j<i; j++)
       newm=savm;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* Covariates have to be included here again */      for(j=i+1; j<=nlstate+ndeath; j++)
       cov[1]=1.;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    } /* end i */
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for (k=1; k<=cptcovprod;k++)      for(jj=1; jj<= nlstate+ndeath; jj++){
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        ps[ii][jj]=0;
         ps[ii][ii]=1;
       }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    }
       /*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));    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       savm=oldm;      for(jj=1; jj<= nlstate+ndeath; jj++){
       oldm=newm;       printf("%lf ",ps[ii][jj]);
     }     }
     for(i=1; i<=nlstate+ndeath; i++)      printf("\n ");
       for(j=1;j<=nlstate+ndeath;j++) {      }
         po[i][j][h]=newm[i][j];      printf("\n ");printf("%lf ",cov[2]);*/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /*
          */    for(i=1; i<= npar; i++) printf("%f ",x[i]);
       }    goto end;*/
   } /* end h */      return ps;
   return po;  }
 }  
   /**************** Product of 2 matrices ******************/
   
 /*************** log-likelihood *************/  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 double func( double *x)  {
 {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   int i, ii, j, k, mi, d, kk;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    /* in, b, out are matrice of pointers which should have been initialized 
   double **out;       before: only the contents of out is modified. The function returns
   double sw; /* Sum of weights */       a pointer to pointers identical to out */
   double lli; /* Individual log likelihood */    long i, j, k;
   long ipmx;    for(i=nrl; i<= nrh; i++)
   /*extern weight */      for(k=ncolol; k<=ncoloh; k++)
   /* We are differentiating ll according to initial status */        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          out[i][k] +=in[i][j]*b[j][k];
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);    return out;
   */  }
   cov[1]=1.;  
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /************* Higher Matrix Product ***************/
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for(mi=1; mi<= wav[i]-1; mi++){  {
       for (ii=1;ii<=nlstate+ndeath;ii++)    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);       duration (i.e. until
       for(d=0; d<dh[mi][i]; d++){       age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
         newm=savm;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;       (typically every 2 years instead of every month which is too big).
         for (kk=1; kk<=cptcovage;kk++) {       Model is determined by parameters x and covariates have to be 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];       included manually here. 
         }  
               */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    int i, j, d, h, k;
         savm=oldm;    double **out, cov[NCOVMAX];
         oldm=newm;    double **newm;
          
            /* Hstepm could be zero and should return the unit matrix */
       } /* end mult */    for (i=1;i<=nlstate+ndeath;i++)
            for (j=1;j<=nlstate+ndeath;j++){
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        oldm[i][j]=(i==j ? 1.0 : 0.0);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        po[i][j][0]=(i==j ? 1.0 : 0.0);
       ipmx +=1;      }
       sw += weight[i];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    for(h=1; h <=nhstepm; h++){
     } /* end of wave */      for(d=1; d <=hstepm; d++){
   } /* end of individual */        newm=savm;
         /* Covariates have to be included here again */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        cov[1]=1.;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   return -l;        for (k=1; k<=cptcovage;k++)
 }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 /*********** Maximum Likelihood Estimation ***************/  
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   int i,j, iter;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double **xi,*delti;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   double fret;        savm=oldm;
   xi=matrix(1,npar,1,npar);        oldm=newm;
   for (i=1;i<=npar;i++)      }
     for (j=1;j<=npar;j++)      for(i=1; i<=nlstate+ndeath; i++)
       xi[i][j]=(i==j ? 1.0 : 0.0);        for(j=1;j<=nlstate+ndeath;j++) {
   printf("Powell\n");          po[i][j][h]=newm[i][j];
   powell(p,xi,npar,ftol,&iter,&fret,func);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
            */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    } /* end h */
     return po;
 }  }
   
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*************** log-likelihood *************/
 {  double func( double *x)
   double  **a,**y,*x,pd;  {
   double **hess;    int i, ii, j, k, mi, d, kk;
   int i, j,jk;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   int *indx;    double **out;
     double sw; /* Sum of weights */
   double hessii(double p[], double delta, int theta, double delti[]);    double lli; /* Individual log likelihood */
   double hessij(double p[], double delti[], int i, int j);    long ipmx;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    /*extern weight */
   void ludcmp(double **a, int npar, int *indx, double *d) ;    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   hess=matrix(1,npar,1,npar);    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   printf("\nCalculation of the hessian matrix. Wait...\n");    */
   for (i=1;i<=npar;i++){    cov[1]=1.;
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);    for(k=1; k<=nlstate; k++) ll[k]=0.;
     /*printf(" %f ",p[i]);*/    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     /*printf(" %lf ",hess[i][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++)
   for (i=1;i<=npar;i++) {          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=1;j<=npar;j++)  {        for(d=0; d<dh[mi][i]; d++){
       if (j>i) {          newm=savm;
         printf(".%d%d",i,j);fflush(stdout);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         hess[i][j]=hessij(p,delti,i,j);          for (kk=1; kk<=cptcovage;kk++) {
         hess[j][i]=hess[i][j];                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         /*printf(" %lf ",hess[i][j]);*/          }
       }          
     }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("\n");          savm=oldm;
           oldm=newm;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          
            
   a=matrix(1,npar,1,npar);        } /* end mult */
   y=matrix(1,npar,1,npar);        
   x=vector(1,npar);        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
   indx=ivector(1,npar);        /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
   for (i=1;i<=npar;i++)        ipmx +=1;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        sw += weight[i];
   ludcmp(a,npar,indx,&pd);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       } /* end of wave */
   for (j=1;j<=npar;j++) {    } /* end of individual */
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     lubksb(a,npar,indx,x);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for (i=1;i<=npar;i++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       matcov[i][j]=x[i];    return -l;
     }  }
   }  
   
   printf("\n#Hessian matrix#\n");  /*********** Maximum Likelihood Estimation ***************/
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       printf("%.3e ",hess[i][j]);  {
     }    int i,j, iter;
     printf("\n");    double **xi,*delti;
   }    double fret;
     xi=matrix(1,npar,1,npar);
   /* Recompute Inverse */    for (i=1;i<=npar;i++)
   for (i=1;i<=npar;i++)      for (j=1;j<=npar;j++)
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        xi[i][j]=(i==j ? 1.0 : 0.0);
   ludcmp(a,npar,indx,&pd);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     powell(p,xi,npar,ftol,&iter,&fret,func);
   /*  printf("\n#Hessian matrix recomputed#\n");  
      printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   for (j=1;j<=npar;j++) {    fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for (i=1;i<=npar;i++) x[i]=0;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     x[j]=1;  
     lubksb(a,npar,indx,x);  }
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  /**** Computes Hessian and covariance matrix ***/
       printf("%.3e ",y[i][j]);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     }  {
     printf("\n");    double  **a,**y,*x,pd;
   }    double **hess;
   */    int i, j,jk;
     int *indx;
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);    double hessii(double p[], double delta, int theta, double delti[]);
   free_vector(x,1,npar);    double hessij(double p[], double delti[], int i, int j);
   free_ivector(indx,1,npar);    void lubksb(double **a, int npar, int *indx, double b[]) ;
   free_matrix(hess,1,npar,1,npar);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   
     hess=matrix(1,npar,1,npar);
 }  
     printf("\nCalculation of the hessian matrix. Wait...\n");
 /*************** hessian matrix ****************/    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 double hessii( double x[], double delta, int theta, double delti[])    for (i=1;i<=npar;i++){
 {      printf("%d",i);fflush(stdout);
   int i;      fprintf(ficlog,"%d",i);fflush(ficlog);
   int l=1, lmax=20;      hess[i][i]=hessii(p,ftolhess,i,delti);
   double k1,k2;      /*printf(" %f ",p[i]);*/
   double p2[NPARMAX+1];      /*printf(" %lf ",hess[i][i]);*/
   double res;    }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    
   double fx;    for (i=1;i<=npar;i++) {
   int k=0,kmax=10;      for (j=1;j<=npar;j++)  {
   double l1;        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
   fx=func(x);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   for (i=1;i<=npar;i++) p2[i]=x[i];          hess[i][j]=hessij(p,delti,i,j);
   for(l=0 ; l <=lmax; l++){          hess[j][i]=hess[i][j];    
     l1=pow(10,l);          /*printf(" %lf ",hess[i][j]);*/
     delts=delt;        }
     for(k=1 ; k <kmax; k=k+1){      }
       delt = delta*(l1*k);    }
       p2[theta]=x[theta] +delt;    printf("\n");
       k1=func(p2)-fx;    fprintf(ficlog,"\n");
       p2[theta]=x[theta]-delt;  
       k2=func(p2)-fx;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       /*res= (k1-2.0*fx+k2)/delt/delt; */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    
          a=matrix(1,npar,1,npar);
 #ifdef DEBUG    y=matrix(1,npar,1,npar);
       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);    x=vector(1,npar);
 #endif    indx=ivector(1,npar);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    for (i=1;i<=npar;i++)
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         k=kmax;    ludcmp(a,npar,indx,&pd);
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    for (j=1;j<=npar;j++) {
         k=kmax; l=lmax*10.;      for (i=1;i<=npar;i++) x[i]=0;
       }      x[j]=1;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      lubksb(a,npar,indx,x);
         delts=delt;      for (i=1;i<=npar;i++){ 
       }        matcov[i][j]=x[i];
     }      }
   }    }
   delti[theta]=delts;  
   return res;    printf("\n#Hessian matrix#\n");
      fprintf(ficlog,"\n#Hessian matrix#\n");
 }    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
 double hessij( double x[], double delti[], int thetai,int thetaj)        printf("%.3e ",hess[i][j]);
 {        fprintf(ficlog,"%.3e ",hess[i][j]);
   int i;      }
   int l=1, l1, lmax=20;      printf("\n");
   double k1,k2,k3,k4,res,fx;      fprintf(ficlog,"\n");
   double p2[NPARMAX+1];    }
   int k;  
     /* Recompute Inverse */
   fx=func(x);    for (i=1;i<=npar;i++)
   for (k=1; k<=2; k++) {      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     for (i=1;i<=npar;i++) p2[i]=x[i];    ludcmp(a,npar,indx,&pd);
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    /*  printf("\n#Hessian matrix recomputed#\n");
     k1=func(p2)-fx;  
      for (j=1;j<=npar;j++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;      for (i=1;i<=npar;i++) x[i]=0;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      x[j]=1;
     k2=func(p2)-fx;      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
     p2[thetai]=x[thetai]-delti[thetai]/k;        y[i][j]=x[i];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        printf("%.3e ",y[i][j]);
     k3=func(p2)-fx;        fprintf(ficlog,"%.3e ",y[i][j]);
        }
     p2[thetai]=x[thetai]-delti[thetai]/k;      printf("\n");
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      fprintf(ficlog,"\n");
     k4=func(p2)-fx;    }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    */
 #ifdef DEBUG  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    free_matrix(a,1,npar,1,npar);
 #endif    free_matrix(y,1,npar,1,npar);
   }    free_vector(x,1,npar);
   return res;    free_ivector(indx,1,npar);
 }    free_matrix(hess,1,npar,1,npar);
   
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)  }
 {  
   int i,imax,j,k;  /*************** hessian matrix ****************/
   double big,dum,sum,temp;  double hessii( double x[], double delta, int theta, double delti[])
   double *vv;  {
      int i;
   vv=vector(1,n);    int l=1, lmax=20;
   *d=1.0;    double k1,k2;
   for (i=1;i<=n;i++) {    double p2[NPARMAX+1];
     big=0.0;    double res;
     for (j=1;j<=n;j++)    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       if ((temp=fabs(a[i][j])) > big) big=temp;    double fx;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    int k=0,kmax=10;
     vv[i]=1.0/big;    double l1;
   }  
   for (j=1;j<=n;j++) {    fx=func(x);
     for (i=1;i<j;i++) {    for (i=1;i<=npar;i++) p2[i]=x[i];
       sum=a[i][j];    for(l=0 ; l <=lmax; l++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      l1=pow(10,l);
       a[i][j]=sum;      delts=delt;
     }      for(k=1 ; k <kmax; k=k+1){
     big=0.0;        delt = delta*(l1*k);
     for (i=j;i<=n;i++) {        p2[theta]=x[theta] +delt;
       sum=a[i][j];        k1=func(p2)-fx;
       for (k=1;k<j;k++)        p2[theta]=x[theta]-delt;
         sum -= a[i][k]*a[k][j];        k2=func(p2)-fx;
       a[i][j]=sum;        /*res= (k1-2.0*fx+k2)/delt/delt; */
       if ( (dum=vv[i]*fabs(sum)) >= big) {        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         big=dum;        
         imax=i;  #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);
     if (j != imax) {  #endif
       for (k=1;k<=n;k++) {        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         dum=a[imax][k];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         a[imax][k]=a[j][k];          k=kmax;
         a[j][k]=dum;        }
       }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       *d = -(*d);          k=kmax; l=lmax*10.;
       vv[imax]=vv[j];        }
     }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     indx[j]=imax;          delts=delt;
     if (a[j][j] == 0.0) a[j][j]=TINY;        }
     if (j != n) {      }
       dum=1.0/(a[j][j]);    }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    delti[theta]=delts;
     }    return res; 
   }    
   free_vector(vv,1,n);  /* Doesn't work */  }
 ;  
 }  double hessij( double x[], double delti[], int thetai,int thetaj)
   {
 void lubksb(double **a, int n, int *indx, double b[])    int i;
 {    int l=1, l1, lmax=20;
   int i,ii=0,ip,j;    double k1,k2,k3,k4,res,fx;
   double sum;    double p2[NPARMAX+1];
      int k;
   for (i=1;i<=n;i++) {  
     ip=indx[i];    fx=func(x);
     sum=b[ip];    for (k=1; k<=2; k++) {
     b[ip]=b[i];      for (i=1;i<=npar;i++) p2[i]=x[i];
     if (ii)      p2[thetai]=x[thetai]+delti[thetai]/k;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     else if (sum) ii=i;      k1=func(p2)-fx;
     b[i]=sum;    
   }      p2[thetai]=x[thetai]+delti[thetai]/k;
   for (i=n;i>=1;i--) {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     sum=b[i];      k2=func(p2)-fx;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    
     b[i]=sum/a[i][i];      p2[thetai]=x[thetai]-delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 }      k3=func(p2)-fx;
     
 /************ Frequencies ********************/      p2[thetai]=x[thetai]-delti[thetai]/k;
 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)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 {  /* Some frequencies */      k4=func(p2)-fx;
        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  #ifdef DEBUG
   double ***freq; /* Frequencies */      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);
   double *pp;      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);
   double pos, k2, dateintsum=0,k2cpt=0;  #endif
   FILE *ficresp;    }
   char fileresp[FILENAMELENGTH];    return res;
   }
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  /************** Inverse of matrix **************/
   strcpy(fileresp,"p");  void ludcmp(double **a, int n, int *indx, double *d) 
   strcat(fileresp,fileres);  { 
   if((ficresp=fopen(fileresp,"w"))==NULL) {    int i,imax,j,k; 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double big,dum,sum,temp; 
     exit(0);    double *vv; 
   }   
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    vv=vector(1,n); 
   j1=0;    *d=1.0; 
     for (i=1;i<=n;i++) { 
   j=cptcoveff;      big=0.0; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
   for(k1=1; k1<=j;k1++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
    for(i1=1; i1<=ncodemax[k1];i1++){      vv[i]=1.0/big; 
        j1++;    } 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    for (j=1;j<=n;j++) { 
          scanf("%d", i);*/      for (i=1;i<j;i++) { 
         for (i=-1; i<=nlstate+ndeath; i++)          sum=a[i][j]; 
          for (jk=-1; jk<=nlstate+ndeath; jk++)          for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
            for(m=agemin; m <= agemax+3; m++)        a[i][j]=sum; 
              freq[i][jk][m]=0;      } 
       big=0.0; 
         dateintsum=0;      for (i=j;i<=n;i++) { 
         k2cpt=0;        sum=a[i][j]; 
        for (i=1; i<=imx; i++) {        for (k=1;k<j;k++) 
          bool=1;          sum -= a[i][k]*a[k][j]; 
          if  (cptcovn>0) {        a[i][j]=sum; 
            for (z1=1; z1<=cptcoveff; z1++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          big=dum; 
                bool=0;          imax=i; 
          }        } 
          if (bool==1) {      } 
            for(m=firstpass; m<=lastpass; m++){      if (j != imax) { 
              k2=anint[m][i]+(mint[m][i]/12.);        for (k=1;k<=n;k++) { 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {          dum=a[imax][k]; 
                if(agev[m][i]==0) agev[m][i]=agemax+1;          a[imax][k]=a[j][k]; 
                if(agev[m][i]==1) agev[m][i]=agemax+2;          a[j][k]=dum; 
                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];        *d = -(*d); 
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        vv[imax]=vv[j]; 
                  dateintsum=dateintsum+k2;      } 
                  k2cpt++;      indx[j]=imax; 
                }      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
              }        dum=1.0/(a[j][j]); 
            }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
          }      } 
        }    } 
         if  (cptcovn>0) {    free_vector(vv,1,n);  /* Doesn't work */
          fprintf(ficresp, "\n#********** Variable ");  ;
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  } 
        fprintf(ficresp, "**********\n#");  
         }  void lubksb(double **a, int n, int *indx, double b[]) 
        for(i=1; i<=nlstate;i++)  { 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    int i,ii=0,ip,j; 
        fprintf(ficresp, "\n");    double sum; 
           
   for(i=(int)agemin; i <= (int)agemax+3; i++){    for (i=1;i<=n;i++) { 
     if(i==(int)agemax+3)      ip=indx[i]; 
       printf("Total");      sum=b[ip]; 
     else      b[ip]=b[i]; 
       printf("Age %d", i);      if (ii) 
     for(jk=1; jk <=nlstate ; jk++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      else if (sum) ii=i; 
         pp[jk] += freq[jk][m][i];      b[i]=sum; 
     }    } 
     for(jk=1; jk <=nlstate ; jk++){    for (i=n;i>=1;i--) { 
       for(m=-1, pos=0; m <=0 ; m++)      sum=b[i]; 
         pos += freq[jk][m][i];      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       if(pp[jk]>=1.e-10)      b[i]=sum/a[i][i]; 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    } 
       else  } 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
     }  /************ 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,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
      for(jk=1; jk <=nlstate ; jk++){  {  /* Some frequencies */
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    
         pp[jk] += freq[jk][m][i];    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
      }    int first;
     double ***freq; /* Frequencies */
     for(jk=1,pos=0; jk <=nlstate ; jk++)    double *pp;
       pos += pp[jk];    double pos, k2, dateintsum=0,k2cpt=0;
     for(jk=1; jk <=nlstate ; jk++){    FILE *ficresp;
       if(pos>=1.e-5)    char fileresp[FILENAMELENGTH];
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    
       else    pp=vector(1,nlstate);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if( i <= (int) agemax){    strcpy(fileresp,"p");
         if(pos>=1.e-5){    strcat(fileresp,fileres);
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    if((ficresp=fopen(fileresp,"w"))==NULL) {
           probs[i][jk][j1]= pp[jk]/pos;      printf("Problem with prevalence resultfile: %s\n", fileresp);
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         }      exit(0);
       else    }
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
       }    j1=0;
     }    
     for(jk=-1; jk <=nlstate+ndeath; jk++)    j=cptcoveff;
       for(m=-1; m <=nlstate+ndeath; m++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)    first=1;
       fprintf(ficresp,"\n");  
     printf("\n");    for(k1=1; k1<=j;k1++){
     }      for(i1=1; i1<=ncodemax[k1];i1++){
     }        j1++;
  }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   dateintmean=dateintsum/k2cpt;          scanf("%d", i);*/
          for (i=-1; i<=nlstate+ndeath; i++)  
   fclose(ficresp);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            for(m=agemin; m <= agemax+3; m++)
   free_vector(pp,1,nlstate);              freq[i][jk][m]=0;
         
   /* End of Freq */        dateintsum=0;
 }        k2cpt=0;
         for (i=1; i<=imx; i++) {
 /************ Prevalence ********************/          bool=1;
 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)          if  (cptcovn>0) {
 {  /* Some frequencies */            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;                bool=0;
   double ***freq; /* Frequencies */          }
   double *pp;          if (bool==1) {
   double pos, k2;            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
   pp=vector(1,nlstate);              if ((k2>=dateprev1) && (k2<=dateprev2)) {
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);                if(agev[m][i]==0) agev[m][i]=agemax+1;
                  if(agev[m][i]==1) agev[m][i]=agemax+2;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);                if (m<lastpass) {
   j1=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];
   j=cptcoveff;                }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}                
                  if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
  for(k1=1; k1<=j;k1++){                  dateintsum=dateintsum+k2;
     for(i1=1; i1<=ncodemax[k1];i1++){                  k2cpt++;
       j1++;                }
                }
       for (i=-1; i<=nlstate+ndeath; i++)              }
         for (jk=-1; jk<=nlstate+ndeath; jk++)            }
           for(m=agemin; m <= agemax+3; m++)        }
             freq[i][jk][m]=0;         
              fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
       for (i=1; i<=imx; i++) {  
         bool=1;        if  (cptcovn>0) {
         if  (cptcovn>0) {          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          fprintf(ficresp, "**********\n#");
               bool=0;        }
         }        for(i=1; i<=nlstate;i++) 
         if (bool==1) {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
           for(m=firstpass; m<=lastpass; m++){        fprintf(ficresp, "\n");
             k2=anint[m][i]+(mint[m][i]/12.);        
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(i=(int)agemin; i <= (int)agemax+3; i++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;          if(i==(int)agemax+3){
               if(agev[m][i]==1) agev[m][i]=agemax+2;            fprintf(ficlog,"Total");
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          }else{
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];              if(first==1){
             }              first=0;
           }              printf("See log file for details...\n");
         }            }
       }            fprintf(ficlog,"Age %d", i);
                }
         for(i=(int)agemin; i <= (int)agemax+3; i++){          for(jk=1; jk <=nlstate ; jk++){
           for(jk=1; jk <=nlstate ; jk++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              pp[jk] += freq[jk][m][i]; 
               pp[jk] += freq[jk][m][i];          }
           }          for(jk=1; jk <=nlstate ; jk++){
           for(jk=1; jk <=nlstate ; jk++){            for(m=-1, pos=0; m <=0 ; m++)
             for(m=-1, pos=0; m <=0 ; m++)              pos += freq[jk][m][i];
             pos += freq[jk][m][i];            if(pp[jk]>=1.e-10){
         }              if(first==1){
                      printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
          for(jk=1; jk <=nlstate ; jk++){              }
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              pp[jk] += freq[jk][m][i];            }else{
          }              if(first==1)
                          printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
          for(jk=1; jk <=nlstate ; jk++){                    }
            if( i <= (int) agemax){  
              if(pos>=1.e-5){          for(jk=1; jk <=nlstate ; jk++){
                probs[i][jk][j1]= pp[jk]/pos;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
              }              pp[jk] += freq[jk][m][i];
            }          }
          }  
                    for(jk=1,pos=0; jk <=nlstate ; jk++)
         }            pos += pp[jk];
     }          for(jk=1; jk <=nlstate ; jk++){
   }            if(pos>=1.e-5){
                if(first==1)
                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   free_vector(pp,1,nlstate);            }else{
                if(first==1)
 }  /* End of Freq */                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 /************* Waves Concatenation ***************/            }
             if( i <= (int) agemax){
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)              if(pos>=1.e-5){
 {                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.                probs[i][jk][j1]= pp[jk]/pos;
      Death is a valid wave (if date is known).                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i              }
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]              else
      and mw[mi+1][i]. dh depends on stepm.                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
      */            }
           }
   int i, mi, m;          
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          for(jk=-1; jk <=nlstate+ndeath; jk++)
      double sum=0., jmean=0.;*/            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
   int j, k=0,jk, ju, jl;              if(first==1)
   double sum=0.;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   jmin=1e+5;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   jmax=-1;              }
   jmean=0.;          if(i <= (int) agemax)
   for(i=1; i<=imx; i++){            fprintf(ficresp,"\n");
     mi=0;          if(first==1)
     m=firstpass;            printf("Others in log...\n");
     while(s[m][i] <= nlstate){          fprintf(ficlog,"\n");
       if(s[m][i]>=1)        }
         mw[++mi][i]=m;      }
       if(m >=lastpass)    }
         break;    dateintmean=dateintsum/k2cpt; 
       else   
         m++;    fclose(ficresp);
     }/* end while */    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     if (s[m][i] > nlstate){    free_vector(pp,1,nlstate);
       mi++;     /* Death is another wave */    
       /* if(mi==0)  never been interviewed correctly before death */    /* End of Freq */
          /* Only death is a correct wave */  }
       mw[mi][i]=m;  
     }  /************ Prevalence ********************/
   void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
     wav[i]=mi;  {  /* Some frequencies */
     if(mi==0)   
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   }    double ***freq; /* Frequencies */
     double *pp;
   for(i=1; i<=imx; i++){    double pos, k2;
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)    pp=vector(1,nlstate);
         dh[mi][i]=1;    
       else{    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
         if (s[mw[mi+1][i]][i] > nlstate) {    j1=0;
           if (agedc[i] < 2*AGESUP) {    
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    j=cptcoveff;
           if(j==0) j=1;  /* Survives at least one month after exam */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           k=k+1;    
           if (j >= jmax) jmax=j;    for(k1=1; k1<=j;k1++){
           if (j <= jmin) jmin=j;      for(i1=1; i1<=ncodemax[k1];i1++){
           sum=sum+j;        j1++;
           /* if (j<10) printf("j=%d num=%d ",j,i); */        
           }        for (i=-1; i<=nlstate+ndeath; i++)  
         }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         else{            for(m=agemin; m <= agemax+3; m++)
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              freq[i][jk][m]=0;
           k=k+1;       
           if (j >= jmax) jmax=j;        for (i=1; i<=imx; i++) {
           else if (j <= jmin)jmin=j;          bool=1;
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          if  (cptcovn>0) {
           sum=sum+j;            for (z1=1; z1<=cptcoveff; z1++) 
         }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         jk= j/stepm;                bool=0;
         jl= j -jk*stepm;          } 
         ju= j -(jk+1)*stepm;          if (bool==1) { 
         if(jl <= -ju)            for(m=firstpass; m<=lastpass; m++){
           dh[mi][i]=jk;              k2=anint[m][i]+(mint[m][i]/12.);
         else              if ((k2>=dateprev1) && (k2<=dateprev2)) {
           dh[mi][i]=jk+1;                if(agev[m][i]==0) agev[m][i]=agemax+1;
         if(dh[mi][i]==0)                if(agev[m][i]==1) agev[m][i]=agemax+2;
           dh[mi][i]=1; /* At least one step */                if (m<lastpass) {
       }                  if (calagedate>0) 
     }                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
   }                  else
   jmean=sum/k;                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
  }                }
 /*********** Tricode ****************************/              }
 void tricode(int *Tvar, int **nbcode, int imx)            }
 {          }
   int Ndum[20],ij=1, k, j, i;        }
   int cptcode=0;        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
   cptcoveff=0;          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   for (k=0; k<19; k++) Ndum[k]=0;              pp[jk] += freq[jk][m][i]; 
   for (k=1; k<=7; k++) ncodemax[k]=0;          }
           for(jk=1; jk <=nlstate ; jk++){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            for(m=-1, pos=0; m <=0 ; m++)
     for (i=1; i<=imx; i++) {              pos += freq[jk][m][i];
       ij=(int)(covar[Tvar[j]][i]);          }
       Ndum[ij]++;          
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          for(jk=1; jk <=nlstate ; jk++){
       if (ij > cptcode) cptcode=ij;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     }              pp[jk] += freq[jk][m][i];
           }
     for (i=0; i<=cptcode; i++) {          
       if(Ndum[i]!=0) ncodemax[j]++;          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
     }          
     ij=1;          for(jk=1; jk <=nlstate ; jk++){    
             if( i <= (int) agemax){
               if(pos>=1.e-5){
     for (i=1; i<=ncodemax[j]; i++) {                probs[i][jk][j1]= pp[jk]/pos;
       for (k=0; k<=19; k++) {              }
         if (Ndum[k] != 0) {            }
           nbcode[Tvar[j]][ij]=k;          }/* end jk */
           ij++;        }/* end i */
         }      } /* end i1 */
         if (ij > ncodemax[j]) break;    } /* end k1 */
       }    
     }    
   }      free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     free_vector(pp,1,nlstate);
  for (k=0; k<19; k++) Ndum[k]=0;    
   }  /* End of Freq */
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];  /************* Waves Concatenation ***************/
       Ndum[ij]++;  
     }  void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   {
  ij=1;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
  for (i=1; i<=10; i++) {       Death is a valid wave (if date is known).
    if((Ndum[i]!=0) && (i<=ncov)){       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      Tvaraff[ij]=i;       dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
      ij++;       and mw[mi+1][i]. dh depends on stepm.
    }       */
  }  
      int i, mi, m;
     cptcoveff=ij-1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 }       double sum=0., jmean=0.;*/
     int first;
 /*********** Health Expectancies ****************/    int j, k=0,jk, ju, jl;
     double sum=0.;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    first=0;
 {    jmin=1e+5;
   /* Health expectancies */    jmax=-1;
   int i, j, nhstepm, hstepm, h;    jmean=0.;
   double age, agelim,hf;    for(i=1; i<=imx; i++){
   double ***p3mat;      mi=0;
        m=firstpass;
   fprintf(ficreseij,"# Health expectancies\n");      while(s[m][i] <= nlstate){
   fprintf(ficreseij,"# Age");        if(s[m][i]>=1)
   for(i=1; i<=nlstate;i++)          mw[++mi][i]=m;
     for(j=1; j<=nlstate;j++)        if(m >=lastpass)
       fprintf(ficreseij," %1d-%1d",i,j);          break;
   fprintf(ficreseij,"\n");        else
           m++;
   hstepm=1*YEARM; /*  Every j years of age (in month) */      }/* end while */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
   agelim=AGESUP;        /* if(mi==0)  never been interviewed correctly before death */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */           /* Only death is a correct wave */
     /* nhstepm age range expressed in number of stepm */        mw[mi][i]=m;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);      }
     /* Typically if 20 years = 20*12/6=40 stepm */  
     if (stepm >= YEARM) hstepm=1;      wav[i]=mi;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      if(mi==0){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if(first==0){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          first=1;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          }
         if(first==1){
           fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
     for(i=1; i<=nlstate;i++)        }
       for(j=1; j<=nlstate;j++)      } /* end mi==0 */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    }
           eij[i][j][(int)age] +=p3mat[i][j][h];  
         }    for(i=1; i<=imx; i++){
          for(mi=1; mi<wav[i];mi++){
     hf=1;        if (stepm <=0)
     if (stepm >= YEARM) hf=stepm/YEARM;          dh[mi][i]=1;
     fprintf(ficreseij,"%.0f",age );        else{
     for(i=1; i<=nlstate;i++)          if (s[mw[mi+1][i]][i] > nlstate) {
       for(j=1; j<=nlstate;j++){            if (agedc[i] < 2*AGESUP) {
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       }            if(j==0) j=1;  /* Survives at least one month after exam */
     fprintf(ficreseij,"\n");            k=k+1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if (j >= jmax) jmax=j;
   }            if (j <= jmin) jmin=j;
 }            sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i); */
 /************ 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)          }
 {          else{
   /* Variance of health expectancies */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            k=k+1;
   double **newm;            if (j >= jmax) jmax=j;
   double **dnewm,**doldm;            else if (j <= jmin)jmin=j;
   int i, j, nhstepm, hstepm, h;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   int k, cptcode;            sum=sum+j;
   double *xp;          }
   double **gp, **gm;          jk= j/stepm;
   double ***gradg, ***trgradg;          jl= j -jk*stepm;
   double ***p3mat;          ju= j -(jk+1)*stepm;
   double age,agelim;          if(jl <= -ju)
   int theta;            dh[mi][i]=jk;
           else
    fprintf(ficresvij,"# Covariances of life expectancies\n");            dh[mi][i]=jk+1;
   fprintf(ficresvij,"# Age");          if(dh[mi][i]==0)
   for(i=1; i<=nlstate;i++)            dh[mi][i]=1; /* At least one step */
     for(j=1; j<=nlstate;j++)        }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      }
   fprintf(ficresvij,"\n");    }
     jmean=sum/k;
   xp=vector(1,npar);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   dnewm=matrix(1,nlstate,1,npar);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   doldm=matrix(1,nlstate,1,nlstate);   }
    
   hstepm=1*YEARM; /* Every year of age */  /*********** Tricode ****************************/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  void tricode(int *Tvar, int **nbcode, int imx)
   agelim = AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int Ndum[20],ij=1, k, j, i;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    int cptcode=0;
     if (stepm >= YEARM) hstepm=1;    cptcoveff=0; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (k=0; k<19; k++) Ndum[k]=0;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    for (k=1; k<=7; k++) ncodemax[k]=0;
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=imx; i++) {
     for(theta=1; theta <=npar; theta++){        ij=(int)(covar[Tvar[j]][i]);
       for(i=1; i<=npar; i++){ /* Computes gradient */        Ndum[ij]++; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       }        if (ij > cptcode) cptcode=ij; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for (i=0; i<=cptcode; i++) {
       if (popbased==1) {        if(Ndum[i]!=0) ncodemax[j]++;
         for(i=1; i<=nlstate;i++)      }
           prlim[i][i]=probs[(int)age][i][ij];      ij=1; 
       }  
        
       for(j=1; j<= nlstate; j++){      for (i=1; i<=ncodemax[j]; i++) {
         for(h=0; h<=nhstepm; h++){        for (k=0; k<=19; k++) {
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          if (Ndum[k] != 0) {
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            nbcode[Tvar[j]][ij]=k; 
         }            
       }            ij++;
              }
       for(i=1; i<=npar; i++) /* Computes gradient */          if (ij > ncodemax[j]) break; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }  
   
       if (popbased==1) {   for (k=0; k<19; k++) Ndum[k]=0;
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];   for (i=1; i<=ncovmodel-2; i++) {
       }     ij=Tvar[i];
      Ndum[ij]++; 
       for(j=1; j<= nlstate; j++){   }
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)   ij=1;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];   for (i=1; i<=10; i++) {
         }     if((Ndum[i]!=0) && (i<=ncovcol)){
       }       Tvaraff[ij]=i; 
        ij++;
       for(j=1; j<= nlstate; j++)     }
         for(h=0; h<=nhstepm; h++){   }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];   
         }   cptcoveff=ij-1;
     } /* End theta */  }
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  /*********** Health Expectancies ****************/
   
     for(h=0; h<=nhstepm; h++)  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(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)  {
           trgradg[h][j][theta]=gradg[h][theta][j];    /* Health expectancies */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     for(i=1;i<=nlstate;i++)    double age, agelim, hf;
       for(j=1;j<=nlstate;j++)    double ***p3mat,***varhe;
         vareij[i][j][(int)age] =0.;    double **dnewm,**doldm;
     for(h=0;h<=nhstepm;h++){    double *xp;
       for(k=0;k<=nhstepm;k++){    double **gp, **gm;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    double ***gradg, ***trgradg;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    int theta;
         for(i=1;i<=nlstate;i++)  
           for(j=1;j<=nlstate;j++)    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
             vareij[i][j][(int)age] += doldm[i][j];    xp=vector(1,npar);
       }    dnewm=matrix(1,nlstate*2,1,npar);
     }    doldm=matrix(1,nlstate*2,1,nlstate*2);
     h=1;    
     if (stepm >= YEARM) h=stepm/YEARM;    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficresvij,"%.0f ",age );    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       }    fprintf(ficreseij,"\n");
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);    if(estepm < stepm){
     free_matrix(gm,0,nhstepm,1,nlstate);      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    else  hstepm=estepm;   
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* We compute the life expectancy from trapezoids spaced every estepm months
   } /* End age */     * This is mainly to measure the difference between two models: for example
       * if stepm=24 months pijx are given only every 2 years and by summing them
   free_vector(xp,1,npar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   free_matrix(doldm,1,nlstate,1,npar);     * progression inbetween and thus overestimating or underestimating according
   free_matrix(dnewm,1,nlstate,1,nlstate);     * 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
 }     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
 /************ Variance of prevlim ******************/     * curvature will be obtained if estepm is as small as stepm. */
 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)  
 {    /* For example we decided to compute the life expectancy with the smallest unit */
   /* Variance of prevalence limit */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       nhstepm is the number of hstepm from age to agelim 
   double **newm;       nstepm is the number of stepm from age to agelin. 
   double **dnewm,**doldm;       Look at hpijx to understand the reason of that which relies in memory size
   int i, j, nhstepm, hstepm;       and note for a fixed period like estepm months */
   int k, cptcode;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double *xp;       survival function given by stepm (the optimization length). Unfortunately it
   double *gp, *gm;       means that if the survival funtion is printed only each two years of age and if
   double **gradg, **trgradg;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double age,agelim;       results. So we changed our mind and took the option of the best precision.
   int theta;    */
        hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  
   fprintf(ficresvpl,"# Age");    agelim=AGESUP;
   for(i=1; i<=nlstate;i++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficresvpl," %1d-%1d",i,i);      /* nhstepm age range expressed in number of stepm */
   fprintf(ficresvpl,"\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   xp=vector(1,npar);      /* if (stepm >= YEARM) hstepm=1;*/
   dnewm=matrix(1,nlstate,1,npar);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   doldm=matrix(1,nlstate,1,nlstate);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   hstepm=1*YEARM; /* Every year of age */      gp=matrix(0,nhstepm,1,nlstate*2);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      gm=matrix(0,nhstepm,1,nlstate*2);
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     if (stepm >= YEARM) hstepm=1;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     gm=vector(1,nlstate);  
       /* Computing Variances of health expectancies */
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */       for(theta=1; theta <=npar; theta++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        for(i=1; i<=npar; i++){ 
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
       for(i=1;i<=nlstate;i++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         gp[i] = prlim[i][i];    
            cptj=0;
       for(i=1; i<=npar; i++) /* Computes gradient */        for(j=1; j<= nlstate; j++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for(i=1; i<=nlstate; i++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            cptj=cptj+1;
       for(i=1;i<=nlstate;i++)            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         gm[i] = prlim[i][i];              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
       for(i=1;i<=nlstate;i++)          }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        }
     } /* End theta */       
        
     trgradg =matrix(1,nlstate,1,npar);        for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for(j=1; j<=nlstate;j++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for(theta=1; theta <=npar; theta++)        
         trgradg[j][theta]=gradg[theta][j];        cptj=0;
         for(j=1; j<= nlstate; j++){
     for(i=1;i<=nlstate;i++)          for(i=1;i<=nlstate;i++){
       varpl[i][(int)age] =0.;            cptj=cptj+1;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     for(i=1;i<=nlstate;i++)            }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          }
         }
     fprintf(ficresvpl,"%.0f ",age );        for(j=1; j<= nlstate*2; j++)
     for(i=1; i<=nlstate;i++)          for(h=0; h<=nhstepm-1; h++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     fprintf(ficresvpl,"\n");          }
     free_vector(gp,1,nlstate);       } 
     free_vector(gm,1,nlstate);     
     free_matrix(gradg,1,npar,1,nlstate);  /* End theta */
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   
   free_vector(xp,1,npar);       for(h=0; h<=nhstepm-1; h++)
   free_matrix(doldm,1,nlstate,1,npar);        for(j=1; j<=nlstate*2;j++)
   free_matrix(dnewm,1,nlstate,1,nlstate);          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
 }       
   
 /************ Variance of one-step probabilities  ******************/       for(i=1;i<=nlstate*2;i++)
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        for(j=1;j<=nlstate*2;j++)
 {          varhe[i][j][(int)age] =0.;
   int i, j;  
   int k=0, cptcode;       printf("%d|",(int)age);fflush(stdout);
   double **dnewm,**doldm;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   double *xp;       for(h=0;h<=nhstepm-1;h++){
   double *gp, *gm;        for(k=0;k<=nhstepm-1;k++){
   double **gradg, **trgradg;          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
   double age,agelim, cov[NCOVMAX];          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
   int theta;          for(i=1;i<=nlstate*2;i++)
   char fileresprob[FILENAMELENGTH];            for(j=1;j<=nlstate*2;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   strcpy(fileresprob,"prob");        }
   strcat(fileresprob,fileres);      }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      /* Computing expectancies */
     printf("Problem with resultfile: %s\n", fileresprob);      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++)
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
              eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
   xp=vector(1,npar);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          }
    
   cov[1]=1;      fprintf(ficreseij,"%3.0f",age );
   for (age=bage; age<=fage; age ++){      cptj=0;
     cov[2]=age;      for(i=1; i<=nlstate;i++)
     gradg=matrix(1,npar,1,9);        for(j=1; j<=nlstate;j++){
     trgradg=matrix(1,9,1,npar);          cptj++;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        }
          fprintf(ficreseij,"\n");
     for(theta=1; theta <=npar; theta++){     
       for(i=1; i<=npar; i++)      free_matrix(gm,0,nhstepm,1,nlstate*2);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      free_matrix(gp,0,nhstepm,1,nlstate*2);
            free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k=0;    }
       for(i=1; i<= (nlstate+ndeath); i++){    printf("\n");
         for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficlog,"\n");
            k=k+1;  
           gp[k]=pmmij[i][j];    free_vector(xp,1,npar);
         }    free_matrix(dnewm,1,nlstate*2,1,npar);
       }    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
     free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
       for(i=1; i<=npar; i++)  }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
      /************ Variance ******************/
   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)
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  {
       k=0;    /* Variance of health expectancies */
       for(i=1; i<=(nlstate+ndeath); i++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         for(j=1; j<=(nlstate+ndeath);j++){    /* double **newm;*/
           k=k+1;    double **dnewm,**doldm;
           gm[k]=pmmij[i][j];    double **dnewmp,**doldmp;
         }    int i, j, nhstepm, hstepm, h, nstepm ;
       }    int k, cptcode;
          double *xp;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    double **gp, **gm;  /* for var eij */
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      double ***gradg, ***trgradg; /*for var eij */
     }    double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       for(theta=1; theta <=npar; theta++)    double ***p3mat;
       trgradg[j][theta]=gradg[theta][j];    double age,agelim, hf;
      double ***mobaverage;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    int theta;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    char digit[4];
     char digitp[25];
      pmij(pmmij,cov,ncovmodel,x,nlstate);  
     char fileresprobmorprev[FILENAMELENGTH];
      k=0;  
      for(i=1; i<=(nlstate+ndeath); i++){    if(popbased==1){
        for(j=1; j<=(nlstate+ndeath);j++){      if(mobilav==1)
          k=k+1;        strcpy(digitp,"-populbased-mobilav-");
          gm[k]=pmmij[i][j];      else strcpy(digitp,"-populbased-nomobil-");
         }    }
      }    else 
            strcpy(digitp,"-stablbased-");
      /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    if (mobilav!=0) {
              mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
      }*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
   fprintf(ficresprob,"\n%d ",(int)age);    }
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    strcpy(fileresprobmorprev,"prmorprev"); 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    sprintf(digit,"%-d",ij);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    strcat(fileresprobmorprev,fileres);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
 }    }
  free_vector(xp,1,npar);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 fclose(ficresprob);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
  exit(0);    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
 }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 /***********************************************/      fprintf(ficresprobmorprev," p.%-d SE",j);
 /**************** Main Program *****************/      for(i=1; i<=nlstate;i++)
 /***********************************************/        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
 /*int main(int argc, char *argv[])*/    fprintf(ficresprobmorprev,"\n");
 int main()    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 {      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      exit(0);
   double agedeb, agefin,hf;    }
   double agemin=1.e20, agemax=-1.e20;    else{
       fprintf(ficgp,"\n# Routine varevsij");
   double fret;    }
   double **xi,tmp,delta;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       printf("Problem with html file: %s\n", optionfilehtm);
   double dum; /* Dummy variable */      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   double ***p3mat;      exit(0);
   int *indx;    }
   char line[MAXLINE], linepar[MAXLINE];    else{
   char title[MAXLINE];      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];    }
   char filerest[FILENAMELENGTH];    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    fprintf(ficresvij,"# Age");
   int firstobs=1, lastobs=10;    for(i=1; i<=nlstate;i++)
   int sdeb, sfin; /* Status at beginning and end */      for(j=1; j<=nlstate;j++)
   int c,  h , cpt,l;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   int ju,jl, mi;    fprintf(ficresvij,"\n");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    xp=vector(1,npar);
   int mobilav=0,popforecast=0;    dnewm=matrix(1,nlstate,1,npar);
   int hstepm, nhstepm;    doldm=matrix(1,nlstate,1,nlstate);
   int *popage;/*boolprev=0 if date and zero if wave*/    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   double bage, fage, age, agelim, agebase;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   double ftolpl=FTOL;    gpp=vector(nlstate+1,nlstate+ndeath);
   double **prlim;    gmp=vector(nlstate+1,nlstate+ndeath);
   double *severity;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   double ***param; /* Matrix of parameters */    
   double  *p;    if(estepm < stepm){
   double **matcov; /* Matrix of covariance */      printf ("Problem %d lower than %d\n",estepm, stepm);
   double ***delti3; /* Scale */    }
   double *delti; /* Scale */    else  hstepm=estepm;   
   double ***eij, ***vareij;    /* For example we decided to compute the life expectancy with the smallest unit */
   double **varpl; /* Variances of prevalence limits by age */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   double *epj, vepp;       nhstepm is the number of hstepm from age to agelim 
   double kk1, kk2;       nstepm is the number of stepm from age to agelin. 
   double *popeffectif,*popcount;       Look at hpijx to understand the reason of that which relies in memory size
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;       and note for a fixed period like k years */
   double yp,yp1,yp2;    /* 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
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";       means that if the survival funtion is printed only each two years of age and if
   char *alph[]={"a","a","b","c","d","e"}, str[4];       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
   char z[1]="c", occ;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 #include <sys/time.h>    agelim = AGESUP;
 #include <time.h>    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   /* long total_usecs;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   struct timeval start_time, end_time;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        gp=matrix(0,nhstepm,1,nlstate);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      gm=matrix(0,nhstepm,1,nlstate);
   
   
   printf("\nIMACH, Version 0.7");      for(theta=1; theta <=npar; theta++){
   printf("\nEnter the parameter file name: ");        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #ifdef windows        }
   scanf("%s",pathtot);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   getcwd(pathcd, size);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        if (popbased==1) {
   /* cutv(path,optionfile,pathtot,'\\');*/          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
 split(pathtot, path,optionfile);              prlim[i][i]=probs[(int)age][i][ij];
   chdir(path);          }else{ /* mobilav */ 
   replace(pathc,path);            for(i=1; i<=nlstate;i++)
 #endif              prlim[i][i]=mobaverage[(int)age][i][ij];
 #ifdef unix          }
   scanf("%s",optionfile);        }
 #endif    
         for(j=1; j<= nlstate; j++){
 /*-------- arguments in the command line --------*/          for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   strcpy(fileres,"r");              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   strcat(fileres, optionfile);          }
         }
   /*---------arguments file --------*/        /* This for computing forces of mortality (h=1)as a weighted average */
         for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          for(i=1; i<= nlstate; i++)
     printf("Problem with optionfile %s\n",optionfile);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     goto end;        }    
   }        /* end force of mortality */
   
   strcpy(filereso,"o");        for(i=1; i<=npar; i++) /* Computes gradient */
   strcat(filereso,fileres);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if((ficparo=fopen(filereso,"w"))==NULL) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }   
         if (popbased==1) {
   /* Reads comments: lines beginning with '#' */          if(mobilav ==0){
   while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);              prlim[i][i]=probs[(int)age][i][ij];
     fgets(line, MAXLINE, ficpar);          }else{ /* mobilav */ 
     puts(line);            for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   ungetc(c,ficpar);        }
   
   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);        for(j=1; j<= nlstate; j++){
   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);          for(h=0; h<=nhstepm; h++){
   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);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 while((c=getc(ficpar))=='#' && c!= EOF){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        /* This for computing force of mortality (h=1)as a weighted average */
     fputs(line,ficparo);        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
   }          for(i=1; i<= nlstate; i++)
   ungetc(c,ficpar);            gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
            /* end force of mortality */
   covar=matrix(0,NCOVMAX,1,n);  
   cptcovn=0;        for(j=1; j<= nlstate; j++) /* vareij */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   ncovmodel=2+cptcovn;          }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   /* Read guess parameters */        }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){      } /* End theta */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     puts(line);  
     fputs(line,ficparo);      for(h=0; h<=nhstepm; h++) /* veij */
   }        for(j=1; j<=nlstate;j++)
   ungetc(c,ficpar);          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     for(j=1; j <=nlstate+ndeath-1; j++){        for(theta=1; theta <=npar; theta++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);          trgradgp[j][theta]=gradgp[theta][j];
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(k=1; k<=ncovmodel;k++){      for(i=1;i<=nlstate;i++)
         fscanf(ficpar," %lf",&param[i][j][k]);        for(j=1;j<=nlstate;j++)
         printf(" %lf",param[i][j][k]);          vareij[i][j][(int)age] =0.;
         fprintf(ficparo," %lf",param[i][j][k]);  
       }      for(h=0;h<=nhstepm;h++){
       fscanf(ficpar,"\n");        for(k=0;k<=nhstepm;k++){
       printf("\n");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       fprintf(ficparo,"\n");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     }          for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   p=param[1][1];      }
    
   /* Reads comments: lines beginning with '#' */      /* pptj */
   while((c=getc(ficpar))=='#' && c!= EOF){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     ungetc(c,ficpar);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     fgets(line, MAXLINE, ficpar);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     puts(line);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     fputs(line,ficparo);          varppt[j][i]=doldmp[j][i];
   }      /* end ppptj */
   ungetc(c,ficpar);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);   
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      if (popbased==1) {
   for(i=1; i <=nlstate; i++){        if(mobilav ==0){
     for(j=1; j <=nlstate+ndeath-1; j++){          for(i=1; i<=nlstate;i++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);            prlim[i][i]=probs[(int)age][i][ij];
       printf("%1d%1d",i,j);        }else{ /* mobilav */ 
       fprintf(ficparo,"%1d%1d",i1,j1);          for(i=1; i<=nlstate;i++)
       for(k=1; k<=ncovmodel;k++){            prlim[i][i]=mobaverage[(int)age][i][ij];
         fscanf(ficpar,"%le",&delti3[i][j][k]);        }
         printf(" %le",delti3[i][j][k]);      }
         fprintf(ficparo," %le",delti3[i][j][k]);      
       }      /* This for computing force of mortality (h=1)as a weighted average */
       fscanf(ficpar,"\n");      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
       printf("\n");        for(i=1; i<= nlstate; i++)
       fprintf(ficparo,"\n");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     }      }    
   }      /* end force of mortality */
   delti=delti3[1][1];  
        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   /* Reads comments: lines beginning with '#' */      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     ungetc(c,ficpar);        for(i=1; i<=nlstate;i++){
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     puts(line);        }
     fputs(line,ficparo);      } 
   }      fprintf(ficresprobmorprev,"\n");
   ungetc(c,ficpar);  
        fprintf(ficresvij,"%.0f ",age );
   matcov=matrix(1,npar,1,npar);      for(i=1; i<=nlstate;i++)
   for(i=1; i <=npar; i++){        for(j=1; j<=nlstate;j++){
     fscanf(ficpar,"%s",&str);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     printf("%s",str);        }
     fprintf(ficparo,"%s",str);      fprintf(ficresvij,"\n");
     for(j=1; j <=i; j++){      free_matrix(gp,0,nhstepm,1,nlstate);
       fscanf(ficpar," %le",&matcov[i][j]);      free_matrix(gm,0,nhstepm,1,nlstate);
       printf(" %.5le",matcov[i][j]);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fprintf(ficparo," %.5le",matcov[i][j]);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fscanf(ficpar,"\n");    } /* End age */
     printf("\n");    free_vector(gpp,nlstate+1,nlstate+ndeath);
     fprintf(ficparo,"\n");    free_vector(gmp,nlstate+1,nlstate+ndeath);
   }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   for(i=1; i <=npar; i++)    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     for(j=i+1;j<=npar;j++)    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       matcov[i][j]=matcov[j][i];    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
        fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   printf("\n");    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);
     /*-------- data file ----------*/    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     if((ficres =fopen(fileres,"w"))==NULL) {    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
       printf("Problem with resultfile: %s\n", fileres);goto end;    /*  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);
     }  */
     fprintf(ficres,"#%s\n",version);    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
      
     if((fic=fopen(datafile,"r"))==NULL)    {    free_vector(xp,1,npar);
       printf("Problem with datafile: %s\n", datafile);goto end;    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);
     n= lastobs;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     severity = vector(1,maxwav);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     outcome=imatrix(1,maxwav+1,1,n);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     num=ivector(1,n);    fclose(ficresprobmorprev);
     moisnais=vector(1,n);    fclose(ficgp);
     annais=vector(1,n);    fclose(fichtm);
     moisdc=vector(1,n);  }
     andc=vector(1,n);  
     agedc=vector(1,n);  /************ Variance of prevlim ******************/
     cod=ivector(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)
     weight=vector(1,n);  {
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    /* Variance of prevalence limit */
     mint=matrix(1,maxwav,1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     anint=matrix(1,maxwav,1,n);    double **newm;
     s=imatrix(1,maxwav+1,1,n);    double **dnewm,**doldm;
     adl=imatrix(1,maxwav+1,1,n);        int i, j, nhstepm, hstepm;
     tab=ivector(1,NCOVMAX);    int k, cptcode;
     ncodemax=ivector(1,8);    double *xp;
     double *gp, *gm;
     i=1;    double **gradg, **trgradg;
     while (fgets(line, MAXLINE, fic) != NULL)    {    double age,agelim;
       if ((i >= firstobs) && (i <=lastobs)) {    int theta;
             
         for (j=maxwav;j>=1;j--){    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    fprintf(ficresvpl,"# Age");
           strcpy(line,stra);    for(i=1; i<=nlstate;i++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficresvpl," %1d-%1d",i,i);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficresvpl,"\n");
         }  
            xp=vector(1,npar);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    dnewm=matrix(1,nlstate,1,npar);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    doldm=matrix(1,nlstate,1,nlstate);
     
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=1*YEARM; /* Every year of age */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         for (j=ncov;j>=1;j--){      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      if (stepm >= YEARM) hstepm=1;
         }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         num[i]=atol(stra);      gradg=matrix(1,npar,1,nlstate);
              gp=vector(1,nlstate);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      gm=vector(1,nlstate);
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  
       for(theta=1; theta <=npar; theta++){
         i=i+1;        for(i=1; i<=npar; i++){ /* Computes gradient */
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     }        }
     /* printf("ii=%d", ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        scanf("%d",i);*/        for(i=1;i<=nlstate;i++)
   imx=i-1; /* Number of individuals */          gp[i] = prlim[i][i];
       
   /* for (i=1; i<=imx; i++){        for(i=1; i<=npar; i++) /* Computes gradient */
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        for(i=1;i<=nlstate;i++)
     }          gm[i] = prlim[i][i];
   
     for (i=1; i<=imx; i++)        for(i=1;i<=nlstate;i++)
     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]));*/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);      trgradg =matrix(1,nlstate,1,npar);
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);      for(j=1; j<=nlstate;j++)
   Tvard=imatrix(1,15,1,2);        for(theta=1; theta <=npar; theta++)
   Tage=ivector(1,15);                trgradg[j][theta]=gradg[theta][j];
      
   if (strlen(model) >1){      for(i=1;i<=nlstate;i++)
     j=0, j1=0, k1=1, k2=1;        varpl[i][(int)age] =0.;
     j=nbocc(model,'+');      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     j1=nbocc(model,'*');      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     cptcovn=j+1;      for(i=1;i<=nlstate;i++)
     cptcovprod=j1;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      
          fprintf(ficresvpl,"%.0f ",age );
     strcpy(modelsav,model);      for(i=1; i<=nlstate;i++)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       printf("Error. Non available option model=%s ",model);      fprintf(ficresvpl,"\n");
       goto end;      free_vector(gp,1,nlstate);
     }      free_vector(gm,1,nlstate);
          free_matrix(gradg,1,npar,1,nlstate);
     for(i=(j+1); i>=1;i--){      free_matrix(trgradg,1,nlstate,1,npar);
       cutv(stra,strb,modelsav,'+');    } /* End age */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    free_vector(xp,1,npar);
       /*scanf("%d",i);*/    free_matrix(doldm,1,nlstate,1,npar);
       if (strchr(strb,'*')) {    free_matrix(dnewm,1,nlstate,1,nlstate);
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {  }
           cptcovprod--;  
           cutv(strb,stre,strd,'V');  /************ Variance of one-step probabilities  ******************/
           Tvar[i]=atoi(stre);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
           cptcovage++;  {
             Tage[cptcovage]=i;    int i, j=0,  i1, k1, l1, t, tj;
             /*printf("stre=%s ", stre);*/    int k2, l2, j1,  z1;
         }    int k=0,l, cptcode;
         else if (strcmp(strd,"age")==0) {    int first=1, first1;
           cptcovprod--;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           cutv(strb,stre,strc,'V');    double **dnewm,**doldm;
           Tvar[i]=atoi(stre);    double *xp;
           cptcovage++;    double *gp, *gm;
           Tage[cptcovage]=i;    double **gradg, **trgradg;
         }    double **mu;
         else {    double age,agelim, cov[NCOVMAX];
           cutv(strb,stre,strc,'V');    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           Tvar[i]=ncov+k1;    int theta;
           cutv(strb,strc,strd,'V');    char fileresprob[FILENAMELENGTH];
           Tprod[k1]=i;    char fileresprobcov[FILENAMELENGTH];
           Tvard[k1][1]=atoi(strc);    char fileresprobcor[FILENAMELENGTH];
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];    double ***varpij;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)    strcpy(fileresprob,"prob"); 
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    strcat(fileresprob,fileres);
           k1++;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           k2=k2+2;      printf("Problem with resultfile: %s\n", fileresprob);
         }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       }    }
       else {    strcpy(fileresprobcov,"probcov"); 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    strcat(fileresprobcov,fileres);
        /*  scanf("%d",i);*/    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       cutv(strd,strc,strb,'V');      printf("Problem with resultfile: %s\n", fileresprobcov);
       Tvar[i]=atoi(strc);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       }    }
       strcpy(modelsav,stra);      strcpy(fileresprobcor,"probcor"); 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    strcat(fileresprobcor,fileres);
         scanf("%d",i);*/    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobcor);
 }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   printf("cptcovprod=%d ", cptcovprod);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   scanf("%d ",i);*/    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fclose(fic);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     /*  if(mle==1){*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     if (weightopt != 1) { /* Maximisation without weights*/    
       for(i=1;i<=n;i++) weight[i]=1.0;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     }    fprintf(ficresprob,"# Age");
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     agev=matrix(1,maxwav,1,imx);    fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
    for (i=1; i<=imx; i++)    fprintf(ficresprobcov,"# Age");
      for(m=2; (m<= maxwav); m++)  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;    for(i=1; i<=nlstate;i++)
          s[m][i]=-1;      for(j=1; j<=(nlstate+ndeath);j++){
        }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
            fprintf(ficresprobcov," p%1d-%1d ",i,j);
     for (i=1; i<=imx; i++)  {        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      }  
       for(m=1; (m<= maxwav); m++){    fprintf(ficresprob,"\n");
         if(s[m][i] >0){    fprintf(ficresprobcov,"\n");
           if (s[m][i] == nlstate+1) {    fprintf(ficresprobcor,"\n");
             if(agedc[i]>0)    xp=vector(1,npar);
               if(moisdc[i]!=99 && andc[i]!=9999)    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               agev[m][i]=agedc[i];    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
             else {    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
               if (andc[i]!=9999){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    first=1;
               agev[m][i]=-1;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
               }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
             }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
           }      exit(0);
           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]);    else{
             if(mint[m][i]==99 || anint[m][i]==9999)      fprintf(ficgp,"\n# Routine varprob");
               agev[m][i]=1;    }
             else if(agev[m][i] <agemin){    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
               agemin=agev[m][i];      printf("Problem with html file: %s\n", optionfilehtm);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
             }      exit(0);
             else if(agev[m][i] >agemax){    }
               agemax=agev[m][i];    else{
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
             }      fprintf(fichtm,"\n");
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
           }      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
           else { /* =9 */      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");
             agev[m][i]=1;  
             s[m][i]=-1;    }
           }  
         }   
         else /*= 0 Unknown */    cov[1]=1;
           agev[m][i]=1;    tj=cptcoveff;
       }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
        j1=0;
     }    for(t=1; t<=tj;t++){
     for (i=1; i<=imx; i++)  {      for(i1=1; i1<=ncodemax[t];i1++){ 
       for(m=1; (m<= maxwav); m++){        j1++;
         if (s[m][i] > (nlstate+ndeath)) {        
           printf("Error: Wrong value in nlstate or ndeath\n");          if  (cptcovn>0) {
           goto end;          fprintf(ficresprob, "\n#********** Variable "); 
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresprob, "**********\n#");
     }          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          fprintf(ficresprobcov, "**********\n#");
           
     free_vector(severity,1,maxwav);          fprintf(ficgp, "\n#********** Variable "); 
     free_imatrix(outcome,1,maxwav+1,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(moisnais,1,n);          fprintf(ficgp, "**********\n#");
     free_vector(annais,1,n);          
     /* free_matrix(mint,1,maxwav,1,n);          
        free_matrix(anint,1,maxwav,1,n);*/          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     free_vector(moisdc,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(andc,1,n);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
              fprintf(ficresprobcor, "\n#********** Variable ");    
     wav=ivector(1,imx);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(ficgp, "**********\n#");    
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        }
            
     /* Concatenates waves */        for (age=bage; age<=fage; age ++){ 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       Tcode=ivector(1,100);          }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       ncodemax[1]=1;          for (k=1; k<=cptcovprod;k++)
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                
    codtab=imatrix(1,100,1,10);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
    h=0;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    m=pow(2,cptcoveff);          gp=vector(1,(nlstate)*(nlstate+ndeath));
            gm=vector(1,(nlstate)*(nlstate+ndeath));
    for(k=1;k<=cptcoveff; k++){      
      for(i=1; i <=(m/pow(2,k));i++){          for(theta=1; theta <=npar; theta++){
        for(j=1; j <= ncodemax[k]; j++){            for(i=1; i<=npar; i++)
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){              xp[i] = x[i] + (i==theta ?delti[theta]:0);
            h++;            
            if (h>m) h=1;codtab[h][k]=j;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
          }            
        }            k=0;
      }            for(i=1; i<= (nlstate); i++){
    }              for(j=1; j<=(nlstate+ndeath);j++){
                    k=k+1;
    /* Calculates basic frequencies. Computes observed prevalence at single age                gp[k]=pmmij[i][j];
        and prints on file fileres'p'. */              }
             }
                
                for(i=1; i<=npar; i++)
     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 */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            k=0;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            for(i=1; i<=(nlstate); i++){
                    for(j=1; j<=(nlstate+ndeath);j++){
     /* For Powell, parameters are in a vector p[] starting at p[1]                k=k+1;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                gm[k]=pmmij[i][j];
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */              }
             }
     if(mle==1){       
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     }              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
              }
     /*--------- results files --------------*/  
     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);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
              for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
    jk=1;          
    fprintf(ficres,"# Parameters\n");          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
    printf("# Parameters\n");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
    for(i=1,jk=1; i <=nlstate; i++){          
      for(k=1; k <=(nlstate+ndeath); k++){          pmij(pmmij,cov,ncovmodel,x,nlstate);
        if (k != i)          
          {          k=0;
            printf("%d%d ",i,k);          for(i=1; i<=(nlstate); i++){
            fprintf(ficres,"%1d%1d ",i,k);            for(j=1; j<=(nlstate+ndeath);j++){
            for(j=1; j <=ncovmodel; j++){              k=k+1;
              printf("%f ",p[jk]);              mu[k][(int) age]=pmmij[i][j];
              fprintf(ficres,"%f ",p[jk]);            }
              jk++;          }
            }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
            printf("\n");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
            fprintf(ficres,"\n");              varpij[i][j][(int)age] = doldm[i][j];
          }  
      }          /*printf("\n%d ",(int)age);
    }       for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
  if(mle==1){         printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     /* Computing hessian and covariance matrix */         fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     ftolhess=ftol; /* Usually correct */       }*/
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }          fprintf(ficresprob,"\n%d ",(int)age);
     fprintf(ficres,"# Scales\n");          fprintf(ficresprobcov,"\n%d ",(int)age);
     printf("# Scales\n");          fprintf(ficresprobcor,"\n%d ",(int)age);
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
         if (j!=i) {            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           fprintf(ficres,"%1d%1d",i,j);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           printf("%1d%1d",i,j);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
           for(k=1; k<=ncovmodel;k++){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
             printf(" %.5e",delti[jk]);          }
             fprintf(ficres," %.5e",delti[jk]);          i=0;
             jk++;          for (k=1; k<=(nlstate);k++){
           }            for (l=1; l<=(nlstate+ndeath);l++){ 
           printf("\n");              i=i++;
           fprintf(ficres,"\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]));
     k=1;              }
     fprintf(ficres,"# Covariance\n");            }
     printf("# Covariance\n");          }/* end of loop for state */
     for(i=1;i<=npar;i++){        } /* end of loop for age */
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;        /* Confidence intervalle of pij  */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        /*
       printf("%s%d%d",alph[k],i1,tab[i]);*/        fprintf(ficgp,"\nset noparametric;unset label");
       fprintf(ficres,"%3d",i);        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       printf("%3d",i);        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       for(j=1; j<=i;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);
         fprintf(ficres," %.5e",matcov[i][j]);        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         printf(" %.5e",matcov[i][j]);        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       }        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       fprintf(ficres,"\n");        */
       printf("\n");  
       k++;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     }        first1=1;
            for (k2=1; k2<=(nlstate);k2++){
     while((c=getc(ficpar))=='#' && c!= EOF){          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       ungetc(c,ficpar);            if(l2==k2) continue;
       fgets(line, MAXLINE, ficpar);            j=(k2-1)*(nlstate+ndeath)+l2;
       puts(line);            for (k1=1; k1<=(nlstate);k1++){
       fputs(line,ficparo);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     }                if(l1==k1) continue;
     ungetc(c,ficpar);                i=(k1-1)*(nlstate+ndeath)+l1;
                  if(i<=j) continue;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                for (age=bage; age<=fage; age ++){ 
                      if ((int)age %5==0){
     if (fage <= 2) {                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       bage = agemin;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       fage = agemax;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     }                    mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
     fprintf(ficres,"# agemin agemax for life expectancy.\n");                    c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                      /* Eigen vectors */
     while((c=getc(ficpar))=='#' && c!= EOF){                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     ungetc(c,ficpar);                    /*v21=sqrt(1.-v11*v11); *//* error */
     fgets(line, MAXLINE, ficpar);                    v21=(lc1-v1)/cv12*v11;
     puts(line);                    v12=-v21;
     fputs(line,ficparo);                    v22=v11;
   }                    tnalp=v21/v11;
   ungetc(c,ficpar);                    if(first1==1){
                        first1=0;
   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);                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   fprintf(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(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                          /*printf(fignu*/
   while((c=getc(ficpar))=='#' && c!= EOF){                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     ungetc(c,ficpar);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     fgets(line, MAXLINE, ficpar);                    if(first==1){
     puts(line);                      first=0;
     fputs(line,ficparo);                      fprintf(ficgp,"\nset parametric;unset label");
   }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   ungetc(c,ficpar);                      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);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   fscanf(ficpar,"pop_based=%d\n",&popbased);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
    fprintf(ficparo,"pop_based=%d\n",popbased);                        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",\
    fprintf(ficres,"pop_based=%d\n",popbased);                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   while((c=getc(ficpar))=='#' && c!= EOF){                    }else{
     ungetc(c,ficpar);                      first=0;
     fgets(line, MAXLINE, ficpar);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
     puts(line);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     fputs(line,ficparo);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   }                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   ungetc(c,ficpar);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   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);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
 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);                    }/* if first */
 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);                  } /* age mod 5 */
                 } /* end loop age */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
  /*------------ gnuplot -------------*/              } /*l12 */
 chdir(pathcd);            } /* k12 */
   if((ficgp=fopen("graph.plt","w"))==NULL) {          } /*l1 */
     printf("Problem with file graph.gp");goto end;        }/* k1 */
   }      } /* loop covariates */
 #ifdef windows      free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   fprintf(ficgp,"cd \"%s\" \n",pathc);      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
 #endif      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
 m=pow(2,cptcoveff);      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
        free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
  /* 1eme*/      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   for (cpt=1; cpt<= nlstate ; cpt ++) {    }
    for (k1=1; k1<= m ; k1 ++) {    free_vector(xp,1,npar);
     fclose(ficresprob);
 #ifdef windows    fclose(ficresprobcov);
     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);    fclose(ficresprobcor);
 #endif    fclose(ficgp);
 #ifdef unix    fclose(fichtm);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);  }
 #endif  
   
 for (i=1; i<= nlstate ; i ++) {  /******************* Printing html file ***********/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   else fprintf(ficgp," \%%*lf (\%%*lf)");                    int lastpass, int stepm, int weightopt, char model[],\
 }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                    int popforecast, int estepm ,\
     for (i=1; i<= nlstate ; i ++) {                    double jprev1, double mprev1,double anprev1, \
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                    double jprev2, double mprev2,double anprev2){
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int jj1, k1, i1, cpt;
 }    /*char optionfilehtm[FILENAMELENGTH];*/
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
      for (i=1; i<= nlstate ; i ++) {      printf("Problem with %s \n",optionfilehtm), exit(0);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
 #ifdef unix   - 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
 fprintf(ficgp,"\nset ter gif small size 400,300");   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
 #endif   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);   - Life expectancies by age and initial health status (estepm=%2d months): 
    }     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   }    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   /*2 eme*/  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);   m=cptcoveff;
       if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     for (i=1; i<= nlstate+1 ; i ++) {  
       k=2*i;   jj1=0;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);   for(k1=1; k1<=m;k1++){
       for (j=1; j<= nlstate+1 ; j ++) {     for(i1=1; i1<=ncodemax[k1];i1++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       jj1++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");       if (cptcovn > 0) {
 }           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");         for (cpt=1; cpt<=cptcoveff;cpt++) 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       for (j=1; j<= nlstate+1 ; j ++) {       }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       /* Pij */
         else fprintf(ficgp," \%%*lf (\%%*lf)");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
 }    <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
       fprintf(ficgp,"\" t\"\" w l 0,");       /* Quasi-incidences */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
       for (j=1; j<= nlstate+1 ; j ++) {  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");         /* Stable prevalence in each health state */
   else fprintf(ficgp," \%%*lf (\%%*lf)");         for(cpt=1; cpt<nlstate;cpt++){
 }             fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       else fprintf(ficgp,"\" t\"\" w l 0,");         }
     }       for(cpt=1; cpt<=nlstate;cpt++) {
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   }  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
         }
   /*3eme*/       fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
   for (k1=1; k1<= m ; k1 ++) {  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     for (cpt=1; cpt<= nlstate ; cpt ++) {     } /* end i1 */
       k=2+nlstate*(cpt-1);   }/* End k1 */
       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);   fprintf(fichtm,"</ul>");
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);  
       }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     }   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
   }   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
   /* CV preval stat */   - 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 (k1=1; k1<= m ; k1 ++) {   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     for (cpt=1; cpt<nlstate ; cpt ++) {   - 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=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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);   if(popforecast==1) fprintf(fichtm,"\n
       for (i=1; i< nlstate ; i ++)   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
         fprintf(ficgp,"+$%d",k+i+1);   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          <br>",fileres,fileres,fileres,fileres);
         else 
       l=3+(nlstate+ndeath)*cpt;     fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;   m=cptcoveff;
         fprintf(ficgp,"+$%d",l+i+1);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);     jj1=0;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);   for(k1=1; k1<=m;k1++){
     }     for(i1=1; i1<=ncodemax[k1];i1++){
   }         jj1++;
        if (cptcovn > 0) {
   /* proba elementaires */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
    for(i=1,jk=1; i <=nlstate; i++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
     for(k=1; k <=(nlstate+ndeath); k++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       if (k != i) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         for(j=1; j <=ncovmodel; j++){       }
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/       for(cpt=1; cpt<=nlstate;cpt++) {
           /*fprintf(ficgp,"%s",alph[1]);*/         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  interval) in state (%d): v%s%d%d.png <br>
           jk++;  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
           fprintf(ficgp,"\n");       }
         }     } /* end i1 */
       }   }/* End k1 */
     }   fprintf(fichtm,"</ul>");
     }  fclose(fichtm);
   }
   for(jk=1; jk <=m; jk++) {  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);  /******************* Gnuplot file **************/
    i=1;  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
      for(k=1; k<=(nlstate+ndeath); k++) {    int ng;
        if (k != k2){    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      printf("Problem with file %s",optionfilegnuplot);
 ij=1;      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
         for(j=3; j <=ncovmodel; j++) {    }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /*#ifdef windows */
             ij++;      fprintf(ficgp,"cd \"%s\" \n",pathc);
           }      /*#endif */
           else  m=pow(2,cptcoveff);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    
         }   /* 1eme*/
           fprintf(ficgp,")/(1");    for (cpt=1; cpt<= nlstate ; cpt ++) {
             for (k1=1; k1<= m ; k1 ++) {
         for(k1=1; k1 <=nlstate; k1++){         fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
 ij=1;  
           for(j=3; j <=ncovmodel; j++){       for (i=1; i<= nlstate ; i ++) {
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
             ij++;       }
           }       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
           else       for (i=1; i<= nlstate ; i ++) {
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           }         else fprintf(ficgp," \%%*lf (\%%*lf)");
           fprintf(ficgp,")");       } 
         }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);       for (i=1; i<= nlstate ; i ++) {
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         i=i+ncovmodel;         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }       }  
      }       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
    }     }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    }
   }    /*2 eme*/
        
   fclose(ficgp);    for (k1=1; k1<= m ; k1 ++) { 
          fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
 chdir(path);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
          
     free_ivector(wav,1,imx);      for (i=1; i<= nlstate+1 ; i ++) {
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        k=2*i;
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
     free_ivector(num,1,n);        for (j=1; j<= nlstate+1 ; j ++) {
     free_vector(agedc,1,n);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     /*free_matrix(covar,1,NCOVMAX,1,n);*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
     fclose(ficparo);        }   
     fclose(ficres);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     /*  }*/        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
            fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
    /*________fin mle=1_________*/        for (j=1; j<= nlstate+1 ; j ++) {
              if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
     /* No more information from the sample is required now */        fprintf(ficgp,"\" t\"\" w l 0,");
   /* Reads comments: lines beginning with '#' */        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
   while((c=getc(ficpar))=='#' && c!= EOF){        for (j=1; j<= nlstate+1 ; j ++) {
     ungetc(c,ficpar);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     fgets(line, MAXLINE, ficpar);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     puts(line);        }   
     fputs(line,ficparo);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   }        else fprintf(ficgp,"\" t\"\" w l 0,");
   ungetc(c,ficpar);      }
      }
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    /*3eme*/
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    
 /*--------- index.htm --------*/    for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
   strcpy(optionfilehtm,optionfile);        k=2+nlstate*(2*cpt-2);
   strcat(optionfilehtm,".htm");        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
     printf("Problem with %s \n",optionfilehtm);goto end;        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
 Total number of observations=%d <br>          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          
 <hr  size=\"2\" color=\"#EC5E5E\">        */
 <li>Outputs files<br><br>\n        for (i=1; i< nlstate ; i ++) {
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          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);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        } 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      }
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    /* CV preval stat */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    for (k1=1; k1<= m ; k1 ++) { 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>      for (cpt=1; cpt<nlstate ; cpt ++) {
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>        k=3;
 <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);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
  fprintf(fichtm," <li>Graphs</li><p>");        
         for (i=1; i< nlstate ; i ++)
  m=cptcoveff;          fprintf(ficgp,"+$%d",k+i+1);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
  j1=0;        l=3+(nlstate+ndeath)*cpt;
  for(k1=1; k1<=m;k1++){        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
    for(i1=1; i1<=ncodemax[k1];i1++){        for (i=1; i< nlstate ; i ++) {
        j1++;          l=3+(nlstate+ndeath)*cpt;
        if (cptcovn > 0) {          fprintf(ficgp,"+$%d",l+i+1);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        }
          for (cpt=1; cpt<=cptcoveff;cpt++)        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      } 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    }  
        }    
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    /* proba elementaires */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        for(i=1,jk=1; i <=nlstate; i++){
        for(cpt=1; cpt<nlstate;cpt++){      for(k=1; k <=(nlstate+ndeath); k++){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        if (k != i) {
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for(j=1; j <=ncovmodel; j++){
        }            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     for(cpt=1; cpt<=nlstate;cpt++) {            jk++; 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            fprintf(ficgp,"\n");
 interval) in state (%d): v%s%d%d.gif <br>          }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          }
      }      }
      for(cpt=1; cpt<=nlstate;cpt++) {     }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
      }       for(jk=1; jk <=m; jk++) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
 health expectancies in states (1) and (2): e%s%d.gif<br>         if (ng==2)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
 fprintf(fichtm,"\n</body>");         else
    }           fprintf(ficgp,"\nset title \"Probability\"\n");
  }         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
 fclose(fichtm);         i=1;
          for(k2=1; k2<=nlstate; k2++) {
   /*--------------- Prevalence limit --------------*/           k3=i;
             for(k=1; k<=(nlstate+ndeath); k++) {
   strcpy(filerespl,"pl");             if (k != k2){
   strcat(filerespl,fileres);               if(ng==2)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;               else
   }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);               ij=1;
   fprintf(ficrespl,"#Prevalence limit\n");               for(j=3; j <=ncovmodel; j++) {
   fprintf(ficrespl,"#Age ");                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   fprintf(ficrespl,"\n");                   ij++;
                   }
   prlim=matrix(1,nlstate,1,nlstate);                 else
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               fprintf(ficgp,")/(1");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */               for(k1=1; k1 <=nlstate; k1++){   
   k=0;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   agebase=agemin;                 ij=1;
   agelim=agemax;                 for(j=3; j <=ncovmodel; j++){
   ftolpl=1.e-10;                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   i1=cptcoveff;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   if (cptcovn < 1){i1=1;}                     ij++;
                    }
   for(cptcov=1;cptcov<=i1;cptcov++){                   else
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         k=k+1;                 }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                 fprintf(ficgp,")");
         fprintf(ficrespl,"\n#******");               }
         for(j=1;j<=cptcoveff;j++)               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
         fprintf(ficrespl,"******\n");               i=i+ncovmodel;
                     }
         for (age=agebase; age<=agelim; age++){           } /* end k */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);         } /* end k2 */
           fprintf(ficrespl,"%.0f",age );       } /* end jk */
           for(i=1; i<=nlstate;i++)     } /* end ng */
           fprintf(ficrespl," %.5f", prlim[i][i]);     fclose(ficgp); 
           fprintf(ficrespl,"\n");  }  /* end gnuplot */
         }  
       }  
     }  /*************** Moving average **************/
   fclose(ficrespl);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
   /*------------- h Pij x at various ages ------------*/    int i, cpt, cptcod;
      int mobilavrange, mob;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    double age;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      if(mobilav==1) mobilavrange=5; /* default */
   }      else mobilavrange=mobilav;
   printf("Computing pij: result on file '%s' \n", filerespij);      for (age=bage; age<=fage; age++)
          for (i=1; i<=nlstate;i++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
   /*if (stepm<=24) stepsize=2;*/            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
   agelim=AGESUP;         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   hstepm=stepsize*YEARM; /* Every year of age */         we use a 5 terms etc. until the borders are no more concerned. 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      */ 
        for (mob=3;mob <=mobilavrange;mob=mob+2){
   k=0;        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   for(cptcov=1;cptcov<=i1;cptcov++){          for (i=1; i<=nlstate;i++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       k=k+1;              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
         fprintf(ficrespij,"\n#****** ");                for (cpt=1;cpt<=(mob-1)/2;cpt++){
         for(j=1;j<=cptcoveff;j++)                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
         fprintf(ficrespij,"******\n");                }
                      mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
         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 */        }/* end age */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }/* end mob */
           oldm=oldms;savm=savms;    }else return -1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      return 0;
           fprintf(ficrespij,"# Age");  }/* End movingaverage */
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);  /************** Forecasting ******************/
           fprintf(ficrespij,"\n");  prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
           for (h=0; h<=nhstepm; h++){    
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
             for(i=1; i<=nlstate;i++)    int *popage;
               for(j=1; j<=nlstate+ndeath;j++)    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    double *popeffectif,*popcount;
             fprintf(ficrespij,"\n");    double ***p3mat;
           }    double ***mobaverage;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    char fileresf[FILENAMELENGTH];
           fprintf(ficrespij,"\n");  
         }   agelim=AGESUP;
     }  calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
   }  
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/   
    
   fclose(ficrespij);    strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
   /*---------- Forecasting ------------------*/    if((ficresf=fopen(fileresf,"w"))==NULL) {
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    if (mobilav!=0) {
   }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   printf("Computing forecasting: result on file '%s' \n", fileresf);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   free_matrix(mint,1,maxwav,1,n);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   free_matrix(anint,1,maxwav,1,n);      }
   free_matrix(agev,1,maxwav,1,imx);    }
   /* Mobile average */  
     stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    if (stepm<=12) stepsize=1;
     
   if (mobilav==1) {    agelim=AGESUP;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)    hstepm=1;
       for (i=1; i<=nlstate;i++)    hstepm=hstepm/stepm; 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    yp1=modf(dateintmean,&yp);
           mobaverage[(int)agedeb][i][cptcod]=0.;    anprojmean=yp;
        yp2=modf((yp1*12),&yp);
     for (agedeb=bage+4; agedeb<=fage; agedeb++){    mprojmean=yp;
       for (i=1; i<=nlstate;i++){    yp1=modf((yp2*30.5),&yp);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    jprojmean=yp;
           for (cpt=0;cpt<=4;cpt++){    if(jprojmean==0) jprojmean=1;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    if(mprojmean==0) jprojmean=1;
           }    
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
         }    
       }    for(cptcov=1;cptcov<=i2;cptcov++){
     }        for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   }        k=k+1;
         fprintf(ficresf,"\n#******");
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(j=1;j<=cptcoveff;j++) {
   if (stepm<=12) stepsize=1;          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
   agelim=AGESUP;        fprintf(ficresf,"******\n");
   /*hstepm=stepsize*YEARM; *//* Every year of age */        fprintf(ficresf,"# StartingAge FinalAge");
   hstepm=1;        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */        
   yp1=modf(dateintmean,&yp);        
   anprojmean=yp;        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
   yp2=modf((yp1*12),&yp);          fprintf(ficresf,"\n");
   mprojmean=yp;          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
   if(jprojmean==0) jprojmean=1;            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   if(mprojmean==0) jprojmean=1;            nhstepm = nhstepm/hstepm; 
             
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
   if (popforecast==1) {            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     if((ficpop=fopen(popfile,"r"))==NULL)    {          
       printf("Problem with population file : %s\n",popfile);goto end;            for (h=0; h<=nhstepm; h++){
     }              if (h==(int) (calagedate+YEARM*cpt)) {
     popage=ivector(0,AGESUP);                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
     popeffectif=vector(0,AGESUP);              } 
     popcount=vector(0,AGESUP);              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
     i=1;                  for(i=1; i<=nlstate;i++) {              
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)                  if (mobilav==1) 
       {                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
         i=i+1;                  else {
       }                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     imx=i;                  }
                      
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                }
   }                if (h==(int)(calagedate+12*cpt)){
                   fprintf(ficresf," %.3f", kk1);
   for(cptcov=1;cptcov<=i1;cptcov++){                          
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                }
       k=k+1;              }
       fprintf(ficresf,"\n#******");            }
       for(j=1;j<=cptcoveff;j++) {            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
       }        }
       fprintf(ficresf,"******\n");      }
       fprintf(ficresf,"# StartingAge FinalAge");    }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);         
       if (popforecast==1)  fprintf(ficresf," [Population]");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    
       for (cpt=0; cpt<=5;cpt++) {    fclose(ficresf);
         fprintf(ficresf,"\n");  }
   fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    /************** Forecasting ******************/
       for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */  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){
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    
         nhstepm = nhstepm/hstepm;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/    int *popage;
     double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double *popeffectif,*popcount;
         oldm=oldms;savm=savms;    double ***p3mat,***tabpop,***tabpopprev;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double ***mobaverage;
                    char filerespop[FILENAMELENGTH];
         for (h=0; h<=nhstepm; h++){  
           if (h==(int) (calagedate+YEARM*cpt)) {    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           }    agelim=AGESUP;
           for(j=1; j<=nlstate+ndeath;j++) {    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
             kk1=0.;kk2=0;    
             for(i=1; i<=nlstate;i++) {            prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
               if (mobilav==1)    
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    
               else {    strcpy(filerespop,"pop"); 
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    strcat(filerespop,fileres);
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/    if((ficrespop=fopen(filerespop,"w"))==NULL) {
               }      printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];    }
             }    printf("Computing forecasting: result on file '%s' \n", filerespop);
              fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
             if (h==(int)(calagedate+12*cpt)){  
               fprintf(ficresf," %.3f", kk1);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
                
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);    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);
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }      }
       }    }
     }  
   }    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (stepm<=12) stepsize=1;
   if (popforecast==1) {    
     free_ivector(popage,0,AGESUP);    agelim=AGESUP;
     free_vector(popeffectif,0,AGESUP);    
     free_vector(popcount,0,AGESUP);    hstepm=1;
   }    hstepm=hstepm/stepm; 
   free_imatrix(s,1,maxwav+1,1,n);    
   free_vector(weight,1,n);    if (popforecast==1) {
   fclose(ficresf);      if((ficpop=fopen(popfile,"r"))==NULL) {
   /*---------- Health expectancies and variances ------------*/        printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
   strcpy(filerest,"t");      } 
   strcat(filerest,fileres);      popage=ivector(0,AGESUP);
   if((ficrest=fopen(filerest,"w"))==NULL) {      popeffectif=vector(0,AGESUP);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      popcount=vector(0,AGESUP);
   }      
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
   strcpy(filerese,"e");      imx=i;
   strcat(filerese,fileres);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   if((ficreseij=fopen(filerese,"w"))==NULL) {    }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }    for(cptcov=1;cptcov<=i2;cptcov++){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
  strcpy(fileresv,"v");        fprintf(ficrespop,"\n#******");
   strcat(fileresv,fileres);        for(j=1;j<=cptcoveff;j++) {
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        }
   }        fprintf(ficrespop,"******\n");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   k=0;        if (popforecast==1)  fprintf(ficrespop," [Population]");
   for(cptcov=1;cptcov<=i1;cptcov++){        
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for (cpt=0; cpt<=0;cpt++) { 
       k=k+1;          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
       fprintf(ficrest,"\n#****** ");          
       for(j=1;j<=cptcoveff;j++)          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       fprintf(ficrest,"******\n");            nhstepm = nhstepm/hstepm; 
             
       fprintf(ficreseij,"\n#****** ");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1;j<=cptcoveff;j++)            oldm=oldms;savm=savms;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
       fprintf(ficreseij,"******\n");          
             for (h=0; h<=nhstepm; h++){
       fprintf(ficresvij,"\n#****** ");              if (h==(int) (calagedate+YEARM*cpt)) {
       for(j=1;j<=cptcoveff;j++)                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);              } 
       fprintf(ficresvij,"******\n");              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                for(i=1; i<=nlstate;i++) {              
       oldm=oldms;savm=savms;                  if (mobilav==1) 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                      kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                  else {
       oldm=oldms;savm=savms;                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                  }
                      }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                if (h==(int)(calagedate+12*cpt)){
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
       fprintf(ficrest,"\n");                    /*fprintf(ficrespop," %.3f", kk1);
                              if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
       hf=1;                }
       if (stepm >= YEARM) hf=stepm/YEARM;              }
       epj=vector(1,nlstate+1);              for(i=1; i<=nlstate;i++){
       for(age=bage; age <=fage ;age++){                kk1=0.;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                  for(j=1; j<=nlstate;j++){
         if (popbased==1) {                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
           for(i=1; i<=nlstate;i++)                  }
             prlim[i][i]=probs[(int)age][i][k];                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
         }              }
          
         fprintf(ficrest," %.0f",age);              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            }
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }          }
           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];        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         for(j=1;j <=nlstate;j++){          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         }            nhstepm = nhstepm/hstepm; 
         fprintf(ficrest,"\n");            
       }            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);
               } 
  fclose(ficreseij);              for(j=1; j<=nlstate+ndeath;j++) {
  fclose(ficresvij);                kk1=0.;kk2=0;
   fclose(ficrest);                for(i=1; i<=nlstate;i++) {              
   fclose(ficpar);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   free_vector(epj,1,nlstate+1);                }
   /*  scanf("%d ",i); */                if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
               }
   /*------- Variance limit prevalence------*/              }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 strcpy(fileresvpl,"vpl");          }
   strcat(fileresvpl,fileres);        }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {     } 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    }
     exit(0);   
   }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
     if (popforecast==1) {
  k=0;      free_ivector(popage,0,AGESUP);
  for(cptcov=1;cptcov<=i1;cptcov++){      free_vector(popeffectif,0,AGESUP);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      free_vector(popcount,0,AGESUP);
      k=k+1;    }
      fprintf(ficresvpl,"\n#****** ");    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      for(j=1;j<=cptcoveff;j++)    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fclose(ficrespop);
      fprintf(ficresvpl,"******\n");  }
        
      varpl=matrix(1,nlstate,(int) bage, (int) fage);  /***********************************************/
      oldm=oldms;savm=savms;  /**************** Main Program *****************/
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  /***********************************************/
    }  
  }  int main(int argc, char *argv[])
   {
   fclose(ficresvpl);  
     int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
   /*---------- End : free ----------------*/    double agedeb, agefin,hf;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double fret;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double **xi,tmp,delta;
    
      double dum; /* Dummy variable */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    double ***p3mat;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    double ***mobaverage;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    int *indx;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    char line[MAXLINE], linepar[MAXLINE];
      char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
   free_matrix(matcov,1,npar,1,npar);    int firstobs=1, lastobs=10;
   free_vector(delti,1,npar);    int sdeb, sfin; /* Status at beginning and end */
      int c,  h , cpt,l;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   printf("End of Imach\n");    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    int mobilav=0,popforecast=0;
      int hstepm, nhstepm;
   /* 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);*/    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/    double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
  end:    double *severity;
 #ifdef windows    double ***param; /* Matrix of parameters */
  chdir(pathcd);    double  *p;
 #endif    double **matcov; /* Matrix of covariance */
      double ***delti3; /* Scale */
  system("..\\gp37mgw\\wgnuplot graph.plt");    double *delti; /* Scale */
     double ***eij, ***vareij;
 #ifdef windows    double **varpl; /* Variances of prevalence limits by age */
   while (z[0] != 'q') {    double *epj, vepp;
     chdir(pathcd);    double kk1, kk2;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
     scanf("%s",z);    
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') {    char *alph[]={"a","a","b","c","d","e"}, str[4];
       chdir(path);  
       system(optionfilehtm);  
     }    char z[1]="c", occ;
     else if (z[0] == 'q') exit(0);  #include <sys/time.h>
   }  #include <time.h>
 #endif    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; 
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn;
     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;
   
     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);
       adl=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){
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+');
       j1=nbocc(model,'*');
       cptcovn=j+1;
       cptcovprod=j1;
       
       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;
       }
       
       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 analyze 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 */
     
     /* 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);
       mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
       /* Concatenates waves */
         concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
   
         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);
      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){
       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");
          }
        }
      }
      
      k=1;
      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      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;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,Tvar,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(mw,1,lastpass-firstpass+1,1,imx);   
    free_ivector(num,1,n);
    free_vector(agedc,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);
     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 */
     k=0;
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1;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*/
   
     k=0;
     for(cptcov=1;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);
       }
     }
   
     k=0;
     for(cptcov=1;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_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
       free_vector(weight,1,n);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     free_vector(epj,1,nlstate+1);
     
     /*------- 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);
   
     k=0;
     for(cptcov=1;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);
       }
    }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
     
     free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     
     
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
    
     free_matrix(matcov,1,npar,1,npar);
     free_vector(delti,1,npar);
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
   
    end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
    strcpy(plotcmd,GNUPLOTPROGRAM);
    strcat(plotcmd," ");
    strcat(plotcmd,optionfilegnuplot);
    printf("Starting: %s\n",plotcmd);fflush(stdout);
    system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.20  
changed lines
  Added in v.1.57


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