Diff for /imach/src/imach.c between versions 1.31 and 1.87

version 1.31, 2002/03/10 13:43:02 version 1.87, 2003/06/18 12:26:01
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.87  2003/06/18 12:26:01  brouard
      Version 0.96
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.86  2003/06/17 20:04:08  brouard
   first survey ("cross") where individuals from different ages are    (Module): Change position of html and gnuplot routines and added
   interviewed on their health status or degree of disability (in the    routine fileappend.
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.85  2003/06/17 13:12:43  brouard
   (if any) in individual health status.  Health expectancies are    * imach.c (Repository): Check when date of death was earlier that
   computed from the time spent in each health state according to a    current date of interview. It may happen when the death was just
   model. More health states you consider, more time is necessary to reach the    prior to the death. In this case, dh was negative and likelihood
   Maximum Likelihood of the parameters involved in the model.  The    was wrong (infinity). We still send an "Error" but patch by
   simplest model is the multinomial logistic model where pij is the    assuming that the date of death was just one stepm after the
   probabibility to be observed in state j at the second wave    interview.
   conditional to be observed in state i at the first wave. Therefore    (Repository): Because some people have very long ID (first column)
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    we changed int to long in num[] and we added a new lvector for
   'age' is age and 'sex' is a covariate. If you want to have a more    memory allocation. But we also truncated to 8 characters (left
   complex model than "constant and age", you should modify the program    truncation)
   where the markup *Covariates have to be included here again* invites    (Repository): No more line truncation errors.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
   The advantage of this computer programme, compared to a simple    place. It differs from routine "prevalence" which may be called
   multinomial logistic model, is clear when the delay between waves is not    many times. Probs is memory consuming and must be used with
   identical for each individual. Also, if a individual missed an    parcimony.
   intermediate interview, the information is lost, but taken into    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   account using an interpolation or extrapolation.    
     Revision 1.83  2003/06/10 13:39:11  lievre
   hPijx is the probability to be observed in state i at age x+h    *** empty log message ***
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.82  2003/06/05 15:57:20  brouard
   states. This elementary transition (by month or quarter trimester,    Add log in  imach.c and  fullversion number is now printed.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices  */
   and the contribution of each individual to the likelihood is simply  /*
   hPijx.     Interpolated Markov Chain
   
   Also this programme outputs the covariance matrix of the parameters but also    Short summary of the programme:
   of the life expectancies. It also computes the prevalence limits.    
      This program computes Healthy Life Expectancies from
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
            Institut national d'études démographiques, Paris.    first survey ("cross") where individuals from different ages are
   This software have been partly granted by Euro-REVES, a concerted action    interviewed on their health status or degree of disability (in the
   from the European Union.    case of a health survey which is our main interest) -2- at least a
   It is copyrighted identically to a GNU software product, ie programme and    second wave of interviews ("longitudinal") which measure each change
   software can be distributed freely for non commercial use. Latest version    (if any) in individual health status.  Health expectancies are
   can be accessed at http://euroreves.ined.fr/imach .    computed from the time spent in each health state according to a
   **********************************************************************/    model. More health states you consider, more time is necessary to reach the
      Maximum Likelihood of the parameters involved in the model.  The
 #include <math.h>    simplest model is the multinomial logistic model where pij is the
 #include <stdio.h>    probability to be observed in state j at the second wave
 #include <stdlib.h>    conditional to be observed in state i at the first wave. Therefore
 #include <unistd.h>    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
 #define MAXLINE 256    complex model than "constant and age", you should modify the program
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    where the markup *Covariates have to be included here again* invites
 #define FILENAMELENGTH 80    you to do it.  More covariates you add, slower the
 /*#define DEBUG*/    convergence.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    The advantage of this computer programme, compared to a simple
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    intermediate interview, the information is lost, but taken into
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    account using an interpolation or extrapolation.  
   
 #define NINTERVMAX 8    hPijx is the probability to be observed in state i at age x+h
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    conditional to the observed state i at age x. The delay 'h' can be
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    split into an exact number (nh*stepm) of unobserved intermediate
 #define NCOVMAX 8 /* Maximum number of covariates */    states. This elementary transition (by month, quarter,
 #define MAXN 20000    semester or year) is modelled as a multinomial logistic.  The hPx
 #define YEARM 12. /* Number of months per year */    matrix is simply the matrix product of nh*stepm elementary matrices
 #define AGESUP 130    and the contribution of each individual to the likelihood is simply
 #define AGEBASE 40    hPijx.
   
     Also this programme outputs the covariance matrix of the parameters but also
 int erreur; /* Error number */    of the life expectancies. It also computes the stable prevalence. 
 int nvar;    
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int npar=NPARMAX;             Institut national d'études démographiques, Paris.
 int nlstate=2; /* Number of live states */    This software have been partly granted by Euro-REVES, a concerted action
 int ndeath=1; /* Number of dead states */    from the European Union.
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    It is copyrighted identically to a GNU software product, ie programme and
 int popbased=0;    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int jmin, jmax; /* min, max spacing between 2 waves */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 int mle, weightopt;    
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    **********************************************************************/
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  /*
 double jmean; /* Mean space between 2 waves */    main
 double **oldm, **newm, **savm; /* Working pointers to matrices */    read parameterfile
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    read datafile
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    concatwav
 FILE *ficgp,*ficresprob,*ficpop;    freqsummary
 FILE *ficreseij;    if (mle >= 1)
   char filerese[FILENAMELENGTH];      mlikeli
  FILE  *ficresvij;    print results files
   char fileresv[FILENAMELENGTH];    if mle==1 
  FILE  *ficresvpl;       computes hessian
   char fileresvpl[FILENAMELENGTH];    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 #define NR_END 1    open gnuplot file
 #define FREE_ARG char*    open html file
 #define FTOL 1.0e-10    stable prevalence
      for age prevalim()
 #define NRANSI    h Pij x
 #define ITMAX 200    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 #define TOL 2.0e-4    health expectancies
     Variance-covariance of DFLE
 #define CGOLD 0.3819660    prevalence()
 #define ZEPS 1.0e-10     movingaverage()
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    varevsij() 
     if popbased==1 varevsij(,popbased)
 #define GOLD 1.618034    total life expectancies
 #define GLIMIT 100.0    Variance of stable prevalence
 #define TINY 1.0e-20   end
   */
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
     
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #include <math.h>
 #define rint(a) floor(a+0.5)  #include <stdio.h>
   #include <stdlib.h>
 static double sqrarg;  #include <unistd.h>
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #include <sys/time.h>
   #include <time.h>
 int imx;  #include "timeval.h"
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 int m,nb;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define FILENAMELENGTH 132
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  /*#define DEBUG*/
 double **pmmij, ***probs, ***mobaverage;  /*#define windows*/
 double dateintmean=0;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 double *weight;  
 int **s; /* Status */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 double *agedc, **covar, idx;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   #define NINTERVMAX 8
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 double ftolhess; /* Tolerance for computing hessian */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 /**************** split *************************/  #define MAXN 20000
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define YEARM 12. /* Number of months per year */
 {  #define AGESUP 130
    char *s;                             /* pointer */  #define AGEBASE 40
    int  l1, l2;                         /* length counters */  #ifdef unix
   #define DIRSEPARATOR '/'
    l1 = strlen( path );                 /* length of path */  #define ODIRSEPARATOR '\\'
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #else
 #ifdef windows  #define DIRSEPARATOR '\\'
    s = strrchr( path, '\\' );           /* find last / */  #define ODIRSEPARATOR '/'
 #else  #endif
    s = strrchr( path, '/' );            /* find last / */  
 #endif  /* $Id$ */
    if ( s == NULL ) {                   /* no directory, so use current */  /* $State$ */
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  char version[]="Imach version 0.96, June 2003, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
       if ( getwd( dirc ) == NULL ) {  int erreur; /* Error number */
 #else  int nvar;
       extern char       *getcwd( );  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int nlstate=2; /* Number of live states */
 #endif  int ndeath=1; /* Number of dead states */
          return( GLOCK_ERROR_GETCWD );  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       }  int popbased=0;
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  int *wav; /* Number of waves for this individuual 0 is possible */
       s++;                              /* after this, the filename */  int maxwav; /* Maxim number of waves */
       l2 = strlen( s );                 /* length of filename */  int jmin, jmax; /* min, max spacing between 2 waves */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int gipmx, gsw; /* Global variables on the number of contributions 
       strcpy( name, s );                /* save file name */                     to the likelihood and the sum of weights (done by funcone)*/
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  int mle, weightopt;
       dirc[l1-l2] = 0;                  /* add zero */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
    }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    l1 = strlen( dirc );                 /* length of directory */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 #ifdef windows             * wave mi and wave mi+1 is not an exact multiple of stepm. */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  double jmean; /* Mean space between 2 waves */
 #else  double **oldm, **newm, **savm; /* Working pointers to matrices */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #endif  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    s = strrchr( name, '.' );            /* find last / */  FILE *ficlog, *ficrespow;
    s++;  int globpr; /* Global variable for printing or not */
    strcpy(ext,s);                       /* save extension */  double fretone; /* Only one call to likelihood */
    l1= strlen( name);  long ipmx; /* Number of contributions */
    l2= strlen( s)+1;  double sw; /* Sum of weights */
    strncpy( finame, name, l1-l2);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
    finame[l1-l2]= 0;  FILE *ficresilk;
    return( 0 );                         /* we're done */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 }  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
   FILE *ficreseij;
 /******************************************/  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 void replace(char *s, char*t)  char fileresv[FILENAMELENGTH];
 {  FILE  *ficresvpl;
   int i;  char fileresvpl[FILENAMELENGTH];
   int lg=20;  char title[MAXLINE];
   i=0;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   lg=strlen(t);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     if (t[i]== '\\') s[i]='/';  char filelog[FILENAMELENGTH]; /* Log file */
   }  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 int nbocc(char *s, char occ)  
 {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   int i,j=0;  
   int lg=20;  #define NR_END 1
   i=0;  #define FREE_ARG char*
   lg=strlen(s);  #define FTOL 1.0e-10
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  #define NRANSI 
   }  #define ITMAX 200 
   return j;  
 }  #define TOL 2.0e-4 
   
 void cutv(char *u,char *v, char*t, char occ)  #define CGOLD 0.3819660 
 {  #define ZEPS 1.0e-10 
   int i,lg,j,p=0;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {  #define GOLD 1.618034 
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #define GLIMIT 100.0 
   }  #define TINY 1.0e-20 
   
   lg=strlen(t);  static double maxarg1,maxarg2;
   for(j=0; j<p; j++) {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     (u[j] = t[j]);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   }    
      u[p]='\0';  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  static double sqrarg;
   }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
 /********************** nrerror ********************/  int imx; 
   int stepm;
 void nrerror(char error_text[])  /* Stepm, step in month: minimum step interpolation*/
 {  
   fprintf(stderr,"ERREUR ...\n");  int estepm;
   fprintf(stderr,"%s\n",error_text);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   exit(1);  
 }  int m,nb;
 /*********************** vector *******************/  long *num;
 double *vector(int nl, int nh)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double *v;  double **pmmij, ***probs;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  double dateintmean=0;
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  double *weight;
 }  int **s; /* Status */
   double *agedc, **covar, idx;
 /************************ free vector ******************/  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 void free_vector(double*v, int nl, int nh)  
 {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   free((FREE_ARG)(v+nl-NR_END));  double ftolhess; /* Tolerance for computing hessian */
 }  
   /**************** split *************************/
 /************************ivector *******************************/  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 int *ivector(long nl,long nh)  {
 {    char  *ss;                            /* pointer */
   int *v;    int   l1, l2;                         /* length counters */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    l1 = strlen(path );                   /* length of path */
   return v-nl+NR_END;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
 /******************free ivector **************************/      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 void free_ivector(int *v, long nl, long nh)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 {      /* get current working directory */
   free((FREE_ARG)(v+nl-NR_END));      /*    extern  char* getcwd ( char *buf , int len);*/
 }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
 /******************* imatrix *******************************/      }
 int **imatrix(long nrl, long nrh, long ncl, long nch)      strcpy( name, path );               /* we've got it */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;      l2 = strlen( ss );                  /* length of filename */
   int **m;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
        strcpy( name, ss );         /* save file name */
   /* allocate pointers to rows */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));      dirc[l1-l2] = 0;                    /* add zero */
   if (!m) nrerror("allocation failure 1 in matrix()");    }
   m += NR_END;    l1 = strlen( dirc );                  /* length of directory */
   m -= nrl;    /*#ifdef windows
      if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
    #else
   /* allocate rows and set pointers to them */    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #endif
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    */
   m[nrl] += NR_END;    ss = strrchr( name, '.' );            /* find last / */
   m[nrl] -= ncl;    ss++;
      strcpy(ext,ss);                       /* save extension */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    l1= strlen( name);
      l2= strlen(ss)+1;
   /* return pointer to array of pointers to rows */    strncpy( finame, name, l1-l2);
   return m;    finame[l1-l2]= 0;
 }    return( 0 );                          /* we're done */
   }
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  /******************************************/
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  void replace(char *s, char*t)
 {  {
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    int i;
   free((FREE_ARG) (m+nrl-NR_END));    int lg=20;
 }    i=0;
     lg=strlen(t);
 /******************* matrix *******************************/    for(i=0; i<= lg; i++) {
 double **matrix(long nrl, long nrh, long ncl, long nch)      (s[i] = t[i]);
 {      if (t[i]== '\\') s[i]='/';
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    }
   double **m;  }
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int nbocc(char *s, char occ)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    int i,j=0;
   m -= nrl;    int lg=20;
     i=0;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    lg=strlen(s);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    for(i=0; i<= lg; i++) {
   m[nrl] += NR_END;    if  (s[i] == occ ) j++;
   m[nrl] -= ncl;    }
     return j;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  
 }  void cutv(char *u,char *v, char*t, char occ)
   {
 /*************************free matrix ************************/    /* cuts string t into u and v where u is ended by char occ excluding it
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 {       gives u="abcedf" and v="ghi2j" */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int i,lg,j,p=0;
   free((FREE_ARG)(m+nrl-NR_END));    i=0;
 }    for(j=0; j<=strlen(t)-1; j++) {
       if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 /******************* ma3x *******************************/    }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    lg=strlen(t);
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    for(j=0; j<p; j++) {
   double ***m;      (u[j] = t[j]);
     }
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));       u[p]='\0';
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;     for(j=0; j<= lg; j++) {
   m -= nrl;      if (j>=(p+1))(v[j-p-1] = t[j]);
     }
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  /********************** nrerror ********************/
   m[nrl] -= ncl;  
   void nrerror(char error_text[])
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  {
     fprintf(stderr,"ERREUR ...\n");
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    fprintf(stderr,"%s\n",error_text);
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    exit(EXIT_FAILURE);
   m[nrl][ncl] += NR_END;  }
   m[nrl][ncl] -= nll;  /*********************** vector *******************/
   for (j=ncl+1; j<=nch; j++)  double *vector(int nl, int nh)
     m[nrl][j]=m[nrl][j-1]+nlay;  {
      double *v;
   for (i=nrl+1; i<=nrh; i++) {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    if (!v) nrerror("allocation failure in vector");
     for (j=ncl+1; j<=nch; j++)    return v-nl+NR_END;
       m[i][j]=m[i][j-1]+nlay;  }
   }  
   return m;  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /*************************free ma3x ************************/    free((FREE_ARG)(v+nl-NR_END));
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  }
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  /************************ivector *******************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int *ivector(long nl,long nh)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 /***************** f1dim *************************/    if (!v) nrerror("allocation failure in ivector");
 extern int ncom;    return v-nl+NR_END;
 extern double *pcom,*xicom;  }
 extern double (*nrfunc)(double []);  
    /******************free ivector **************************/
 double f1dim(double x)  void free_ivector(int *v, long nl, long nh)
 {  {
   int j;    free((FREE_ARG)(v+nl-NR_END));
   double f;  }
   double *xt;  
    /************************lvector *******************************/
   xt=vector(1,ncom);  long *lvector(long nl,long nh)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  {
   f=(*nrfunc)(xt);    long *v;
   free_vector(xt,1,ncom);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   return f;    if (!v) nrerror("allocation failure in ivector");
 }    return v-nl+NR_END;
   }
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /******************free lvector **************************/
 {  void free_lvector(long *v, long nl, long nh)
   int iter;  {
   double a,b,d,etemp;    free((FREE_ARG)(v+nl-NR_END));
   double fu,fv,fw,fx;  }
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  /******************* imatrix *******************************/
   double e=0.0;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   a=(ax < cx ? ax : cx);  { 
   b=(ax > cx ? ax : cx);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   x=w=v=bx;    int **m; 
   fw=fv=fx=(*f)(x);    
   for (iter=1;iter<=ITMAX;iter++) {    /* allocate pointers to rows */ 
     xm=0.5*(a+b);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    if (!m) nrerror("allocation failure 1 in matrix()"); 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m += NR_END; 
     printf(".");fflush(stdout);    m -= nrl; 
 #ifdef DEBUG    
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    /* allocate rows and set pointers to them */ 
 #endif    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       *xmin=x;    m[nrl] += NR_END; 
       return fx;    m[nrl] -= ncl; 
     }    
     ftemp=fu;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     if (fabs(e) > tol1) {    
       r=(x-w)*(fx-fv);    /* return pointer to array of pointers to rows */ 
       q=(x-v)*(fx-fw);    return m; 
       p=(x-v)*q-(x-w)*r;  } 
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /****************** free_imatrix *************************/
       q=fabs(q);  void free_imatrix(m,nrl,nrh,ncl,nch)
       etemp=e;        int **m;
       e=d;        long nch,ncl,nrh,nrl; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))       /* free an int matrix allocated by imatrix() */ 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  { 
       else {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         d=p/q;    free((FREE_ARG) (m+nrl-NR_END)); 
         u=x+d;  } 
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
     } else {  {
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     }    double **m;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (fu <= fx) {    if (!m) nrerror("allocation failure 1 in matrix()");
       if (u >= x) a=x; else b=x;    m += NR_END;
       SHFT(v,w,x,u)    m -= nrl;
         SHFT(fv,fw,fx,fu)  
         } else {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
           if (u < x) a=u; else b=u;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
           if (fu <= fw || w == x) {    m[nrl] += NR_END;
             v=w;    m[nrl] -= ncl;
             w=u;  
             fv=fw;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
             fw=fu;    return m;
           } else if (fu <= fv || v == x || v == w) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
             v=u;     */
             fv=fu;  }
           }  
         }  /*************************free matrix ************************/
   }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   nrerror("Too many iterations in brent");  {
   *xmin=x;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   return fx;    free((FREE_ARG)(m+nrl-NR_END));
 }  }
   
 /****************** mnbrak ***********************/  /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  {
             double (*func)(double))    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 {    double ***m;
   double ulim,u,r,q, dum;  
   double fu;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      if (!m) nrerror("allocation failure 1 in matrix()");
   *fa=(*func)(*ax);    m += NR_END;
   *fb=(*func)(*bx);    m -= nrl;
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       SHFT(dum,*fb,*fa,dum)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       }    m[nrl] += NR_END;
   *cx=(*bx)+GOLD*(*bx-*ax);    m[nrl] -= ncl;
   *fc=(*func)(*cx);  
   while (*fb > *fc) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    m[nrl][ncl] += NR_END;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    m[nrl][ncl] -= nll;
     if ((*bx-u)*(u-*cx) > 0.0) {    for (j=ncl+1; j<=nch; j++) 
       fu=(*func)(u);      m[nrl][j]=m[nrl][j-1]+nlay;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    
       fu=(*func)(u);    for (i=nrl+1; i<=nrh; i++) {
       if (fu < *fc) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      for (j=ncl+1; j<=nch; j++) 
           SHFT(*fb,*fc,fu,(*func)(u))        m[i][j]=m[i][j-1]+nlay;
           }    }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    return m; 
       u=ulim;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       fu=(*func)(u);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     } else {    */
       u=(*cx)+GOLD*(*cx-*bx);  }
       fu=(*func)(u);  
     }  /*************************free ma3x ************************/
     SHFT(*ax,*bx,*cx,u)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       SHFT(*fa,*fb,*fc,fu)  {
       }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 /*************** linmin ************************/  }
   
 int ncom;  /***************** f1dim *************************/
 double *pcom,*xicom;  extern int ncom; 
 double (*nrfunc)(double []);  extern double *pcom,*xicom;
    extern double (*nrfunc)(double []); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))   
 {  double f1dim(double x) 
   double brent(double ax, double bx, double cx,  { 
                double (*f)(double), double tol, double *xmin);    int j; 
   double f1dim(double x);    double f;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    double *xt; 
               double *fc, double (*func)(double));   
   int j;    xt=vector(1,ncom); 
   double xx,xmin,bx,ax;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double fx,fb,fa;    f=(*nrfunc)(xt); 
      free_vector(xt,1,ncom); 
   ncom=n;    return f; 
   pcom=vector(1,n);  } 
   xicom=vector(1,n);  
   nrfunc=func;  /*****************brent *************************/
   for (j=1;j<=n;j++) {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     pcom[j]=p[j];  { 
     xicom[j]=xi[j];    int iter; 
   }    double a,b,d,etemp;
   ax=0.0;    double fu,fv,fw,fx;
   xx=1.0;    double ftemp;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    double e=0.0; 
 #ifdef DEBUG   
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    a=(ax < cx ? ax : cx); 
 #endif    b=(ax > cx ? ax : cx); 
   for (j=1;j<=n;j++) {    x=w=v=bx; 
     xi[j] *= xmin;    fw=fv=fx=(*f)(x); 
     p[j] += xi[j];    for (iter=1;iter<=ITMAX;iter++) { 
   }      xm=0.5*(a+b); 
   free_vector(xicom,1,n);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   free_vector(pcom,1,n);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 }      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
 /*************** powell ************************/  #ifdef DEBUG
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
             double (*func)(double []))      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   void linmin(double p[], double xi[], int n, double *fret,  #endif
               double (*func)(double []));      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   int i,ibig,j;        *xmin=x; 
   double del,t,*pt,*ptt,*xit;        return fx; 
   double fp,fptt;      } 
   double *xits;      ftemp=fu;
   pt=vector(1,n);      if (fabs(e) > tol1) { 
   ptt=vector(1,n);        r=(x-w)*(fx-fv); 
   xit=vector(1,n);        q=(x-v)*(fx-fw); 
   xits=vector(1,n);        p=(x-v)*q-(x-w)*r; 
   *fret=(*func)(p);        q=2.0*(q-r); 
   for (j=1;j<=n;j++) pt[j]=p[j];        if (q > 0.0) p = -p; 
   for (*iter=1;;++(*iter)) {        q=fabs(q); 
     fp=(*fret);        etemp=e; 
     ibig=0;        e=d; 
     del=0.0;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for (i=1;i<=n;i++)        else { 
       printf(" %d %.12f",i, p[i]);          d=p/q; 
     printf("\n");          u=x+d; 
     for (i=1;i<=n;i++) {          if (u-a < tol2 || b-u < tol2) 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];            d=SIGN(tol1,xm-x); 
       fptt=(*fret);        } 
 #ifdef DEBUG      } else { 
       printf("fret=%lf \n",*fret);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 #endif      } 
       printf("%d",i);fflush(stdout);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       linmin(p,xit,n,fret,func);      fu=(*f)(u); 
       if (fabs(fptt-(*fret)) > del) {      if (fu <= fx) { 
         del=fabs(fptt-(*fret));        if (u >= x) a=x; else b=x; 
         ibig=i;        SHFT(v,w,x,u) 
       }          SHFT(fv,fw,fx,fu) 
 #ifdef DEBUG          } else { 
       printf("%d %.12e",i,(*fret));            if (u < x) a=u; else b=u; 
       for (j=1;j<=n;j++) {            if (fu <= fw || w == x) { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);              v=w; 
         printf(" x(%d)=%.12e",j,xit[j]);              w=u; 
       }              fv=fw; 
       for(j=1;j<=n;j++)              fw=fu; 
         printf(" p=%.12e",p[j]);            } else if (fu <= fv || v == x || v == w) { 
       printf("\n");              v=u; 
 #endif              fv=fu; 
     }            } 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {          } 
 #ifdef DEBUG    } 
       int k[2],l;    nrerror("Too many iterations in brent"); 
       k[0]=1;    *xmin=x; 
       k[1]=-1;    return fx; 
       printf("Max: %.12e",(*func)(p));  } 
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /****************** mnbrak ***********************/
       printf("\n");  
       for(l=0;l<=1;l++) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         for (j=1;j<=n;j++) {              double (*func)(double)) 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  { 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    double ulim,u,r,q, dum;
         }    double fu; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));   
       }    *fa=(*func)(*ax); 
 #endif    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
       free_vector(xit,1,n);        SHFT(dum,*fb,*fa,dum) 
       free_vector(xits,1,n);        } 
       free_vector(ptt,1,n);    *cx=(*bx)+GOLD*(*bx-*ax); 
       free_vector(pt,1,n);    *fc=(*func)(*cx); 
       return;    while (*fb > *fc) { 
     }      r=(*bx-*ax)*(*fb-*fc); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      q=(*bx-*cx)*(*fb-*fa); 
     for (j=1;j<=n;j++) {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       ptt[j]=2.0*p[j]-pt[j];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       xit[j]=p[j]-pt[j];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       pt[j]=p[j];      if ((*bx-u)*(u-*cx) > 0.0) { 
     }        fu=(*func)(u); 
     fptt=(*func)(ptt);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     if (fptt < fp) {        fu=(*func)(u); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        if (fu < *fc) { 
       if (t < 0.0) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         linmin(p,xit,n,fret,func);            SHFT(*fb,*fc,fu,(*func)(u)) 
         for (j=1;j<=n;j++) {            } 
           xi[j][ibig]=xi[j][n];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
           xi[j][n]=xit[j];        u=ulim; 
         }        fu=(*func)(u); 
 #ifdef DEBUG      } else { 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        u=(*cx)+GOLD*(*cx-*bx); 
         for(j=1;j<=n;j++)        fu=(*func)(u); 
           printf(" %.12e",xit[j]);      } 
         printf("\n");      SHFT(*ax,*bx,*cx,u) 
 #endif        SHFT(*fa,*fb,*fc,fu) 
       }        } 
     }  } 
   }  
 }  /*************** linmin ************************/
   
 /**** Prevalence limit ****************/  int ncom; 
   double *pcom,*xicom;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  double (*nrfunc)(double []); 
 {   
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
      matrix by transitions matrix until convergence is reached */  { 
     double brent(double ax, double bx, double cx, 
   int i, ii,j,k;                 double (*f)(double), double tol, double *xmin); 
   double min, max, maxmin, maxmax,sumnew=0.;    double f1dim(double x); 
   double **matprod2();    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   double **out, cov[NCOVMAX], **pmij();                double *fc, double (*func)(double)); 
   double **newm;    int j; 
   double agefin, delaymax=50 ; /* Max number of years to converge */    double xx,xmin,bx,ax; 
     double fx,fb,fa;
   for (ii=1;ii<=nlstate+ndeath;ii++)   
     for (j=1;j<=nlstate+ndeath;j++){    ncom=n; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    pcom=vector(1,n); 
     }    xicom=vector(1,n); 
     nrfunc=func; 
    cov[1]=1.;    for (j=1;j<=n;j++) { 
        pcom[j]=p[j]; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      xicom[j]=xi[j]; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    } 
     newm=savm;    ax=0.0; 
     /* Covariates have to be included here again */    xx=1.0; 
      cov[2]=agefin;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
      *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       for (k=1; k<=cptcovn;k++) {  #ifdef DEBUG
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       }  #endif
       for (k=1; k<=cptcovage;k++)    for (j=1;j<=n;j++) { 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      xi[j] *= xmin; 
       for (k=1; k<=cptcovprod;k++)      p[j] += xi[j]; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    } 
     free_vector(xicom,1,n); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    free_vector(pcom,1,n); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  } 
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     savm=oldm;              double (*func)(double [])) 
     oldm=newm;  { 
     maxmax=0.;    void linmin(double p[], double xi[], int n, double *fret, 
     for(j=1;j<=nlstate;j++){                double (*func)(double [])); 
       min=1.;    int i,ibig,j; 
       max=0.;    double del,t,*pt,*ptt,*xit;
       for(i=1; i<=nlstate; i++) {    double fp,fptt;
         sumnew=0;    double *xits;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    pt=vector(1,n); 
         prlim[i][j]= newm[i][j]/(1-sumnew);    ptt=vector(1,n); 
         max=FMAX(max,prlim[i][j]);    xit=vector(1,n); 
         min=FMIN(min,prlim[i][j]);    xits=vector(1,n); 
       }    *fret=(*func)(p); 
       maxmin=max-min;    for (j=1;j<=n;j++) pt[j]=p[j]; 
       maxmax=FMAX(maxmax,maxmin);    for (*iter=1;;++(*iter)) { 
     }      fp=(*fret); 
     if(maxmax < ftolpl){      ibig=0; 
       return prlim;      del=0.0; 
     }      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 }      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       for (i=1;i<=n;i++) {
 /*************** transition probabilities ***************/        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        fprintf(ficrespow," %.12lf", p[i]);
 {      }
   double s1, s2;      printf("\n");
   /*double t34;*/      fprintf(ficlog,"\n");
   int i,j,j1, nc, ii, jj;      fprintf(ficrespow,"\n");
       for (i=1;i<=n;i++) { 
     for(i=1; i<= nlstate; i++){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     for(j=1; j<i;j++){        fptt=(*fret); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #ifdef DEBUG
         /*s2 += param[i][j][nc]*cov[nc];*/        printf("fret=%lf \n",*fret);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        fprintf(ficlog,"fret=%lf \n",*fret);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  #endif
       }        printf("%d",i);fflush(stdout);
       ps[i][j]=s2;        fprintf(ficlog,"%d",i);fflush(ficlog);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
     for(j=i+1; j<=nlstate+ndeath;j++){          del=fabs(fptt-(*fret)); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          ibig=i; 
         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);*/  #ifdef DEBUG
       }        printf("%d %.12e",i,(*fret));
       ps[i][j]=s2;        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
   }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     /*ps[3][2]=1;*/          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   for(i=1; i<= nlstate; i++){        }
      s1=0;        for(j=1;j<=n;j++) {
     for(j=1; j<i; j++)          printf(" p=%.12e",p[j]);
       s1+=exp(ps[i][j]);          fprintf(ficlog," p=%.12e",p[j]);
     for(j=i+1; j<=nlstate+ndeath; j++)        }
       s1+=exp(ps[i][j]);        printf("\n");
     ps[i][i]=1./(s1+1.);        fprintf(ficlog,"\n");
     for(j=1; j<i; j++)  #endif
       ps[i][j]= exp(ps[i][j])*ps[i][i];      } 
     for(j=i+1; j<=nlstate+ndeath; j++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #ifdef DEBUG
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        int k[2],l;
   } /* end i */        k[0]=1;
         k[1]=-1;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        printf("Max: %.12e",(*func)(p));
     for(jj=1; jj<= nlstate+ndeath; jj++){        fprintf(ficlog,"Max: %.12e",(*func)(p));
       ps[ii][jj]=0;        for (j=1;j<=n;j++) {
       ps[ii][ii]=1;          printf(" %.12e",p[j]);
     }          fprintf(ficlog," %.12e",p[j]);
   }        }
         printf("\n");
         fprintf(ficlog,"\n");
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        for(l=0;l<=1;l++) {
     for(jj=1; jj<= nlstate+ndeath; jj++){          for (j=1;j<=n;j++) {
      printf("%lf ",ps[ii][jj]);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
    }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     printf("\n ");            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }          }
     printf("\n ");printf("%lf ",cov[2]);*/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 /*          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        }
   goto end;*/  #endif
     return ps;  
 }  
         free_vector(xit,1,n); 
 /**************** Product of 2 matrices ******************/        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        free_vector(pt,1,n); 
 {        return; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      } 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   /* in, b, out are matrice of pointers which should have been initialized      for (j=1;j<=n;j++) { 
      before: only the contents of out is modified. The function returns        ptt[j]=2.0*p[j]-pt[j]; 
      a pointer to pointers identical to out */        xit[j]=p[j]-pt[j]; 
   long i, j, k;        pt[j]=p[j]; 
   for(i=nrl; i<= nrh; i++)      } 
     for(k=ncolol; k<=ncoloh; k++)      fptt=(*func)(ptt); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      if (fptt < fp) { 
         out[i][k] +=in[i][j]*b[j][k];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
   return out;          linmin(p,xit,n,fret,func); 
 }          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
 /************* Higher Matrix Product ***************/          }
   #ifdef DEBUG
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )          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);
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          for(j=1;j<=n;j++){
      duration (i.e. until            printf(" %.12e",xit[j]);
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.            fprintf(ficlog," %.12e",xit[j]);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          }
      (typically every 2 years instead of every month which is too big).          printf("\n");
      Model is determined by parameters x and covariates have to be          fprintf(ficlog,"\n");
      included manually here.  #endif
         }
      */      } 
     } 
   int i, j, d, h, k;  } 
   double **out, cov[NCOVMAX];  
   double **newm;  /**** Prevalence limit (stable prevalence)  ****************/
   
   /* Hstepm could be zero and should return the unit matrix */  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   for (i=1;i<=nlstate+ndeath;i++)  {
     for (j=1;j<=nlstate+ndeath;j++){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       oldm[i][j]=(i==j ? 1.0 : 0.0);       matrix by transitions matrix until convergence is reached */
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }    int i, ii,j,k;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double min, max, maxmin, maxmax,sumnew=0.;
   for(h=1; h <=nhstepm; h++){    double **matprod2();
     for(d=1; d <=hstepm; d++){    double **out, cov[NCOVMAX], **pmij();
       newm=savm;    double **newm;
       /* Covariates have to be included here again */    double agefin, delaymax=50 ; /* Max number of years to converge */
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      for (j=1;j<=nlstate+ndeath;j++){
       for (k=1; k<=cptcovage;k++)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         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]]];     cov[1]=1.;
    
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      newm=savm;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      /* Covariates have to be included here again */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));       cov[2]=agefin;
       savm=oldm;    
       oldm=newm;        for (k=1; k<=cptcovn;k++) {
     }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for(i=1; i<=nlstate+ndeath; 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(j=1;j<=nlstate+ndeath;j++) {        }
         po[i][j][h]=newm[i][j];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        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]]];
       }  
   } /* end h */        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   return po;        /*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);
   
 /*************** log-likelihood *************/      savm=oldm;
 double func( double *x)      oldm=newm;
 {      maxmax=0.;
   int i, ii, j, k, mi, d, kk;      for(j=1;j<=nlstate;j++){
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        min=1.;
   double **out;        max=0.;
   double sw; /* Sum of weights */        for(i=1; i<=nlstate; i++) {
   double lli; /* Individual log likelihood */          sumnew=0;
   long ipmx;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /*extern weight */          prlim[i][j]= newm[i][j]/(1-sumnew);
   /* We are differentiating ll according to initial status */          max=FMAX(max,prlim[i][j]);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          min=FMIN(min,prlim[i][j]);
   /*for(i=1;i<imx;i++)        }
     printf(" %d\n",s[4][i]);        maxmin=max-min;
   */        maxmax=FMAX(maxmax,maxmin);
   cov[1]=1.;      }
       if(maxmax < ftolpl){
   for(k=1; k<=nlstate; k++) ll[k]=0.;        return prlim;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      }
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    }
     for(mi=1; mi<= wav[i]-1; mi++){  }
       for (ii=1;ii<=nlstate+ndeath;ii++)  
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*************** transition probabilities ***************/ 
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  {
         for (kk=1; kk<=cptcovage;kk++) {    double s1, s2;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    /*double t34;*/
         }    int i,j,j1, nc, ii, jj;
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      for(i=1; i<= nlstate; i++){
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      for(j=1; j<i;j++){
         savm=oldm;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         oldm=newm;          /*s2 += param[i][j][nc]*cov[nc];*/
                  s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
                  /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
       } /* end mult */        }
              ps[i][j]=s2;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      }
       ipmx +=1;      for(j=i+1; j<=nlstate+ndeath;j++){
       sw += weight[i];        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     } /* end of wave */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   } /* end of individual */        }
         ps[i][j]=s2;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    }
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      /*ps[3][2]=1;*/
   return -l;  
 }    for(i=1; i<= nlstate; i++){
        s1=0;
       for(j=1; j<i; j++)
 /*********** Maximum Likelihood Estimation ***************/        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        s1+=exp(ps[i][j]);
 {      ps[i][i]=1./(s1+1.);
   int i,j, iter;      for(j=1; j<i; j++)
   double **xi,*delti;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   double fret;      for(j=i+1; j<=nlstate+ndeath; j++)
   xi=matrix(1,npar,1,npar);        ps[i][j]= exp(ps[i][j])*ps[i][i];
   for (i=1;i<=npar;i++)      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     for (j=1;j<=npar;j++)    } /* end i */
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   powell(p,xi,npar,ftol,&iter,&fret,func);      for(jj=1; jj<= nlstate+ndeath; jj++){
         ps[ii][jj]=0;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        ps[ii][ii]=1;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      }
     }
 }  
   
 /**** Computes Hessian and covariance matrix ***/    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      for(jj=1; jj<= nlstate+ndeath; jj++){
 {       printf("%lf ",ps[ii][jj]);
   double  **a,**y,*x,pd;     }
   double **hess;      printf("\n ");
   int i, j,jk;      }
   int *indx;      printf("\n ");printf("%lf ",cov[2]);*/
   /*
   double hessii(double p[], double delta, int theta, double delti[]);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double hessij(double p[], double delti[], int i, int j);    goto end;*/
   void lubksb(double **a, int npar, int *indx, double b[]) ;      return ps;
   void ludcmp(double **a, int npar, int *indx, double *d) ;  }
   
   hess=matrix(1,npar,1,npar);  /**************** Product of 2 matrices ******************/
   
   printf("\nCalculation of the hessian matrix. Wait...\n");  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   for (i=1;i<=npar;i++){  {
     printf("%d",i);fflush(stdout);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     hess[i][i]=hessii(p,ftolhess,i,delti);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /*printf(" %f ",p[i]);*/    /* in, b, out are matrice of pointers which should have been initialized 
     /*printf(" %lf ",hess[i][i]);*/       before: only the contents of out is modified. The function returns
   }       a pointer to pointers identical to out */
      long i, j, k;
   for (i=1;i<=npar;i++) {    for(i=nrl; i<= nrh; i++)
     for (j=1;j<=npar;j++)  {      for(k=ncolol; k<=ncoloh; k++)
       if (j>i) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         printf(".%d%d",i,j);fflush(stdout);          out[i][k] +=in[i][j]*b[j][k];
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];        return out;
         /*printf(" %lf ",hess[i][j]);*/  }
       }  
     }  
   }  /************* Higher Matrix Product ***************/
   printf("\n");  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  {
      /* Computes the transition matrix starting at age 'age' over 
   a=matrix(1,npar,1,npar);       'nhstepm*hstepm*stepm' months (i.e. until
   y=matrix(1,npar,1,npar);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   x=vector(1,npar);       nhstepm*hstepm matrices. 
   indx=ivector(1,npar);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   for (i=1;i<=npar;i++)       (typically every 2 years instead of every month which is too big 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];       for the memory).
   ludcmp(a,npar,indx,&pd);       Model is determined by parameters x and covariates have to be 
        included manually here. 
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;       */
     x[j]=1;  
     lubksb(a,npar,indx,x);    int i, j, d, h, k;
     for (i=1;i<=npar;i++){    double **out, cov[NCOVMAX];
       matcov[i][j]=x[i];    double **newm;
     }  
   }    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
   printf("\n#Hessian matrix#\n");      for (j=1;j<=nlstate+ndeath;j++){
   for (i=1;i<=npar;i++) {        oldm[i][j]=(i==j ? 1.0 : 0.0);
     for (j=1;j<=npar;j++) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
       printf("%.3e ",hess[i][j]);      }
     }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     printf("\n");    for(h=1; h <=nhstepm; h++){
   }      for(d=1; d <=hstepm; d++){
         newm=savm;
   /* Recompute Inverse */        /* Covariates have to be included here again */
   for (i=1;i<=npar;i++)        cov[1]=1.;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   ludcmp(a,npar,indx,&pd);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
   /*  printf("\n#Hessian matrix recomputed#\n");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   for (j=1;j<=npar;j++) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  
     lubksb(a,npar,indx,x);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for (i=1;i<=npar;i++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       y[i][j]=x[i];        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       printf("%.3e ",y[i][j]);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     }        savm=oldm;
     printf("\n");        oldm=newm;
   }      }
   */      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
   free_matrix(a,1,npar,1,npar);          po[i][j][h]=newm[i][j];
   free_matrix(y,1,npar,1,npar);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   free_vector(x,1,npar);           */
   free_ivector(indx,1,npar);        }
   free_matrix(hess,1,npar,1,npar);    } /* end h */
     return po;
   }
 }  
   
 /*************** hessian matrix ****************/  /*************** log-likelihood *************/
 double hessii( double x[], double delta, int theta, double delti[])  double func( double *x)
 {  {
   int i;    int i, ii, j, k, mi, d, kk;
   int l=1, lmax=20;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double k1,k2;    double **out;
   double p2[NPARMAX+1];    double sw; /* Sum of weights */
   double res;    double lli; /* Individual log likelihood */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    int s1, s2;
   double fx;    double bbh, survp;
   int k=0,kmax=10;    long ipmx;
   double l1;    /*extern weight */
     /* We are differentiating ll according to initial status */
   fx=func(x);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for (i=1;i<=npar;i++) p2[i]=x[i];    /*for(i=1;i<imx;i++) 
   for(l=0 ; l <=lmax; l++){      printf(" %d\n",s[4][i]);
     l1=pow(10,l);    */
     delts=delt;    cov[1]=1.;
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);    for(k=1; k<=nlstate; k++) ll[k]=0.;
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;    if(mle==1){
       p2[theta]=x[theta]-delt;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       k2=func(p2)-fx;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       /*res= (k1-2.0*fx+k2)/delt/delt; */        for(mi=1; mi<= wav[i]-1; mi++){
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          for (ii=1;ii<=nlstate+ndeath;ii++)
                  for (j=1;j<=nlstate+ndeath;j++){
 #ifdef DEBUG              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 #endif            }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          for(d=0; d<dh[mi][i]; d++){
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            newm=savm;
         k=kmax;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         k=kmax; l=lmax*10.;            }
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         delts=delt;            savm=oldm;
       }            oldm=newm;
     }          } /* end mult */
   }        
   delti[theta]=delts;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   return res;          /* But now since version 0.9 we anticipate for bias and large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
 }           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
 double hessij( double x[], double delti[], int thetai,int thetaj)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   int i;           * probability in order to take into account the bias as a fraction of the way
   int l=1, l1, lmax=20;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   double k1,k2,k3,k4,res,fx;           * -stepm/2 to stepm/2 .
   double p2[NPARMAX+1];           * For stepm=1 the results are the same as for previous versions of Imach.
   int k;           * For stepm > 1 the results are less biased than in previous versions. 
            */
   fx=func(x);          s1=s[mw[mi][i]][i];
   for (k=1; k<=2; k++) {          s2=s[mw[mi+1][i]][i];
     for (i=1;i<=npar;i++) p2[i]=x[i];          bbh=(double)bh[mi][i]/(double)stepm; 
     p2[thetai]=x[thetai]+delti[thetai]/k;          /* bias is positive if real duration
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * is higher than the multiple of stepm and negative otherwise.
     k1=func(p2)-fx;           */
            /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     p2[thetai]=x[thetai]+delti[thetai]/k;          if( s2 > nlstate){ 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     k2=func(p2)-fx;               to the likelihood is the probability to die between last step unit time and current 
                 step unit time, which is also the differences between probability to die before dh 
     p2[thetai]=x[thetai]-delti[thetai]/k;               and probability to die before dh-stepm . 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;               In version up to 0.92 likelihood was computed
     k3=func(p2)-fx;          as if date of death was unknown. Death was treated as any other
            health state: the date of the interview describes the actual state
     p2[thetai]=x[thetai]-delti[thetai]/k;          and not the date of a change in health state. The former idea was
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          to consider that at each interview the state was recorded
     k4=func(p2)-fx;          (healthy, disable or death) and IMaCh was corrected; but when we
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          introduced the exact date of death then we should have modified
 #ifdef DEBUG          the contribution of an exact death to the likelihood. This new
     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);          contribution is smaller and very dependent of the step unit
 #endif          stepm. It is no more the probability to die between last interview
   }          and month of death but the probability to survive from last
   return res;          interview up to one month before death multiplied by the
 }          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
 /************** Inverse of matrix **************/          mortality artificially. The bad side is that we add another loop
 void ludcmp(double **a, int n, int *indx, double *d)          which slows down the processing. The difference can be up to 10%
 {          lower mortality.
   int i,imax,j,k;            */
   double big,dum,sum,temp;            lli=log(out[s1][s2] - savm[s1][s2]);
   double *vv;          }else{
              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   vv=vector(1,n);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   *d=1.0;          } 
   for (i=1;i<=n;i++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     big=0.0;          /*if(lli ==000.0)*/
     for (j=1;j<=n;j++)          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       if ((temp=fabs(a[i][j])) > big) big=temp;          ipmx +=1;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          sw += weight[i];
     vv[i]=1.0/big;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
   for (j=1;j<=n;j++) {      } /* end of individual */
     for (i=1;i<j;i++) {    }  else if(mle==2){
       sum=a[i][j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       a[i][j]=sum;        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
     big=0.0;            for (j=1;j<=nlstate+ndeath;j++){
     for (i=j;i<=n;i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       sum=a[i][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (k=1;k<j;k++)            }
         sum -= a[i][k]*a[k][j];          for(d=0; d<=dh[mi][i]; d++){
       a[i][j]=sum;            newm=savm;
       if ( (dum=vv[i]*fabs(sum)) >= big) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         big=dum;            for (kk=1; kk<=cptcovage;kk++) {
         imax=i;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if (j != imax) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (k=1;k<=n;k++) {            savm=oldm;
         dum=a[imax][k];            oldm=newm;
         a[imax][k]=a[j][k];          } /* end mult */
         a[j][k]=dum;        
       }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       *d = -(*d);          /* But now since version 0.9 we anticipate for bias and large stepm.
       vv[imax]=vv[j];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     }           * (in months) between two waves is not a multiple of stepm, we rounded to 
     indx[j]=imax;           * the nearest (and in case of equal distance, to the lowest) interval but now
     if (a[j][j] == 0.0) a[j][j]=TINY;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     if (j != n) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       dum=1.0/(a[j][j]);           * probability in order to take into account the bias as a fraction of the way
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     }           * -stepm/2 to stepm/2 .
   }           * For stepm=1 the results are the same as for previous versions of Imach.
   free_vector(vv,1,n);  /* Doesn't work */           * For stepm > 1 the results are less biased than in previous versions. 
 ;           */
 }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 void lubksb(double **a, int n, int *indx, double b[])          bbh=(double)bh[mi][i]/(double)stepm; 
 {          /* bias is positive if real duration
   int i,ii=0,ip,j;           * is higher than the multiple of stepm and negative otherwise.
   double sum;           */
            lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   for (i=1;i<=n;i++) {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     ip=indx[i];          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
     sum=b[ip];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     b[ip]=b[i];          /*if(lli ==000.0)*/
     if (ii)          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          ipmx +=1;
     else if (sum) ii=i;          sw += weight[i];
     b[i]=sum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
   for (i=n;i>=1;i--) {      } /* end of individual */
     sum=b[i];    }  else if(mle==3){  /* exponential inter-extrapolation */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     b[i]=sum/a[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 (j=1;j<=nlstate+ndeath;j++){
 /************ Frequencies ********************/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 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)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {  /* Some frequencies */            }
            for(d=0; d<dh[mi][i]; d++){
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            newm=savm;
   double ***freq; /* Frequencies */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double *pp;            for (kk=1; kk<=cptcovage;kk++) {
   double pos, k2, dateintsum=0,k2cpt=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   FILE *ficresp;            }
   char fileresp[FILENAMELENGTH];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   pp=vector(1,nlstate);            savm=oldm;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            oldm=newm;
   strcpy(fileresp,"p");          } /* end mult */
   strcat(fileresp,fileres);        
   if((ficresp=fopen(fileresp,"w"))==NULL) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     printf("Problem with prevalence resultfile: %s\n", fileresp);          /* But now since version 0.9 we anticipate for bias and large stepm.
     exit(0);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   }           * (in months) between two waves is not a multiple of stepm, we rounded to 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           * the nearest (and in case of equal distance, to the lowest) interval but now
   j1=0;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   j=cptcoveff;           * probability in order to take into account the bias as a fraction of the way
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
   for(k1=1; k1<=j;k1++){           * For stepm=1 the results are the same as for previous versions of Imach.
    for(i1=1; i1<=ncodemax[k1];i1++){           * For stepm > 1 the results are less biased than in previous versions. 
        j1++;           */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          s1=s[mw[mi][i]][i];
          scanf("%d", i);*/          s2=s[mw[mi+1][i]][i];
         for (i=-1; i<=nlstate+ndeath; i++)            bbh=(double)bh[mi][i]/(double)stepm; 
          for (jk=-1; jk<=nlstate+ndeath; jk++)            /* bias is positive if real duration
            for(m=agemin; m <= agemax+3; m++)           * is higher than the multiple of stepm and negative otherwise.
              freq[i][jk][m]=0;           */
           /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
         dateintsum=0;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         k2cpt=0;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
        for (i=1; i<=imx; i++) {          /*if(lli ==000.0)*/
          bool=1;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          if  (cptcovn>0) {          ipmx +=1;
            for (z1=1; z1<=cptcoveff; z1++)          sw += weight[i];
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                bool=0;        } /* end of wave */
          }      } /* end of individual */
          if (bool==1) {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
            for(m=firstpass; m<=lastpass; m++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
              k2=anint[m][i]+(mint[m][i]/12.);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(mi=1; mi<= wav[i]-1; mi++){
                if(agev[m][i]==0) agev[m][i]=agemax+1;          for (ii=1;ii<=nlstate+ndeath;ii++)
                if(agev[m][i]==1) agev[m][i]=agemax+2;            for (j=1;j<=nlstate+ndeath;j++){
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            }
                  dateintsum=dateintsum+k2;          for(d=0; d<dh[mi][i]; d++){
                  k2cpt++;            newm=savm;
                }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
              }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
            }            }
          }          
        }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            savm=oldm;
             oldm=newm;
         if  (cptcovn>0) {          } /* end mult */
          fprintf(ficresp, "\n#********** Variable ");        
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          s1=s[mw[mi][i]][i];
        fprintf(ficresp, "**********\n#");          s2=s[mw[mi+1][i]][i];
         }          if( s2 > nlstate){ 
        for(i=1; i<=nlstate;i++)            lli=log(out[s1][s2] - savm[s1][s2]);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          }else{
        fprintf(ficresp, "\n");            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                  }
   for(i=(int)agemin; i <= (int)agemax+3; i++){          ipmx +=1;
     if(i==(int)agemax+3)          sw += weight[i];
       printf("Total");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     else  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       printf("Age %d", i);        } /* end of wave */
     for(jk=1; jk <=nlstate ; jk++){      } /* end of individual */
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         pp[jk] += freq[jk][m][i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(jk=1; jk <=nlstate ; jk++){        for(mi=1; mi<= wav[i]-1; mi++){
       for(m=-1, pos=0; m <=0 ; m++)          for (ii=1;ii<=nlstate+ndeath;ii++)
         pos += freq[jk][m][i];            for (j=1;j<=nlstate+ndeath;j++){
       if(pp[jk]>=1.e-10)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       else            }
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      for(jk=1; jk <=nlstate ; jk++){            for (kk=1; kk<=cptcovage;kk++) {
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         pp[jk] += freq[jk][m][i];            }
      }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(jk=1,pos=0; jk <=nlstate ; jk++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       pos += pp[jk];            savm=oldm;
     for(jk=1; jk <=nlstate ; jk++){            oldm=newm;
       if(pos>=1.e-5)          } /* end mult */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        
       else          s1=s[mw[mi][i]][i];
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          s2=s[mw[mi+1][i]][i];
       if( i <= (int) agemax){          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         if(pos>=1.e-5){          ipmx +=1;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          sw += weight[i];
           probs[i][jk][j1]= pp[jk]/pos;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         }        } /* end of wave */
       else      } /* end of individual */
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    } /* End of if */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for(jk=-1; jk <=nlstate+ndeath; jk++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       for(m=-1; m <=nlstate+ndeath; m++)    return -l;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  }
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");  /*************** log-likelihood *************/
     printf("\n");  double funcone( double *x)
     }  {
     }    /* Same as likeli but slower because of a lot of printf and if */
  }    int i, ii, j, k, mi, d, kk;
   dateintmean=dateintsum/k2cpt;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
   fclose(ficresp);    double lli; /* Individual log likelihood */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double llt;
   free_vector(pp,1,nlstate);    int s1, s2;
     double bbh, survp;
   /* End of Freq */    /*extern weight */
 }    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 /************ Prevalence ********************/    /*for(i=1;i<imx;i++) 
 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)      printf(" %d\n",s[4][i]);
 {  /* Some frequencies */    */
      cov[1]=1.;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double *pp;  
   double pos, k2;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   pp=vector(1,nlstate);      for(mi=1; mi<= wav[i]-1; mi++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   j1=0;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
            }
   j=cptcoveff;        for(d=0; d<dh[mi][i]; d++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          newm=savm;
            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  for(k1=1; k1<=j;k1++){          for (kk=1; kk<=cptcovage;kk++) {
     for(i1=1; i1<=ncodemax[k1];i1++){            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       j1++;          }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (i=-1; i<=nlstate+ndeath; i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for (jk=-1; jk<=nlstate+ndeath; jk++)            savm=oldm;
           for(m=agemin; m <= agemax+3; m++)          oldm=newm;
             freq[i][jk][m]=0;        } /* end mult */
              
       for (i=1; i<=imx; i++) {        s1=s[mw[mi][i]][i];
         bool=1;        s2=s[mw[mi+1][i]][i];
         if  (cptcovn>0) {        bbh=(double)bh[mi][i]/(double)stepm; 
           for (z1=1; z1<=cptcoveff; z1++)        /* bias is positive if real duration
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])         * is higher than the multiple of stepm and negative otherwise.
               bool=0;         */
         }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         if (bool==1) {          lli=log(out[s1][s2] - savm[s1][s2]);
           for(m=firstpass; m<=lastpass; m++){        } else if (mle==1){
             k2=anint[m][i]+(mint[m][i]/12.);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        } else if(mle==2){
               if(agev[m][i]==0) agev[m][i]=agemax+1;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
               if(agev[m][i]==1) agev[m][i]=agemax+2;        } else if(mle==3){  /* exponential inter-extrapolation */
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
             }          lli=log(out[s1][s2]); /* Original formula */
           }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
         }          lli=log(out[s1][s2]); /* Original formula */
       }        } /* End of if */
         for(i=(int)agemin; i <= (int)agemax+3; i++){        ipmx +=1;
           for(jk=1; jk <=nlstate ; jk++){        sw += weight[i];
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               pp[jk] += freq[jk][m][i];  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
           }        if(globpr){
           for(jk=1; jk <=nlstate ; jk++){          fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
             for(m=-1, pos=0; m <=0 ; m++)   %10.6f %10.6f %10.6f ", \
             pos += freq[jk][m][i];                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
                  for(k=1,llt=0.,l=0.; k<=nlstate; k++){
          for(jk=1; jk <=nlstate ; jk++){            llt +=ll[k]*gipmx/gsw;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
              pp[jk] += freq[jk][m][i];          }
          }          fprintf(ficresilk," %10.6f\n", -llt);
                  }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      } /* end of wave */
     } /* end of individual */
          for(jk=1; jk <=nlstate ; jk++){              for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
            if( i <= (int) agemax){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
              if(pos>=1.e-5){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                probs[i][jk][j1]= pp[jk]/pos;    if(globpr==0){ /* First time we count the contributions and weights */
              }      gipmx=ipmx;
            }      gsw=sw;
          }    }
              return -l;
         }  }
     }  
   }  
    void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
    {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /* This routine should help understanding what is done with 
   free_vector(pp,1,nlstate);       the selection of individuals/waves and
         to check the exact contribution to the likelihood.
 }  /* End of Freq */       Plotting could be done.
      */
 /************* Waves Concatenation ***************/    int k;
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    if(*globpri !=0){ /* Just counts and sums no printings */
 {      strcpy(fileresilk,"ilk"); 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      strcat(fileresilk,fileres);
      Death is a valid wave (if date is known).      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        printf("Problem with resultfile: %s\n", fileresilk);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
      and mw[mi+1][i]. dh depends on stepm.      }
      */      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight out sav ");
   int i, mi, m;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      for(k=1; k<=nlstate; k++) 
      double sum=0., jmean=0.;*/        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   int j, k=0,jk, ju, jl;    }
   double sum=0.;  
   jmin=1e+5;    *fretone=(*funcone)(p);
   jmax=-1;    if(*globpri !=0){
   jmean=0.;      fclose(ficresilk);
   for(i=1; i<=imx; i++){      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",fileresilk,fileresilk);
     mi=0;      fflush(fichtm); 
     m=firstpass;    } 
     while(s[m][i] <= nlstate){    return;
       if(s[m][i]>=1)  }
         mw[++mi][i]=m;  
       if(m >=lastpass)  /*********** Maximum Likelihood Estimation ***************/
         break;  
       else  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         m++;  {
     }/* end while */    int i,j, iter;
     if (s[m][i] > nlstate){    double **xi;
       mi++;     /* Death is another wave */    double fret;
       /* if(mi==0)  never been interviewed correctly before death */    double fretone; /* Only one call to likelihood */
          /* Only death is a correct wave */    char filerespow[FILENAMELENGTH];
       mw[mi][i]=m;    xi=matrix(1,npar,1,npar);
     }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
     wav[i]=mi;        xi[i][j]=(i==j ? 1.0 : 0.0);
     if(mi==0)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    strcpy(filerespow,"pow"); 
   }    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
   for(i=1; i<=imx; i++){      printf("Problem with resultfile: %s\n", filerespow);
     for(mi=1; mi<wav[i];mi++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       if (stepm <=0)    }
         dh[mi][i]=1;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       else{    for (i=1;i<=nlstate;i++)
         if (s[mw[mi+1][i]][i] > nlstate) {      for(j=1;j<=nlstate+ndeath;j++)
           if (agedc[i] < 2*AGESUP) {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    fprintf(ficrespow,"\n");
           if(j==0) j=1;  /* Survives at least one month after exam */  
           k=k+1;    powell(p,xi,npar,ftol,&iter,&fret,func);
           if (j >= jmax) jmax=j;  
           if (j <= jmin) jmin=j;    fclose(ficrespow);
           sum=sum+j;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         }  
         else{  }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;  /**** Computes Hessian and covariance matrix ***/
           if (j >= jmax) jmax=j;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           else if (j <= jmin)jmin=j;  {
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    double  **a,**y,*x,pd;
           sum=sum+j;    double **hess;
         }    int i, j,jk;
         jk= j/stepm;    int *indx;
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;    double hessii(double p[], double delta, int theta, double delti[]);
         if(jl <= -ju)    double hessij(double p[], double delti[], int i, int j);
           dh[mi][i]=jk;    void lubksb(double **a, int npar, int *indx, double b[]) ;
         else    void ludcmp(double **a, int npar, int *indx, double *d) ;
           dh[mi][i]=jk+1;  
         if(dh[mi][i]==0)    hess=matrix(1,npar,1,npar);
           dh[mi][i]=1; /* At least one step */  
       }    printf("\nCalculation of the hessian matrix. Wait...\n");
     }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   }    for (i=1;i<=npar;i++){
   jmean=sum/k;      printf("%d",i);fflush(stdout);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      fprintf(ficlog,"%d",i);fflush(ficlog);
  }      hess[i][i]=hessii(p,ftolhess,i,delti);
 /*********** Tricode ****************************/      /*printf(" %f ",p[i]);*/
 void tricode(int *Tvar, int **nbcode, int imx)      /*printf(" %lf ",hess[i][i]);*/
 {    }
   int Ndum[20],ij=1, k, j, i;    
   int cptcode=0;    for (i=1;i<=npar;i++) {
   cptcoveff=0;      for (j=1;j<=npar;j++)  {
          if (j>i) { 
   for (k=0; k<19; k++) Ndum[k]=0;          printf(".%d%d",i,j);fflush(stdout);
   for (k=1; k<=7; k++) ncodemax[k]=0;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          hess[j][i]=hess[i][j];    
     for (i=1; i<=imx; i++) {          /*printf(" %lf ",hess[i][j]);*/
       ij=(int)(covar[Tvar[j]][i]);        }
       Ndum[ij]++;      }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    }
       if (ij > cptcode) cptcode=ij;    printf("\n");
     }    fprintf(ficlog,"\n");
   
     for (i=0; i<=cptcode; i++) {    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       if(Ndum[i]!=0) ncodemax[j]++;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     }    
     ij=1;    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
     x=vector(1,npar);
     for (i=1; i<=ncodemax[j]; i++) {    indx=ivector(1,npar);
       for (k=0; k<=19; k++) {    for (i=1;i<=npar;i++)
         if (Ndum[k] != 0) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           nbcode[Tvar[j]][ij]=k;    ludcmp(a,npar,indx,&pd);
           ij++;  
         }    for (j=1;j<=npar;j++) {
         if (ij > ncodemax[j]) break;      for (i=1;i<=npar;i++) x[i]=0;
       }        x[j]=1;
     }      lubksb(a,npar,indx,x);
   }        for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
  for (k=0; k<19; k++) Ndum[k]=0;      }
     }
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];    printf("\n#Hessian matrix#\n");
       Ndum[ij]++;    fprintf(ficlog,"\n#Hessian matrix#\n");
     }    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
  ij=1;        printf("%.3e ",hess[i][j]);
  for (i=1; i<=10; i++) {        fprintf(ficlog,"%.3e ",hess[i][j]);
    if((Ndum[i]!=0) && (i<=ncov)){      }
      Tvaraff[ij]=i;      printf("\n");
      ij++;      fprintf(ficlog,"\n");
    }    }
  }  
      /* Recompute Inverse */
     cptcoveff=ij-1;    for (i=1;i<=npar;i++)
 }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
 /*********** Health Expectancies ****************/  
     /*  printf("\n#Hessian matrix recomputed#\n");
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  
 {    for (j=1;j<=npar;j++) {
   /* Health expectancies */      for (i=1;i<=npar;i++) x[i]=0;
   int i, j, nhstepm, hstepm, h, nstepm, k;      x[j]=1;
   double age, agelim,hf;      lubksb(a,npar,indx,x);
   double ***p3mat;      for (i=1;i<=npar;i++){ 
          y[i][j]=x[i];
   fprintf(ficreseij,"# Health expectancies\n");        printf("%.3e ",y[i][j]);
   fprintf(ficreseij,"# Age");        fprintf(ficlog,"%.3e ",y[i][j]);
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)      printf("\n");
       fprintf(ficreseij," %1d-%1d",i,j);      fprintf(ficlog,"\n");
   fprintf(ficreseij,"\n");    }
     */
   k=1;             /* For example stepm=6 months */  
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */    free_matrix(a,1,npar,1,npar);
   hstepm=1;   /* or (b) We decided to compute the life expectancy with the smallest unit */    free_matrix(y,1,npar,1,npar);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    free_vector(x,1,npar);
      nhstepm is the number of hstepm from age to agelim    free_ivector(indx,1,npar);
      nstepm is the number of stepm from age to agelin.    free_matrix(hess,1,npar,1,npar);
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  }
      survival function given par stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed only each two years of age and if  /*************** hessian matrix ****************/
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  double hessii( double x[], double delta, int theta, double delti[])
      results. So we changed our mind and took the option of the best precision.  {
   */    int i;
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */    int l=1, lmax=20;
     double k1,k2;
   agelim=AGESUP;    double p2[NPARMAX+1];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double res;
     /* nhstepm age range expressed in number of stepm */    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    double fx;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    int k=0,kmax=10;
     if (stepm >= YEARM) hstepm=1;    double l1;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fx=func(x);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    for (i=1;i<=npar;i++) p2[i]=x[i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    for(l=0 ; l <=lmax; l++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        l1=pow(10,l);
     hf=hstepm/YEARM;  /* Duration of hstepm expressed in year unit. */      delts=delt;
     for(i=1; i<=nlstate;i++)      for(k=1 ; k <kmax; k=k+1){
       for(j=1; j<=nlstate;j++)        delt = delta*(l1*k);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        p2[theta]=x[theta] +delt;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        k1=func(p2)-fx;
           /* 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]);*/        p2[theta]=x[theta]-delt;
         }        k2=func(p2)-fx;
     fprintf(ficreseij,"%3.0f",age );        /*res= (k1-2.0*fx+k2)/delt/delt; */
     for(i=1; i<=nlstate;i++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       for(j=1; j<=nlstate;j++){        
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);  #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(ficreseij,"\n");        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);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #endif
   }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
 /************ 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 if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 {          k=kmax; l=lmax*10.;
   /* Variance of health expectancies */        }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   double **newm;          delts=delt;
   double **dnewm,**doldm;        }
   int i, j, nhstepm, hstepm, h;      }
   int k, cptcode;    }
   double *xp;    delti[theta]=delts;
   double **gp, **gm;    return res; 
   double ***gradg, ***trgradg;    
   double ***p3mat;  }
   double age,agelim;  
   int theta;  double hessij( double x[], double delti[], int thetai,int thetaj)
   {
    fprintf(ficresvij,"# Covariances of life expectancies\n");    int i;
   fprintf(ficresvij,"# Age");    int l=1, l1, lmax=20;
   for(i=1; i<=nlstate;i++)    double k1,k2,k3,k4,res,fx;
     for(j=1; j<=nlstate;j++)    double p2[NPARMAX+1];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    int k;
   fprintf(ficresvij,"\n");  
     fx=func(x);
   xp=vector(1,npar);    for (k=1; k<=2; k++) {
   dnewm=matrix(1,nlstate,1,npar);      for (i=1;i<=npar;i++) p2[i]=x[i];
   doldm=matrix(1,nlstate,1,nlstate);      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   hstepm=1*YEARM; /* Every year of age */      k1=func(p2)-fx;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    
   agelim = AGESUP;      p2[thetai]=x[thetai]+delti[thetai]/k;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      k2=func(p2)-fx;
     if (stepm >= YEARM) hstepm=1;    
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      p2[thetai]=x[thetai]-delti[thetai]/k;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      k3=func(p2)-fx;
     gp=matrix(0,nhstepm,1,nlstate);    
     gm=matrix(0,nhstepm,1,nlstate);      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(theta=1; theta <=npar; theta++){      k4=func(p2)-fx;
       for(i=1; i<=npar; i++){ /* Computes gradient */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  #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);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        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);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  #endif
     }
       if (popbased==1) {    return res;
         for(i=1; i<=nlstate;i++)  }
           prlim[i][i]=probs[(int)age][i][ij];  
       }  /************** Inverse of matrix **************/
    void ludcmp(double **a, int n, int *indx, double *d) 
       for(j=1; j<= nlstate; j++){  { 
         for(h=0; h<=nhstepm; h++){    int i,imax,j,k; 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    double big,dum,sum,temp; 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    double *vv; 
         }   
       }    vv=vector(1,n); 
        *d=1.0; 
       for(i=1; i<=npar; i++) /* Computes gradient */    for (i=1;i<=n;i++) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      big=0.0; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (j=1;j<=n;j++) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        if ((temp=fabs(a[i][j])) > big) big=temp; 
        if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       if (popbased==1) {      vv[i]=1.0/big; 
         for(i=1; i<=nlstate;i++)    } 
           prlim[i][i]=probs[(int)age][i][ij];    for (j=1;j<=n;j++) { 
       }      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
       for(j=1; j<= nlstate; j++){        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         for(h=0; h<=nhstepm; h++){        a[i][j]=sum; 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      } 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      big=0.0; 
         }      for (i=j;i<=n;i++) { 
       }        sum=a[i][j]; 
         for (k=1;k<j;k++) 
       for(j=1; j<= nlstate; j++)          sum -= a[i][k]*a[k][j]; 
         for(h=0; h<=nhstepm; h++){        a[i][j]=sum; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         }          big=dum; 
     } /* End theta */          imax=i; 
         } 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      } 
       if (j != imax) { 
     for(h=0; h<=nhstepm; h++)        for (k=1;k<=n;k++) { 
       for(j=1; j<=nlstate;j++)          dum=a[imax][k]; 
         for(theta=1; theta <=npar; theta++)          a[imax][k]=a[j][k]; 
           trgradg[h][j][theta]=gradg[h][theta][j];          a[j][k]=dum; 
         } 
     for(i=1;i<=nlstate;i++)        *d = -(*d); 
       for(j=1;j<=nlstate;j++)        vv[imax]=vv[j]; 
         vareij[i][j][(int)age] =0.;      } 
     for(h=0;h<=nhstepm;h++){      indx[j]=imax; 
       for(k=0;k<=nhstepm;k++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      if (j != n) { 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        dum=1.0/(a[j][j]); 
         for(i=1;i<=nlstate;i++)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           for(j=1;j<=nlstate;j++)      } 
             vareij[i][j][(int)age] += doldm[i][j];    } 
       }    free_vector(vv,1,n);  /* Doesn't work */
     }  ;
     h=1;  } 
     if (stepm >= YEARM) h=stepm/YEARM;  
     fprintf(ficresvij,"%.0f ",age );  void lubksb(double **a, int n, int *indx, double b[]) 
     for(i=1; i<=nlstate;i++)  { 
       for(j=1; j<=nlstate;j++){    int i,ii=0,ip,j; 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    double sum; 
       }   
     fprintf(ficresvij,"\n");    for (i=1;i<=n;i++) { 
     free_matrix(gp,0,nhstepm,1,nlstate);      ip=indx[i]; 
     free_matrix(gm,0,nhstepm,1,nlstate);      sum=b[ip]; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      b[ip]=b[i]; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      if (ii) 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   } /* End age */      else if (sum) ii=i; 
        b[i]=sum; 
   free_vector(xp,1,npar);    } 
   free_matrix(doldm,1,nlstate,1,npar);    for (i=n;i>=1;i--) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 }      b[i]=sum/a[i][i]; 
     } 
 /************ Variance of prevlim ******************/  } 
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  
 {  /************ Frequencies ********************/
   /* Variance of prevalence limit */  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  {  /* Some frequencies */
   double **newm;    
   double **dnewm,**doldm;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   int i, j, nhstepm, hstepm;    int first;
   int k, cptcode;    double ***freq; /* Frequencies */
   double *xp;    double *pp, **prop;
   double *gp, *gm;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   double **gradg, **trgradg;    FILE *ficresp;
   double age,agelim;    char fileresp[FILENAMELENGTH];
   int theta;    
        pp=vector(1,nlstate);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    prop=matrix(1,nlstate,iagemin,iagemax+3);
   fprintf(ficresvpl,"# Age");    strcpy(fileresp,"p");
   for(i=1; i<=nlstate;i++)    strcat(fileresp,fileres);
       fprintf(ficresvpl," %1d-%1d",i,i);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   fprintf(ficresvpl,"\n");      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   xp=vector(1,npar);      exit(0);
   dnewm=matrix(1,nlstate,1,npar);    }
   doldm=matrix(1,nlstate,1,nlstate);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
      j1=0;
   hstepm=1*YEARM; /* Every year of age */    
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    j=cptcoveff;
   agelim = AGESUP;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    first=1;
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for(k1=1; k1<=j;k1++){
     gradg=matrix(1,npar,1,nlstate);      for(i1=1; i1<=ncodemax[k1];i1++){
     gp=vector(1,nlstate);        j1++;
     gm=vector(1,nlstate);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
     for(theta=1; theta <=npar; theta++){        for (i=-1; i<=nlstate+ndeath; i++)  
       for(i=1; i<=npar; i++){ /* Computes gradient */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            for(m=iagemin; m <= iagemax+3; m++)
       }              freq[i][jk][m]=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)      for (i=1; i<=nlstate; i++)  
         gp[i] = prlim[i][i];        for(m=iagemin; m <= iagemax+3; m++)
              prop[i][m]=0;
       for(i=1; i<=npar; i++) /* Computes gradient */        
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        dateintsum=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        k2cpt=0;
       for(i=1;i<=nlstate;i++)        for (i=1; i<=imx; i++) {
         gm[i] = prlim[i][i];          bool=1;
           if  (cptcovn>0) {
       for(i=1;i<=nlstate;i++)            for (z1=1; z1<=cptcoveff; z1++) 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     } /* End theta */                bool=0;
           }
     trgradg =matrix(1,nlstate,1,npar);          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
     for(j=1; j<=nlstate;j++)              k2=anint[m][i]+(mint[m][i]/12.);
       for(theta=1; theta <=npar; theta++)              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         trgradg[j][theta]=gradg[theta][j];                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
     for(i=1;i<=nlstate;i++)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       varpl[i][(int)age] =0.;                if (m<lastpass) {
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     for(i=1;i<=nlstate;i++)                }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     fprintf(ficresvpl,"%.0f ",age );                  dateintsum=dateintsum+k2;
     for(i=1; i<=nlstate;i++)                  k2cpt++;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));                }
     fprintf(ficresvpl,"\n");                /*}*/
     free_vector(gp,1,nlstate);            }
     free_vector(gm,1,nlstate);          }
     free_matrix(gradg,1,npar,1,nlstate);        }
     free_matrix(trgradg,1,nlstate,1,npar);         
   } /* End age */        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
   free_vector(xp,1,npar);        if  (cptcovn>0) {
   free_matrix(doldm,1,nlstate,1,npar);          fprintf(ficresp, "\n#********** Variable "); 
   free_matrix(dnewm,1,nlstate,1,nlstate);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
 }        }
         for(i=1; i<=nlstate;i++) 
 /************ Variance of one-step probabilities  ******************/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        fprintf(ficresp, "\n");
 {        
   int i, j;        for(i=iagemin; i <= iagemax+3; i++){
   int k=0, cptcode;          if(i==iagemax+3){
   double **dnewm,**doldm;            fprintf(ficlog,"Total");
   double *xp;          }else{
   double *gp, *gm;            if(first==1){
   double **gradg, **trgradg;              first=0;
   double age,agelim, cov[NCOVMAX];              printf("See log file for details...\n");
   int theta;            }
   char fileresprob[FILENAMELENGTH];            fprintf(ficlog,"Age %d", i);
           }
   strcpy(fileresprob,"prob");          for(jk=1; jk <=nlstate ; jk++){
   strcat(fileresprob,fileres);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {              pp[jk] += freq[jk][m][i]; 
     printf("Problem with resultfile: %s\n", fileresprob);          }
   }          for(jk=1; jk <=nlstate ; jk++){
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);            for(m=-1, pos=0; m <=0 ; m++)
                pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
   xp=vector(1,npar);              if(first==1){
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));              }
                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   cov[1]=1;            }else{
   for (age=bage; age<=fage; age ++){              if(first==1)
     cov[2]=age;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     gradg=matrix(1,npar,1,9);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     trgradg=matrix(1,9,1,npar);            }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          }
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
              for(jk=1; jk <=nlstate ; jk++){
     for(theta=1; theta <=npar; theta++){            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for(i=1; i<=npar; i++)              pp[jk] += freq[jk][m][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }       
                for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            pos += pp[jk];
                posprop += prop[jk][i];
       k=0;          }
       for(i=1; i<= (nlstate+ndeath); i++){          for(jk=1; jk <=nlstate ; jk++){
         for(j=1; j<=(nlstate+ndeath);j++){            if(pos>=1.e-5){
            k=k+1;              if(first==1)
           gp[k]=pmmij[i][j];                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       }            }else{
               if(first==1)
       for(i=1; i<=npar; i++)                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                }
             if( i <= iagemax){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              if(pos>=1.e-5){
       k=0;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       for(i=1; i<=(nlstate+ndeath); i++){                /*probs[i][jk][j1]= pp[jk]/pos;*/
         for(j=1; j<=(nlstate+ndeath);j++){                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
           k=k+1;              }
           gm[k]=pmmij[i][j];              else
         }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       }            }
                }
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            for(jk=-1; jk <=nlstate+ndeath; jk++)
     }            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)              if(first==1)
       for(theta=1; theta <=npar; theta++)                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       trgradg[j][theta]=gradg[theta][j];                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                }
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          if(i <= iagemax)
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);            fprintf(ficresp,"\n");
           if(first==1)
      pmij(pmmij,cov,ncovmodel,x,nlstate);            printf("Others in log...\n");
           fprintf(ficlog,"\n");
      k=0;        }
      for(i=1; i<=(nlstate+ndeath); i++){      }
        for(j=1; j<=(nlstate+ndeath);j++){    }
          k=k+1;    dateintmean=dateintsum/k2cpt; 
          gm[k]=pmmij[i][j];   
         }    fclose(ficresp);
      }    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
          free_vector(pp,1,nlstate);
      /*printf("\n%d ",(int)age);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    /* End of Freq */
          }
   
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  /************ Prevalence ********************/
      }*/  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
   fprintf(ficresprob,"\n%d ",(int)age);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){       We still use firstpass and lastpass as another selection.
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    */
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);   
   }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    double *pp, **prop;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    double pos,posprop; 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double  y2; /* in fractional years */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int iagemin, iagemax;
 }  
  free_vector(xp,1,npar);    iagemin= (int) agemin;
 fclose(ficresprob);    iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
 }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 /******************* Printing html file ***********/    j1=0;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){    
   int jj1, k1, i1, cpt;    j=cptcoveff;
   FILE *fichtm;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   /*char optionfilehtm[FILENAMELENGTH];*/    
     for(k1=1; k1<=j;k1++){
   strcpy(optionfilehtm,optionfile);      for(i1=1; i1<=ncodemax[k1];i1++){
   strcat(optionfilehtm,".htm");        j1++;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        
     printf("Problem with %s \n",optionfilehtm), exit(0);        for (i=1; i<=nlstate; i++)  
   }          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71a </font> <hr size=\"2\" color=\"#EC5E5E\">       
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
 Total number of observations=%d <br>          if  (cptcovn>0) {
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>            for (z1=1; z1<=cptcoveff; z1++) 
 <hr  size=\"2\" color=\"#EC5E5E\">              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 <li>Outputs files<br><br>\n                bool=0;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          } 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          if (bool==1) { 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>                if (s[m][i]>0 && s[m][i]<=nlstate) { 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);                  prop[s[m][i]][iagemax+3] += weight[i]; 
                  } 
 fprintf(fichtm," <li>Graphs</li><p>");              }
             } /* end selection of waves */
  m=cptcoveff;          }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        }
         for(i=iagemin; i <= iagemax+3; i++){  
  jj1=0;          
  for(k1=1; k1<=m;k1++){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
    for(i1=1; i1<=ncodemax[k1];i1++){            posprop += prop[jk][i]; 
        jj1++;          } 
        if (cptcovn > 0) {  
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          for(jk=1; jk <=nlstate ; jk++){     
          for (cpt=1; cpt<=cptcoveff;cpt++)            if( i <=  iagemax){ 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);              if(posprop>=1.e-5){ 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                probs[i][jk][j1]= prop[jk][i]/posprop;
        }              } 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>            } 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              }/* end jk */ 
        for(cpt=1; cpt<nlstate;cpt++){        }/* end i */ 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      } /* end i1 */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    } /* end k1 */
        }    
     for(cpt=1; cpt<=nlstate;cpt++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    /*free_vector(pp,1,nlstate);*/
 interval) in state (%d): v%s%d%d.gif <br>    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    }  /* End of prevalence */
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {  /************* Waves Concatenation ***************/
         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,jj1,strtok(optionfile, "."),cpt,jj1);  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
      }  {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 health expectancies in states (1) and (2): e%s%d.gif<br>       Death is a valid wave (if date is known).
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 fprintf(fichtm,"\n</body>");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
    }       and mw[mi+1][i]. dh depends on stepm.
    }       */
 fclose(fichtm);  
 }    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 /******************* Gnuplot file **************/       double sum=0., jmean=0.;*/
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){    int first;
     int j, k=0,jk, ju, jl;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    double sum=0.;
     first=0;
   strcpy(optionfilegnuplot,optionfilefiname);    jmin=1e+5;
   strcat(optionfilegnuplot,".plt");    jmax=-1;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    jmean=0.;
     printf("Problem with file %s",optionfilegnuplot);    for(i=1; i<=imx; i++){
   }      mi=0;
       m=firstpass;
 #ifdef windows      while(s[m][i] <= nlstate){
     fprintf(ficgp,"cd \"%s\" \n",pathc);        if(s[m][i]>=1)
 #endif          mw[++mi][i]=m;
 m=pow(2,cptcoveff);        if(m >=lastpass)
            break;
  /* 1eme*/        else
   for (cpt=1; cpt<= nlstate ; cpt ++) {          m++;
    for (k1=1; k1<= m ; k1 ++) {      }/* end while */
       if (s[m][i] > nlstate){
 #ifdef windows        mi++;     /* Death is another wave */
     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);        /* if(mi==0)  never been interviewed correctly before death */
 #endif           /* Only death is a correct wave */
 #ifdef unix        mw[mi][i]=m;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      }
 #endif  
       wav[i]=mi;
 for (i=1; i<= nlstate ; i ++) {      if(mi==0){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if(first==0){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 }          first=1;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        }
     for (i=1; i<= nlstate ; i ++) {        if(first==1){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }      } /* end mi==0 */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    } /* End individuals */
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for(i=1; i<=imx; i++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(mi=1; mi<wav[i];mi++){
 }          if (stepm <=0)
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          dh[mi][i]=1;
 #ifdef unix        else{
 fprintf(ficgp,"\nset ter gif small size 400,300");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 #endif            if (agedc[i] < 2*AGESUP) {
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
    }              if(j==0) j=1;  /* Survives at least one month after exam */
   }              else if(j<0){
   /*2 eme*/                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 j=1; /* Careful Patch */
   for (k1=1; k1<= m ; k1 ++) {                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                    fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
     for (i=1; i<= nlstate+1 ; i ++) {              }
       k=2*i;              k=k+1;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              if (j >= jmax) jmax=j;
       for (j=1; j<= nlstate+1 ; j ++) {              if (j <= jmin) jmin=j;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              sum=sum+j;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
 }                /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       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);          else{
       for (j=1; j<= nlstate+1 ; j ++) {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");            k=k+1;
 }              if (j >= jmax) jmax=j;
       fprintf(ficgp,"\" t\"\" w l 0,");            else if (j <= jmin)jmin=j;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       for (j=1; j<= nlstate+1 ; j ++) {            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            if(j<0){
   else fprintf(ficgp," \%%*lf (\%%*lf)");              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 }                fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            }
       else fprintf(ficgp,"\" t\"\" w l 0,");            sum=sum+j;
     }          }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          jk= j/stepm;
   }          jl= j -jk*stepm;
            ju= j -(jk+1)*stepm;
   /*3eme*/          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
   for (k1=1; k1<= m ; k1 ++) {              dh[mi][i]=jk;
     for (cpt=1; cpt<= nlstate ; cpt ++) {              bh[mi][i]=0;
       k=2+nlstate*(cpt-1);            }else{ /* We want a negative bias in order to only have interpolation ie
       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);                    * at the price of an extra matrix product in likelihood */
       for (i=1; i< nlstate ; i ++) {              dh[mi][i]=jk+1;
         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);              bh[mi][i]=ju;
       }            }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          }else{
     }            if(jl <= -ju){
     }              dh[mi][i]=jk;
                bh[mi][i]=jl;       /* bias is positive if real duration
   /* CV preval stat */                                   * is higher than the multiple of stepm and negative otherwise.
     for (k1=1; k1<= m ; k1 ++) {                                   */
     for (cpt=1; cpt<nlstate ; cpt ++) {            }
       k=3;            else{
       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/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
       for (i=1; i< nlstate ; i ++)            }
         fprintf(ficgp,"+$%d",k+i+1);            if(dh[mi][i]==0){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              dh[mi][i]=1; /* At least one step */
                    bh[mi][i]=ju; /* At least one step */
       l=3+(nlstate+ndeath)*cpt;              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            }
       for (i=1; i< nlstate ; i ++) {          } /* end if mle */
         l=3+(nlstate+ndeath)*cpt;        }
         fprintf(ficgp,"+$%d",l+i+1);      } /* end wave */
       }    }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      jmean=sum/k;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     }    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   }     }
    
   /* proba elementaires */  /*********** Tricode ****************************/
    for(i=1,jk=1; i <=nlstate; i++){  void tricode(int *Tvar, int **nbcode, int imx)
     for(k=1; k <=(nlstate+ndeath); k++){  {
       if (k != i) {    
         for(j=1; j <=ncovmodel; j++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
            int cptcode=0;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    cptcoveff=0; 
           jk++;   
           fprintf(ficgp,"\n");    for (k=0; k<maxncov; k++) Ndum[k]=0;
         }    for (k=1; k<=7; k++) ncodemax[k]=0;
       }  
     }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
     for(jk=1; jk <=m; jk++) {        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);        Ndum[ij]++; /*store the modality */
    i=1;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
    for(k2=1; k2<=nlstate; k2++) {        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
      k3=i;                                         Tvar[j]. If V=sex and male is 0 and 
      for(k=1; k<=(nlstate+ndeath); k++) {                                         female is 1, then  cptcode=1.*/
        if (k != k2){      }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;      for (i=0; i<=cptcode; i++) {
         for(j=3; j <=ncovmodel; j++) {        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      }
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;      ij=1; 
           }      for (i=1; i<=ncodemax[j]; i++) {
           else        for (k=0; k<= maxncov; k++) {
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          if (Ndum[k] != 0) {
         }            nbcode[Tvar[j]][ij]=k; 
           fprintf(ficgp,")/(1");            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                    
         for(k1=1; k1 <=nlstate; k1++){              ij++;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          }
 ij=1;          if (ij > ncodemax[j]) break; 
           for(j=3; j <=ncovmodel; j++){        }  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      } 
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    }  
             ij++;  
           }   for (k=0; k< maxncov; k++) Ndum[k]=0;
           else  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);   for (i=1; i<=ncovmodel-2; i++) { 
           }     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           fprintf(ficgp,")");     ij=Tvar[i];
         }     Ndum[ij]++;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);   }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
         i=i+ncovmodel;   ij=1;
        }   for (i=1; i<= maxncov; i++) {
      }     if((Ndum[i]!=0) && (i<=ncovcol)){
    }       Tvaraff[ij]=i; /*For printing */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);       ij++;
    }     }
       }
   fclose(ficgp);   
 }  /* end gnuplot */   cptcoveff=ij-1; /*Number of simple covariates*/
   }
   
 /*************** Moving average **************/  /*********** Health Expectancies ****************/
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){  
   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 )
   int i, cpt, cptcod;  
     for (agedeb=agemin; agedeb<=fage; agedeb++)  {
       for (i=1; i<=nlstate;i++)    /* Health expectancies */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
           mobaverage[(int)agedeb][i][cptcod]=0.;    double age, agelim, hf;
        double ***p3mat,***varhe;
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    double **dnewm,**doldm;
       for (i=1; i<=nlstate;i++){    double *xp;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double **gp, **gm;
           for (cpt=0;cpt<=4;cpt++){    double ***gradg, ***trgradg;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    int theta;
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         }    xp=vector(1,npar);
       }    dnewm=matrix(1,nlstate*nlstate,1,npar);
     }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
        
 }    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
 /************** Forecasting ******************/      for(j=1; j<=nlstate;j++)
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
      fprintf(ficreseij,"\n");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;    if(estepm < stepm){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      printf ("Problem %d lower than %d\n",estepm, stepm);
   double *popeffectif,*popcount;    }
   double ***p3mat;    else  hstepm=estepm;   
   char fileresf[FILENAMELENGTH];    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
  agelim=AGESUP;     * if stepm=24 months pijx are given only every 2 years and by summing them
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     * 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 
   strcpy(fileresf,"f");     * hypothesis. A more precise result, taking into account a more precise
   strcat(fileresf,fileres);     * curvature will be obtained if estepm is as small as stepm. */
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);    /* For example we decided to compute the life expectancy with the smallest unit */
   }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   printf("Computing forecasting: result on file '%s' \n", fileresf);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
   if (mobilav==1) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       survival function given by stepm (the optimization length). Unfortunately it
     movingaverage(agedeb, fage, agemin, mobaverage);       means that if the survival funtion is printed only each two years of age and if
   }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
   stepsize=(int) (stepm+YEARM-1)/YEARM;    */
   if (stepm<=12) stepsize=1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    
   agelim=AGESUP;    agelim=AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   hstepm=1;      /* nhstepm age range expressed in number of stepm */
   hstepm=hstepm/stepm;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   yp1=modf(dateintmean,&yp);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   anprojmean=yp;      /* if (stepm >= YEARM) hstepm=1;*/
   yp2=modf((yp1*12),&yp);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   mprojmean=yp;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   yp1=modf((yp2*30.5),&yp);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   jprojmean=yp;      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   if(jprojmean==0) jprojmean=1;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   if(mprojmean==0) jprojmean=1;  
        /* Computed by stepm unit matrices, product of hstepm matrices, stored
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   for(cptcov=1;cptcov<=i2;cptcov++){   
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fprintf(ficresf,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {      /* Computing Variances of health expectancies */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }       for(theta=1; theta <=npar; theta++){
       fprintf(ficresf,"******\n");        for(i=1; i<=npar; i++){ 
       fprintf(ficresf,"# StartingAge FinalAge");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        }
              hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        cptj=0;
         fprintf(ficresf,"\n");        for(j=1; j<= nlstate; j++){
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            for(i=1; i<=nlstate; i++){
             cptj=cptj+1;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           nhstepm = nhstepm/hstepm;            }
                    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
           oldm=oldms;savm=savms;       
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         
                for(i=1; i<=npar; i++) 
           for (h=0; h<=nhstepm; h++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             if (h==(int) (calagedate+YEARM*cpt)) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);        
             }        cptj=0;
             for(j=1; j<=nlstate+ndeath;j++) {        for(j=1; j<= nlstate; j++){
               kk1=0.;kk2=0;          for(i=1;i<=nlstate;i++){
               for(i=1; i<=nlstate;i++) {                          cptj=cptj+1;
                 if (mobilav==1)            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            }
                 }          }
                        }
               }        for(j=1; j<= nlstate*nlstate; j++)
               if (h==(int)(calagedate+12*cpt)){          for(h=0; h<=nhstepm-1; h++){
                 fprintf(ficresf," %.3f", kk1);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                                  }
               }       } 
             }     
           }  /* End theta */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       }  
     }       for(h=0; h<=nhstepm-1; h++)
   }        for(j=1; j<=nlstate*nlstate;j++)
                  for(theta=1; theta <=npar; theta++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            trgradg[h][j][theta]=gradg[h][theta][j];
        
   fclose(ficresf);  
 }       for(i=1;i<=nlstate*nlstate;i++)
 /************** Forecasting ******************/        for(j=1;j<=nlstate*nlstate;j++)
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){          varhe[i][j][(int)age] =0.;
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       printf("%d|",(int)age);fflush(stdout);
   int *popage;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;       for(h=0;h<=nhstepm-1;h++){
   double *popeffectif,*popcount;        for(k=0;k<=nhstepm-1;k++){
   double ***p3mat,***tabpop,***tabpopprev;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   char filerespop[FILENAMELENGTH];          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(i=1;i<=nlstate*nlstate;i++)
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(j=1;j<=nlstate*nlstate;j++)
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   agelim=AGESUP;        }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      }
        /* Computing expectancies */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
            for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   strcpy(filerespop,"pop");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   strcat(filerespop,fileres);            
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     printf("Problem with forecast resultfile: %s\n", filerespop);  
   }          }
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
       fprintf(ficreseij,"%3.0f",age );
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      cptj=0;
       for(i=1; i<=nlstate;i++)
   if (mobilav==1) {        for(j=1; j<=nlstate;j++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          cptj++;
     movingaverage(agedeb, fage, agemin, mobaverage);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   }        }
       fprintf(ficreseij,"\n");
   stepsize=(int) (stepm+YEARM-1)/YEARM;     
   if (stepm<=12) stepsize=1;      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
        free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   agelim=AGESUP;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   hstepm=1;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   hstepm=hstepm/stepm;    }
      printf("\n");
   if (popforecast==1) {    fprintf(ficlog,"\n");
     if((ficpop=fopen(popfile,"r"))==NULL) {  
       printf("Problem with population file : %s\n",popfile);exit(0);    free_vector(xp,1,npar);
     }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     popage=ivector(0,AGESUP);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     popeffectif=vector(0,AGESUP);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     popcount=vector(0,AGESUP);  }
      
     i=1;    /************ Variance ******************/
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  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)
      {
     imx=i;    /* Variance of health expectancies */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   }    /* double **newm;*/
     double **dnewm,**doldm;
   for(cptcov=1;cptcov<=i2;cptcov++){    double **dnewmp,**doldmp;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int i, j, nhstepm, hstepm, h, nstepm ;
       k=k+1;    int k, cptcode;
       fprintf(ficrespop,"\n#******");    double *xp;
       for(j=1;j<=cptcoveff;j++) {    double **gp, **gm;  /* for var eij */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ***gradg, ***trgradg; /*for var eij */
       }    double **gradgp, **trgradgp; /* for var p point j */
       fprintf(ficrespop,"******\n");    double *gpp, *gmp; /* for var p point j */
       fprintf(ficrespop,"# Age");    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    double ***p3mat;
       if (popforecast==1)  fprintf(ficrespop," [Population]");    double age,agelim, hf;
          double ***mobaverage;
       for (cpt=0; cpt<=0;cpt++) {    int theta;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      char digit[4];
            char digitp[25];
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    char fileresprobmorprev[FILENAMELENGTH];
           nhstepm = nhstepm/hstepm;  
              if(popbased==1){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if(mobilav!=0)
           oldm=oldms;savm=savms;        strcpy(digitp,"-populbased-mobilav-");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        else strcpy(digitp,"-populbased-nomobil-");
            }
           for (h=0; h<=nhstepm; h++){    else 
             if (h==(int) (calagedate+YEARM*cpt)) {      strcpy(digitp,"-stablbased-");
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }    if (mobilav!=0) {
             for(j=1; j<=nlstate+ndeath;j++) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               kk1=0.;kk2=0;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
               for(i=1; i<=nlstate;i++) {                      fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                 if (mobilav==1)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      }
                 else {    }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }    strcpy(fileresprobmorprev,"prmorprev"); 
               }    sprintf(digit,"%-d",ij);
               if (h==(int)(calagedate+12*cpt)){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
                   /*fprintf(ficrespop," %.3f", kk1);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    strcat(fileresprobmorprev,fileres);
               }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
             }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
             for(i=1; i<=nlstate;i++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
               kk1=0.;    }
                 for(j=1; j<=nlstate;j++){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                 }    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
             }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      for(i=1; i<=nlstate;i++)
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           }    }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresprobmorprev,"\n");
         }    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);
     }
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    else{
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        fprintf(ficgp,"\n# Routine varevsij");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
           nhstepm = nhstepm/hstepm;  /*     printf("Problem with html file: %s\n", optionfilehtm); */
            /*     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*     exit(0); */
           oldm=oldms;savm=savms;  /*   } */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*   else{ */
           for (h=0; h<=nhstepm; h++){    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  /*   } */
             }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    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");
               for(i=1; i<=nlstate;i++) {                  fprintf(ficresvij,"# Age");
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        for(i=1; i<=nlstate;i++)
               }      for(j=1; j<=nlstate;j++)
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
             }    fprintf(ficresvij,"\n");
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    xp=vector(1,npar);
         }    dnewm=matrix(1,nlstate,1,npar);
       }    doldm=matrix(1,nlstate,1,nlstate);
    }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
   if (popforecast==1) {    gmp=vector(nlstate+1,nlstate+ndeath);
     free_ivector(popage,0,AGESUP);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     free_vector(popeffectif,0,AGESUP);    
     free_vector(popcount,0,AGESUP);    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    else  hstepm=estepm;   
   fclose(ficrespop);    /* For example we decided to compute the life expectancy with the smallest unit */
 }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
 /***********************************************/       nstepm is the number of stepm from age to agelin. 
 /**************** Main Program *****************/       Look at hpijx to understand the reason of that which relies in memory size
 /***********************************************/       and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 int main(int argc, char *argv[])       survival function given by stepm (the optimization length). Unfortunately it
 {       means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;       results. So we changed our mind and took the option of the best precision.
   double agedeb, agefin,hf;    */
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   double fret;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double **xi,tmp,delta;      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 */
   double dum; /* Dummy variable */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double ***p3mat;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   int *indx;      gp=matrix(0,nhstepm,1,nlstate);
   char line[MAXLINE], linepar[MAXLINE];      gm=matrix(0,nhstepm,1,nlstate);
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   char filerest[FILENAMELENGTH];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   char fileregp[FILENAMELENGTH];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        if (popbased==1) {
   int firstobs=1, lastobs=10;          if(mobilav ==0){
   int sdeb, sfin; /* Status at beginning and end */            for(i=1; i<=nlstate;i++)
   int c,  h , cpt,l;              prlim[i][i]=probs[(int)age][i][ij];
   int ju,jl, mi;          }else{ /* mobilav */ 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            for(i=1; i<=nlstate;i++)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              prlim[i][i]=mobaverage[(int)age][i][ij];
   int mobilav=0,popforecast=0;          }
   int hstepm, nhstepm;        }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    
         for(j=1; j<= nlstate; j++){
   double bage, fage, age, agelim, agebase;          for(h=0; h<=nhstepm; h++){
   double ftolpl=FTOL;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   double **prlim;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   double *severity;          }
   double ***param; /* Matrix of parameters */        }
   double  *p;        /* This for computing probability of death (h=1 means
   double **matcov; /* Matrix of covariance */           computed over hstepm matrices product = hstepm*stepm months) 
   double ***delti3; /* Scale */           as a weighted average of prlim.
   double *delti; /* Scale */        */
   double ***eij, ***vareij;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   double **varpl; /* Variances of prevalence limits by age */          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   double *epj, vepp;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   double kk1, kk2;        }    
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        /* end probability of death */
    
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   char version[80]="Imach version 0.71a, March 2002, INED-EUROREVES ";          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   char *alph[]={"a","a","b","c","d","e"}, str[4];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   char z[1]="c", occ;        if (popbased==1) {
 #include <sys/time.h>          if(mobilav ==0){
 #include <time.h>            for(i=1; i<=nlstate;i++)
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
   /* long total_usecs;            for(i=1; i<=nlstate;i++)
   struct timeval start_time, end_time;              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        }
   
         for(j=1; j<= nlstate; j++){
   printf("\n%s",version);          for(h=0; h<=nhstepm; h++){
   if(argc <=1){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     printf("\nEnter the parameter file name: ");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     scanf("%s",pathtot);          }
   }        }
   else{        /* This for computing probability of death (h=1 means
     strcpy(pathtot,argv[1]);           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        */
   /*cygwin_split_path(pathtot,path,optionfile);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   /* cutv(path,optionfile,pathtot,'\\');*/           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        /* end probability of death */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);        for(j=1; j<= nlstate; j++) /* vareij */
   replace(pathc,path);          for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 /*-------- arguments in the command line --------*/          }
   
   strcpy(fileres,"r");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   strcat(fileres, optionfilefiname);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   strcat(fileres,".txt");    /* Other files have txt extension */        }
   
   /*---------arguments file --------*/      } /* End theta */
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;      for(h=0; h<=nhstepm; h++) /* veij */
   }        for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   strcpy(filereso,"o");            trgradg[h][j][theta]=gradg[h][theta][j];
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        for(theta=1; theta <=npar; theta++)
   }          trgradgp[j][theta]=gradgp[theta][j];
     
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     ungetc(c,ficpar);      for(i=1;i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);        for(j=1;j<=nlstate;j++)
     puts(line);          vareij[i][j][(int)age] =0.;
     fputs(line,ficparo);  
   }      for(h=0;h<=nhstepm;h++){
   ungetc(c,ficpar);        for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   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);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   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(i=1;i<=nlstate;i++)
   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(j=1;j<=nlstate;j++)
 while((c=getc(ficpar))=='#' && c!= EOF){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      }
     puts(line);    
     fputs(line,ficparo);      /* pptj */
   }      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);
        for(j=nlstate+1;j<=nlstate+ndeath;j++)
            for(i=nlstate+1;i<=nlstate+ndeath;i++)
   covar=matrix(0,NCOVMAX,1,n);          varppt[j][i]=doldmp[j][i];
   cptcovn=0;      /* end ppptj */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   ncovmodel=2+cptcovn;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */   
        if (popbased==1) {
   /* Read guess parameters */        if(mobilav ==0){
   /* Reads comments: lines beginning with '#' */          for(i=1; i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){            prlim[i][i]=probs[(int)age][i][ij];
     ungetc(c,ficpar);        }else{ /* mobilav */ 
     fgets(line, MAXLINE, ficpar);          for(i=1; i<=nlstate;i++)
     puts(line);            prlim[i][i]=mobaverage[(int)age][i][ij];
     fputs(line,ficparo);        }
   }      }
   ungetc(c,ficpar);               
        /* This for computing probability of death (h=1 means
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     for(i=1; i <=nlstate; i++)         as a weighted average of prlim.
     for(j=1; j <=nlstate+ndeath-1; j++){      */
       fscanf(ficpar,"%1d%1d",&i1,&j1);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fprintf(ficparo,"%1d%1d",i1,j1);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       printf("%1d%1d",i,j);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       for(k=1; k<=ncovmodel;k++){      }    
         fscanf(ficpar," %lf",&param[i][j][k]);      /* end probability of death */
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fscanf(ficpar,"\n");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       printf("\n");        for(i=1; i<=nlstate;i++){
       fprintf(ficparo,"\n");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     }        }
        } 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      fprintf(ficresprobmorprev,"\n");
   
   p=param[1][1];      fprintf(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */        for(j=1; j<=nlstate;j++){
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      fprintf(ficresvij,"\n");
     puts(line);      free_matrix(gp,0,nhstepm,1,nlstate);
     fputs(line,ficparo);      free_matrix(gm,0,nhstepm,1,nlstate);
   }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   ungetc(c,ficpar);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    } /* End age */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    free_vector(gpp,nlstate+1,nlstate+ndeath);
   for(i=1; i <=nlstate; i++){    free_vector(gmp,nlstate+1,nlstate+ndeath);
     for(j=1; j <=nlstate+ndeath-1; j++){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       printf("%1d%1d",i,j);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       fprintf(ficparo,"%1d%1d",i1,j1);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       for(k=1; k<=ncovmodel;k++){    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         fscanf(ficpar,"%le",&delti3[i][j][k]);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
         printf(" %le",delti3[i][j][k]);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
         fprintf(ficparo," %le",delti3[i][j][k]);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
       fscanf(ficpar,"\n");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
       printf("\n");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
       fprintf(ficparo,"\n");    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
   }    /*  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);
   delti=delti3[1][1];  */
      fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    free_vector(xp,1,npar);
     ungetc(c,ficpar);    free_matrix(doldm,1,nlstate,1,nlstate);
     fgets(line, MAXLINE, ficpar);    free_matrix(dnewm,1,nlstate,1,npar);
     puts(line);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   ungetc(c,ficpar);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fclose(ficresprobmorprev);
   matcov=matrix(1,npar,1,npar);    fclose(ficgp);
   for(i=1; i <=npar; i++){  /*   fclose(fichtm); */
     fscanf(ficpar,"%s",&str);  }  /* end varevsij */
     printf("%s",str);  
     fprintf(ficparo,"%s",str);  /************ Variance of prevlim ******************/
     for(j=1; j <=i; j++){  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)
       fscanf(ficpar," %le",&matcov[i][j]);  {
       printf(" %.5le",matcov[i][j]);    /* Variance of prevalence limit */
       fprintf(ficparo," %.5le",matcov[i][j]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     }    double **newm;
     fscanf(ficpar,"\n");    double **dnewm,**doldm;
     printf("\n");    int i, j, nhstepm, hstepm;
     fprintf(ficparo,"\n");    int k, cptcode;
   }    double *xp;
   for(i=1; i <=npar; i++)    double *gp, *gm;
     for(j=i+1;j<=npar;j++)    double **gradg, **trgradg;
       matcov[i][j]=matcov[j][i];    double age,agelim;
        int theta;
   printf("\n");     
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
     /*-------- Rewriting paramater file ----------*/    for(i=1; i<=nlstate;i++)
      strcpy(rfileres,"r");    /* "Rparameterfile */        fprintf(ficresvpl," %1d-%1d",i,i);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    fprintf(ficresvpl,"\n");
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    xp=vector(1,npar);
     if((ficres =fopen(rfileres,"w"))==NULL) {    dnewm=matrix(1,nlstate,1,npar);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    doldm=matrix(1,nlstate,1,nlstate);
     }    
     fprintf(ficres,"#%s\n",version);    hstepm=1*YEARM; /* Every year of age */
        hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     /*-------- data file ----------*/    agelim = AGESUP;
     if((fic=fopen(datafile,"r"))==NULL)    {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       printf("Problem with datafile: %s\n", datafile);goto end;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     }      if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     n= lastobs;      gradg=matrix(1,npar,1,nlstate);
     severity = vector(1,maxwav);      gp=vector(1,nlstate);
     outcome=imatrix(1,maxwav+1,1,n);      gm=vector(1,nlstate);
     num=ivector(1,n);  
     moisnais=vector(1,n);      for(theta=1; theta <=npar; theta++){
     annais=vector(1,n);        for(i=1; i<=npar; i++){ /* Computes gradient */
     moisdc=vector(1,n);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     andc=vector(1,n);        }
     agedc=vector(1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     cod=ivector(1,n);        for(i=1;i<=nlstate;i++)
     weight=vector(1,n);          gp[i] = prlim[i][i];
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      
     mint=matrix(1,maxwav,1,n);        for(i=1; i<=npar; i++) /* Computes gradient */
     anint=matrix(1,maxwav,1,n);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     s=imatrix(1,maxwav+1,1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     adl=imatrix(1,maxwav+1,1,n);            for(i=1;i<=nlstate;i++)
     tab=ivector(1,NCOVMAX);          gm[i] = prlim[i][i];
     ncodemax=ivector(1,8);  
         for(i=1;i<=nlstate;i++)
     i=1;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     while (fgets(line, MAXLINE, fic) != NULL)    {      } /* End theta */
       if ((i >= firstobs) && (i <=lastobs)) {  
              trgradg =matrix(1,nlstate,1,npar);
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      for(j=1; j<=nlstate;j++)
           strcpy(line,stra);        for(theta=1; theta <=npar; theta++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          trgradg[j][theta]=gradg[theta][j];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }      for(i=1;i<=nlstate;i++)
                varpl[i][(int)age] =0.;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
       fprintf(ficresvpl,"%.0f ",age );
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      for(i=1; i<=nlstate;i++)
         for (j=ncov;j>=1;j--){        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficresvpl,"\n");
         }      free_vector(gp,1,nlstate);
         num[i]=atol(stra);      free_vector(gm,1,nlstate);
              free_matrix(gradg,1,npar,1,nlstate);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      free_matrix(trgradg,1,nlstate,1,npar);
           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;}*/    } /* End age */
   
         i=i+1;    free_vector(xp,1,npar);
       }    free_matrix(doldm,1,nlstate,1,npar);
     }    free_matrix(dnewm,1,nlstate,1,nlstate);
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/  }
   imx=i-1; /* Number of individuals */  
   /************ Variance of one-step probabilities  ******************/
   /* for (i=1; i<=imx; i++){  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
     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;    int i, j=0,  i1, k1, l1, t, tj;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    int k2, l2, j1,  z1;
     }    int k=0,l, cptcode;
     int first=1, first1;
     for (i=1; i<=imx; i++)    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     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]));*/    double **dnewm,**doldm;
     double *xp;
   /* Calculation of the number of parameter from char model*/    double *gp, *gm;
   Tvar=ivector(1,15);    double **gradg, **trgradg;
   Tprod=ivector(1,15);    double **mu;
   Tvaraff=ivector(1,15);    double age,agelim, cov[NCOVMAX];
   Tvard=imatrix(1,15,1,2);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   Tage=ivector(1,15);          int theta;
        char fileresprob[FILENAMELENGTH];
   if (strlen(model) >1){    char fileresprobcov[FILENAMELENGTH];
     j=0, j1=0, k1=1, k2=1;    char fileresprobcor[FILENAMELENGTH];
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');    double ***varpij;
     cptcovn=j+1;  
     cptcovprod=j1;    strcpy(fileresprob,"prob"); 
        strcat(fileresprob,fileres);
        if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     strcpy(modelsav,model);      printf("Problem with resultfile: %s\n", fileresprob);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       printf("Error. Non available option model=%s ",model);    }
       goto end;    strcpy(fileresprobcov,"probcov"); 
     }    strcat(fileresprobcov,fileres);
        if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     for(i=(j+1); i>=1;i--){      printf("Problem with resultfile: %s\n", fileresprobcov);
       cutv(stra,strb,modelsav,'+');      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    strcpy(fileresprobcor,"probcor"); 
       /*scanf("%d",i);*/    strcat(fileresprobcor,fileres);
       if (strchr(strb,'*')) {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         cutv(strd,strc,strb,'*');      printf("Problem with resultfile: %s\n", fileresprobcor);
         if (strcmp(strc,"age")==0) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
           cptcovprod--;    }
           cutv(strb,stre,strd,'V');    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           Tvar[i]=atoi(stre);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           cptcovage++;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
             Tage[cptcovage]=i;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
             /*printf("stre=%s ", stre);*/    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         else if (strcmp(strd,"age")==0) {    
           cptcovprod--;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           cutv(strb,stre,strc,'V');    fprintf(ficresprob,"# Age");
           Tvar[i]=atoi(stre);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           cptcovage++;    fprintf(ficresprobcov,"# Age");
           Tage[cptcovage]=i;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
         }    fprintf(ficresprobcov,"# Age");
         else {  
           cutv(strb,stre,strc,'V');  
           Tvar[i]=ncov+k1;    for(i=1; i<=nlstate;i++)
           cutv(strb,strc,strd,'V');      for(j=1; j<=(nlstate+ndeath);j++){
           Tprod[k1]=i;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
           Tvard[k1][1]=atoi(strc);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
           Tvard[k1][2]=atoi(stre);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           Tvar[cptcovn+k2]=Tvard[k1][1];      }  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];   /* fprintf(ficresprob,"\n");
           for (k=1; k<=lastobs;k++)    fprintf(ficresprobcov,"\n");
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    fprintf(ficresprobcor,"\n");
           k1++;   */
           k2=k2+2;   xp=vector(1,npar);
         }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       else {    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
        /*  scanf("%d",i);*/    first=1;
       cutv(strd,strc,strb,'V');    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       Tvar[i]=atoi(strc);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       strcpy(modelsav,stra);        exit(0);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    }
         scanf("%d",i);*/    else{
     }      fprintf(ficgp,"\n# Routine varprob");
 }    }
    /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  /*     printf("Problem with html file: %s\n", optionfilehtm); */
   printf("cptcovprod=%d ", cptcovprod);  /*     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); */
   scanf("%d ",i);*/  /*     exit(0); */
     fclose(fic);  /*   } */
   /*   else{ */
     /*  if(mle==1){*/      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     if (weightopt != 1) { /* Maximisation without weights*/      fprintf(fichtm,"\n");
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
     /*-calculation of age at interview from date of interview and age at death -*/      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");
     agev=matrix(1,maxwav,1,imx);      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");
   
    for (i=1; i<=imx; i++)  /*   } */
      for(m=2; (m<= maxwav); m++)  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    cov[1]=1;
          anint[m][i]=9999;    tj=cptcoveff;
          s[m][i]=-1;    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++){ 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        j1++;
       for(m=1; (m<= maxwav); m++){        if  (cptcovn>0) {
         if(s[m][i] >0){          fprintf(ficresprob, "\n#********** Variable "); 
           if (s[m][i] == nlstate+1) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             if(agedc[i]>0)          fprintf(ficresprob, "**********\n#\n");
               if(moisdc[i]!=99 && andc[i]!=9999)          fprintf(ficresprobcov, "\n#********** Variable "); 
               agev[m][i]=agedc[i];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             else {          fprintf(ficresprobcov, "**********\n#\n");
               if (andc[i]!=9999){          
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          fprintf(ficgp, "\n#********** Variable "); 
               agev[m][i]=-1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               }          fprintf(ficgp, "**********\n#\n");
             }          
           }          
           else if(s[m][i] !=9){ /* Should no more exist */          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             if(mint[m][i]==99 || anint[m][i]==9999)          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
               agev[m][i]=1;          
             else if(agev[m][i] <agemin){          fprintf(ficresprobcor, "\n#********** Variable ");    
               agemin=agev[m][i];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          fprintf(ficresprobcor, "**********\n#");    
             }        }
             else if(agev[m][i] >agemax){        
               agemax=agev[m][i];        for (age=bage; age<=fage; age ++){ 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          cov[2]=age;
             }          for (k=1; k<=cptcovn;k++) {
             /*agev[m][i]=anint[m][i]-annais[i];*/            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
             /*   agev[m][i] = age[i]+2*m;*/          }
           }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           else { /* =9 */          for (k=1; k<=cptcovprod;k++)
             agev[m][i]=1;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             s[m][i]=-1;          
           }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         }          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         else /*= 0 Unknown */          gp=vector(1,(nlstate)*(nlstate+ndeath));
           agev[m][i]=1;          gm=vector(1,(nlstate)*(nlstate+ndeath));
       }      
              for(theta=1; theta <=npar; theta++){
     }            for(i=1; i<=npar; i++)
     for (i=1; i<=imx; i++)  {              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       for(m=1; (m<= maxwav); m++){            
         if (s[m][i] > (nlstate+ndeath)) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           printf("Error: Wrong value in nlstate or ndeath\n");              
           goto end;            k=0;
         }            for(i=1; i<= (nlstate); i++){
       }              for(j=1; j<=(nlstate+ndeath);j++){
     }                k=k+1;
                 gp[k]=pmmij[i][j];
 printf("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);            for(i=1; i<=npar; i++)
     free_vector(moisnais,1,n);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     free_vector(annais,1,n);      
     /* free_matrix(mint,1,maxwav,1,n);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
        free_matrix(anint,1,maxwav,1,n);*/            k=0;
     free_vector(moisdc,1,n);            for(i=1; i<=(nlstate); i++){
     free_vector(andc,1,n);              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                    gm[k]=pmmij[i][j];
     wav=ivector(1,imx);              }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);       
                for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     /* Concatenates waves */              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       Tcode=ivector(1,100);            for(theta=1; theta <=npar; theta++)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              trgradg[j][theta]=gradg[theta][j];
       ncodemax[1]=1;          
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
    codtab=imatrix(1,100,1,10);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
    h=0;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
    m=pow(2,cptcoveff);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
            free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){          pmij(pmmij,cov,ncovmodel,x,nlstate);
        for(j=1; j <= ncodemax[k]; j++){          
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          k=0;
            h++;          for(i=1; i<=(nlstate); i++){
            if (h>m) h=1;codtab[h][k]=j;            for(j=1; j<=(nlstate+ndeath);j++){
          }              k=k+1;
        }              mu[k][(int) age]=pmmij[i][j];
      }            }
    }          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
    /*for(i=1; i <=m ;i++){              varpij[i][j][(int)age] = doldm[i][j];
      for(k=1; k <=cptcovn; k++){  
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          /*printf("\n%d ",(int)age);
      }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
      printf("\n");            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
    }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
    scanf("%d",i);*/            }*/
      
    /* Calculates basic frequencies. Computes observed prevalence at single age          fprintf(ficresprob,"\n%d ",(int)age);
        and prints on file fileres'p'. */          fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
      
              for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          }
                i=0;
     /* For Powell, parameters are in a vector p[] starting at p[1]          for (k=1; k<=(nlstate);k++){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */            for (l=1; l<=(nlstate+ndeath);l++){ 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */              i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     if(mle==1){              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              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]));
     /*--------- 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= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);            }
            }/* end of loop for state */
         } /* end of loop for age */
    jk=1;  
    fprintf(ficres,"# Parameters\n");        /* Confidence intervalle of pij  */
    printf("# Parameters\n");        /*
    for(i=1,jk=1; i <=nlstate; i++){          fprintf(ficgp,"\nset noparametric;unset label");
      for(k=1; k <=(nlstate+ndeath); k++){          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
        if (k != i)          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
          {          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
            printf("%d%d ",i,k);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
            fprintf(ficres,"%1d%1d ",i,k);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
            for(j=1; j <=ncovmodel; j++){          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
              printf("%f ",p[jk]);        */
              fprintf(ficres,"%f ",p[jk]);  
              jk++;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
            }        first1=1;
            printf("\n");        for (k2=1; k2<=(nlstate);k2++){
            fprintf(ficres,"\n");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
          }            if(l2==k2) continue;
      }            j=(k2-1)*(nlstate+ndeath)+l2;
    }            for (k1=1; k1<=(nlstate);k1++){
  if(mle==1){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     /* Computing hessian and covariance matrix */                if(l1==k1) continue;
     ftolhess=ftol; /* Usually correct */                i=(k1-1)*(nlstate+ndeath)+l1;
     hesscov(matcov, p, npar, delti, ftolhess, func);                if(i<=j) continue;
  }                for (age=bage; age<=fage; age ++){ 
     fprintf(ficres,"# Scales\n");                  if ((int)age %5==0){
     printf("# Scales\n");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
      for(i=1,jk=1; i <=nlstate; i++){                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       for(j=1; j <=nlstate+ndeath; j++){                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         if (j!=i) {                    mu1=mu[i][(int) age]/stepm*YEARM ;
           fprintf(ficres,"%1d%1d",i,j);                    mu2=mu[j][(int) age]/stepm*YEARM;
           printf("%1d%1d",i,j);                    c12=cv12/sqrt(v1*v2);
           for(k=1; k<=ncovmodel;k++){                    /* Computing eigen value of matrix of covariance */
             printf(" %.5e",delti[jk]);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
             fprintf(ficres," %.5e",delti[jk]);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
             jk++;                    /* Eigen vectors */
           }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           printf("\n");                    /*v21=sqrt(1.-v11*v11); *//* error */
           fprintf(ficres,"\n");                    v21=(lc1-v1)/cv12*v11;
         }                    v12=-v21;
       }                    v22=v11;
      }                    tnalp=v21/v11;
                        if(first1==1){
     k=1;                      first1=0;
     fprintf(ficres,"# Covariance\n");                      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);
     printf("# Covariance\n");                    }
     for(i=1;i<=npar;i++){                    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);
       /*  if (k>nlstate) k=1;                    /*printf(fignu*/
       i1=(i-1)/(ncovmodel*nlstate)+1;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       printf("%s%d%d",alph[k],i1,tab[i]);*/                    if(first==1){
       fprintf(ficres,"%3d",i);                      first=0;
       printf("%3d",i);                      fprintf(ficgp,"\nset parametric;unset label");
       for(j=1; j<=i;j++){                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
         fprintf(ficres," %.5e",matcov[i][j]);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         printf(" %.5e",matcov[i][j]);                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
       }                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
       fprintf(ficres,"\n");                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       printf("\n");                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
       k++;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                          fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     while((c=getc(ficpar))=='#' && c!= EOF){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       ungetc(c,ficpar);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       fgets(line, MAXLINE, ficpar);                    }else{
       puts(line);                      first=0;
       fputs(line,ficparo);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
     }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     ungetc(c,ficpar);                      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",\
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                  mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     if (fage <= 2) {                    }/* if first */
       bage = agemin;                  } /* age mod 5 */
       fage = agemaxpar;                } /* end loop age */
     }                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                    first=1;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");              } /*l12 */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);            } /* k12 */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          } /*l1 */
          }/* k1 */
     while((c=getc(ficpar))=='#' && c!= EOF){      } /* loop covariates */
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     puts(line);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     fputs(line,ficparo);    free_vector(xp,1,npar);
   }    fclose(ficresprob);
   ungetc(c,ficpar);    fclose(ficresprobcov);
      fclose(ficresprobcor);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    fclose(ficgp);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  }
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
        
   while((c=getc(ficpar))=='#' && c!= EOF){  /******************* Printing html file ***********/
     ungetc(c,ficpar);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     fgets(line, MAXLINE, ficpar);                    int lastpass, int stepm, int weightopt, char model[],\
     puts(line);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     fputs(line,ficparo);                    int popforecast, int estepm ,\
   }                    double jprev1, double mprev1,double anprev1, \
   ungetc(c,ficpar);                    double jprev2, double mprev2,double anprev2){
      int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   fscanf(ficpar,"pop_based=%d\n",&popbased);  /*   } */
   fprintf(ficparo,"pop_based=%d\n",popbased);    
   fprintf(ficres,"pop_based=%d\n",popbased);       fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
     - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n \
   while((c=getc(ficpar))=='#' && c!= EOF){   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
     ungetc(c,ficpar);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
     fgets(line, MAXLINE, ficpar);   - Life expectancies by age and initial health status (estepm=%2d months): \
     puts(line);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
     fputs(line,ficparo);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   }  
   ungetc(c,ficpar);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);   m=cptcoveff;
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
    jj1=0;
    for(k1=1; k1<=m;k1++){
 while((c=getc(ficpar))=='#' && c!= EOF){     for(i1=1; i1<=ncodemax[k1];i1++){
     ungetc(c,ficpar);       jj1++;
     fgets(line, MAXLINE, ficpar);       if (cptcovn > 0) {
     puts(line);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fputs(line,ficparo);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   ungetc(c,ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);       /* Pij */
   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(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> \
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       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> \
 /*------------ gnuplot -------------*/  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);         /* Stable prevalence in each health state */
           for(cpt=1; cpt<nlstate;cpt++){
 /*------------ free_vector  -------------*/           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
  chdir(path);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           }
  free_ivector(wav,1,imx);       for(cpt=1; cpt<=nlstate;cpt++) {
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
  free_ivector(num,1,n);       }
  free_vector(agedc,1,n);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  health expectancies in states (1) and (2): e%s%d.png<br>\
  fclose(ficparo);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
  fclose(ficres);     } /* end i1 */
    }/* End k1 */
 /*--------- index.htm --------*/   fprintf(fichtm,"</ul>");
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);  
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
     - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
   /*--------------- Prevalence limit --------------*/   - 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\
   strcpy(filerespl,"pl");   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
   strcat(filerespl,fileres);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
   if((ficrespl=fopen(filerespl,"w"))==NULL) {   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;   - 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);
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  /*  if(popforecast==1) fprintf(fichtm,"\n */
   fprintf(ficrespl,"#Prevalence limit\n");  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   fprintf(ficrespl,"#Age ");  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  /*      <br>",fileres,fileres,fileres,fileres); */
   fprintf(ficrespl,"\n");  /*  else  */
    /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   prlim=matrix(1,nlstate,1,nlstate);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   m=cptcoveff;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */   jj1=0;
   k=0;   for(k1=1; k1<=m;k1++){
   agebase=agemin;     for(i1=1; i1<=ncodemax[k1];i1++){
   agelim=agemaxpar;       jj1++;
   ftolpl=1.e-10;       if (cptcovn > 0) {
   i1=cptcoveff;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   if (cptcovn < 1){i1=1;}         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   for(cptcov=1;cptcov<=i1;cptcov++){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       }
         k=k+1;       for(cpt=1; cpt<=nlstate;cpt++) {
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
         fprintf(ficrespl,"\n#******");  interval) in state (%d): v%s%d%d.png <br>\
         for(j=1;j<=cptcoveff;j++)  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       }
         fprintf(ficrespl,"******\n");     } /* end i1 */
           }/* End k1 */
         for (age=agebase; age<=agelim; age++){   fprintf(fichtm,"</ul>");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   fflush(fichtm);
           fprintf(ficrespl,"%.0f",age );  }
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);  /******************* Gnuplot file **************/
           fprintf(ficrespl,"\n");  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         }  
       }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     }    int ng;
   fclose(ficrespl);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
   /*------------- h Pij x at various ages ------------*/      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
      }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    /*#ifdef windows */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      fprintf(ficgp,"cd \"%s\" \n",pathc);
   }      /*#endif */
   printf("Computing pij: result on file '%s' \n", filerespij);  m=pow(2,cptcoveff);
      
   stepsize=(int) (stepm+YEARM-1)/YEARM;   /* 1eme*/
   /*if (stepm<=24) stepsize=2;*/    for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
   agelim=AGESUP;       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   hstepm=stepsize*YEARM; /* Every year of age */       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);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
         for (i=1; i<= nlstate ; i ++) {
   k=0;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   for(cptcov=1;cptcov<=i1;cptcov++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       }
       k=k+1;       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
         fprintf(ficrespij,"\n#****** ");       for (i=1; i<= nlstate ; i ++) {
         for(j=1;j<=cptcoveff;j++)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         fprintf(ficrespij,"******\n");       } 
               fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */       for (i=1; i<= nlstate ; i ++) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */         else fprintf(ficgp," \%%*lf (\%%*lf)");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       }  
           oldm=oldms;savm=savms;       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       }
           fprintf(ficrespij,"# Age");    }
           for(i=1; i<=nlstate;i++)    /*2 eme*/
             for(j=1; j<=nlstate+ndeath;j++)    
               fprintf(ficrespij," %1d-%1d",i,j);    for (k1=1; k1<= m ; k1 ++) { 
           fprintf(ficrespij,"\n");      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
           for (h=0; h<=nhstepm; h++){      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      
             for(i=1; i<=nlstate;i++)      for (i=1; i<= nlstate+1 ; i ++) {
               for(j=1; j<=nlstate+ndeath;j++)        k=2*i;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
             fprintf(ficrespij,"\n");        for (j=1; j<= nlstate+1 ; j ++) {
           }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          else fprintf(ficgp," \%%*lf (\%%*lf)");
           fprintf(ficrespij,"\n");        }   
         }        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     }        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   fclose(ficrespij);        }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
   /*---------- Forecasting ------------------*/        for (j=1; j<= nlstate+1 ; j ++) {
   if((stepm == 1) && (model==".")){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          else fprintf(ficgp," \%%*lf (\%%*lf)");
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        }   
     free_matrix(mint,1,maxwav,1,n);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        else fprintf(ficgp,"\" t\"\" w l 0,");
     free_vector(weight,1,n);}      }
   else{    }
     erreur=108;    
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);    /*3eme*/
   }    
      for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
   /*---------- Health expectancies and variances ------------*/        k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   strcpy(filerest,"t");        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
   strcat(filerest,fileres);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   if((ficrest=fopen(filerest,"w"))==NULL) {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
   strcpy(filerese,"e");        */
   strcat(filerese,fileres);        for (i=1; i< nlstate ; i ++) {
   if((ficreseij=fopen(filerese,"w"))==NULL) {          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);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          
   }        } 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      }
     }
  strcpy(fileresv,"v");    
   strcat(fileresv,fileres);    /* CV preval stable (period) */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    for (k1=1; k1<= m ; k1 ++) { 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      for (cpt=1; cpt<=nlstate ; cpt ++) {
   }        k=3;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
   k=0;        
   for(cptcov=1;cptcov<=i1;cptcov++){        for (i=1; i< nlstate ; i ++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficgp,"+$%d",k+i+1);
       k=k+1;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
       fprintf(ficrest,"\n#****** ");        
       for(j=1;j<=cptcoveff;j++)        l=3+(nlstate+ndeath)*cpt;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
       fprintf(ficrest,"******\n");        for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
       fprintf(ficreseij,"\n#****** ");          fprintf(ficgp,"+$%d",l+i+1);
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       fprintf(ficreseij,"******\n");      } 
     }  
       fprintf(ficresvij,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    /* proba elementaires */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficresvij,"******\n");      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for(j=1; j <=ncovmodel; j++){
       oldm=oldms;savm=savms;            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);              jk++; 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            fprintf(ficgp,"\n");
       oldm=oldms;savm=savms;          }
        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) ");     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);       for(jk=1; jk <=m; jk++) {
       fprintf(ficrest,"\n");         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
       hf=1;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
       if (stepm >= YEARM) hf=stepm/YEARM;         else
       epj=vector(1,nlstate+1);           fprintf(ficgp,"\nset title \"Probability\"\n");
       for(age=bage; age <=fage ;age++){         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);         i=1;
         if (popbased==1) {         for(k2=1; k2<=nlstate; k2++) {
           for(i=1; i<=nlstate;i++)           k3=i;
             prlim[i][i]=probs[(int)age][i][k];           for(k=1; k<=(nlstate+ndeath); k++) {
         }             if (k != k2){
                       if(ng==2)
         fprintf(ficrest," %.0f",age);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){               else
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];               ij=1;
           }               for(j=3; j <=ncovmodel; j++) {
           epj[nlstate+1] +=epj[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]]]);
         for(i=1, vepp=0.;i <=nlstate;i++)                   ij++;
           for(j=1;j <=nlstate;j++)                 }
             vepp += vareij[i][j][(int)age];                 else
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         for(j=1;j <=nlstate;j++){               }
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));               fprintf(ficgp,")/(1");
         }               
         fprintf(ficrest,"\n");               for(k1=1; k1 <=nlstate; k1++){   
       }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     }                 ij=1;
   }                 for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   fclose(ficreseij);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   fclose(ficresvij);                     ij++;
   fclose(ficrest);                   }
   fclose(ficpar);                   else
   free_vector(epj,1,nlstate+1);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   }
   /*------- Variance limit prevalence------*/                   fprintf(ficgp,")");
                }
   strcpy(fileresvpl,"vpl");               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   strcat(fileresvpl,fileres);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {               i=i+ncovmodel;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);             }
     exit(0);           } /* end k */
   }         } /* end k2 */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);       } /* end jk */
      } /* end ng */
   k=0;     fclose(ficgp); 
   for(cptcov=1;cptcov<=i1;cptcov++){  }  /* end gnuplot */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;  
       fprintf(ficresvpl,"\n#****** ");  /*************** Moving average **************/
       for(j=1;j<=cptcoveff;j++)  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\n");    int i, cpt, cptcod;
          int modcovmax =1;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    int mobilavrange, mob;
       oldm=oldms;savm=savms;    double age;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
     }    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
  }                             a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   fclose(ficresvpl);  
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   /*---------- End : free ----------------*/      if(mobilav==1) mobilavrange=5; /* default */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      else mobilavrange=mobilav;
        for (age=bage; age<=fage; age++)
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        for (i=1; i<=nlstate;i++)
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        /* We keep the original values on the extreme ages bage, fage and for 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);         we use a 5 terms etc. until the borders are no more concerned. 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      */ 
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      for (mob=3;mob <=mobilavrange;mob=mob+2){
          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   free_matrix(matcov,1,npar,1,npar);          for (i=1; i<=nlstate;i++){
   free_vector(delti,1,npar);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   free_matrix(agev,1,maxwav,1,imx);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   if(erreur >0)                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     printf("End of Imach with error %d\n",erreur);                }
   else   printf("End of Imach\n");              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   /*  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);*/        }/* end age */
   /*printf("Total time was %d uSec.\n", total_usecs);*/      }/* end mob */
   /*------ End -----------*/    }else return -1;
     return 0;
   }/* End movingaverage */
  end:  
 #ifdef windows  
   /* chdir(pathcd);*/  /************** Forecasting ******************/
 #endif  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
  /*system("wgnuplot graph.plt");*/    /* proj1, year, month, day of starting projection 
  /*system("../gp37mgw/wgnuplot graph.plt");*/       agemin, agemax range of age
  /*system("cd ../gp37mgw");*/       dateprev1 dateprev2 range of dates during which prevalence is computed
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/       anproj2 year of en of projection (same day and month as proj1).
  strcpy(plotcmd,GNUPLOTPROGRAM);    */
  strcat(plotcmd," ");    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
  strcat(plotcmd,optionfilegnuplot);    int *popage;
  system(plotcmd);    double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
 #ifdef windows    double *popeffectif,*popcount;
   while (z[0] != 'q') {    double ***p3mat;
     chdir(path);    double ***mobaverage;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    char fileresf[FILENAMELENGTH];
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");    agelim=AGESUP;
     else if (z[0] == 'e') {    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       chdir(path);   
       system(optionfilehtm);    strcpy(fileresf,"f"); 
     }    strcat(fileresf,fileres);
     else if (z[0] == 'q') exit(0);    if((ficresf=fopen(fileresf,"w"))==NULL) {
   }      printf("Problem with forecast resultfile: %s\n", fileresf);
 #endif      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
 }    }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[132],pathc[132],pathcd[132],pathtot[132],model[132];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char *strt, *strtend;
     char *stratrunc;
     int lstra;
   
     long total_usecs;
     struct timeval start_time, end_time, curr_time;
     struct timezone tzp;
     extern int gettimeofday();
     struct tm tmg, tm, *gmtime(), *localtime();
     long time_value;
     extern long time();
    
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strt=asctime(&tm);
   
   /*  printf("Localtime (at start)=%s",strt); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strt);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strt=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strt); 
   */
   
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 132)!= 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,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%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\n%s",version,fullversion);
     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);
   
     printf("Localtime (at start)=%s",strt);
     fprintf(ficlog,"Localtime (at start)=%s",strt);
     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);
       fflush(ficlog);
       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);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     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);
     numlinepar++;
     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);
     fprintf(ficlog,"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);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         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");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     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);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%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]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     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]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       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");
   
     fflush(ficlog);
   
     /*-------- 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=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.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("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ 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);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %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\
   <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><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
             model,fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strt);
     /*fclose(fichtm);*/
     fflush(fichtm);
   
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
   /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
   /*     printf("Problem with file: %s\n", optionfilehtm); */
   /*     fprintf(ficlog,"Problem with file: %s\n", optionfilehtm); */
   /*   } */
   
   
   /*   if(fileappend(fichtm, optionfilehtm)){ */
       fprintf(fichtm,"\n");
       fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
           imx,agemin,agemax,jmin,jmax,jmean);
   /*     fclose(fichtm); */
   /*   } */
   
       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) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strtend=asctime(&tm);
     printf("Localtime at start %s and at end=%s",strt, strtend); 
     fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend); 
     /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
   
     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);
     fprintf(ficlog,"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);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Localtime at start %s and at end=%s<br>",strt, strtend);
     fclose(fichtm);
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.31  
changed lines
  Added in v.1.87


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