Diff for /imach/src/imach.c between versions 1.27 and 1.87

version 1.27, 2002/02/28 17:49:07 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, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      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 */
              ipmx +=1;
         for(i=(int)agemin; i <= (int)agemax+3; i++){        sw += weight[i];
           for(jk=1; jk <=nlstate ; jk++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  /*       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]); */
               pp[jk] += freq[jk][m][i];        if(globpr){
           }          fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
           for(jk=1; jk <=nlstate ; jk++){   %10.6f %10.6f %10.6f ", \
             for(m=-1, pos=0; m <=0 ; m++)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
             pos += freq[jk][m][i];                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                    llt +=ll[k]*gipmx/gsw;
          for(jk=1; jk <=nlstate ; jk++){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          }
              pp[jk] += freq[jk][m][i];          fprintf(ficresilk," %10.6f\n", -llt);
          }        }
                } /* end of wave */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
          for(jk=1; jk <=nlstate ; jk++){              /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
            if( i <= (int) agemax){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
              if(pos>=1.e-5){    if(globpr==0){ /* First time we count the contributions and weights */
                probs[i][jk][j1]= pp[jk]/pos;      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 []))
    {
      /* This routine should help understanding what is done with 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);       the selection of individuals/waves and
   free_vector(pp,1,nlstate);       to check the exact contribution to the likelihood.
         Plotting could be done.
 }  /* End of Freq */     */
     int k;
 /************* Waves Concatenation ***************/  
     if(*globpri !=0){ /* Just counts and sums no printings */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      strcpy(fileresilk,"ilk"); 
 {      strcat(fileresilk,fileres);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
      Death is a valid wave (if date is known).        printf("Problem with resultfile: %s\n", fileresilk);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        fprintf(ficlog,"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]      }
      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 ");
       /*  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 i, mi, m;      for(k=1; k<=nlstate; k++) 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
      double sum=0., jmean=0.;*/      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   int j, k=0,jk, ju, jl;  
   double sum=0.;    *fretone=(*funcone)(p);
   jmin=1e+5;    if(*globpri !=0){
   jmax=-1;      fclose(ficresilk);
   jmean=0.;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",fileresilk,fileresilk);
   for(i=1; i<=imx; i++){      fflush(fichtm); 
     mi=0;    } 
     m=firstpass;    return;
     while(s[m][i] <= nlstate){  }
       if(s[m][i]>=1)  
         mw[++mi][i]=m;  /*********** Maximum Likelihood Estimation ***************/
       if(m >=lastpass)  
         break;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       else  {
         m++;    int i,j, iter;
     }/* end while */    double **xi;
     if (s[m][i] > nlstate){    double fret;
       mi++;     /* Death is another wave */    double fretone; /* Only one call to likelihood */
       /* if(mi==0)  never been interviewed correctly before death */    char filerespow[FILENAMELENGTH];
          /* Only death is a correct wave */    xi=matrix(1,npar,1,npar);
       mw[mi][i]=m;    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
     wav[i]=mi;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     if(mi==0)    strcpy(filerespow,"pow"); 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    strcat(filerespow,fileres);
   }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
   for(i=1; i<=imx; i++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for(mi=1; mi<wav[i];mi++){    }
       if (stepm <=0)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         dh[mi][i]=1;    for (i=1;i<=nlstate;i++)
       else{      for(j=1;j<=nlstate+ndeath;j++)
         if (s[mw[mi+1][i]][i] > nlstate) {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
           if (agedc[i] < 2*AGESUP) {    fprintf(ficrespow,"\n");
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */    powell(p,xi,npar,ftol,&iter,&fret,func);
           k=k+1;  
           if (j >= jmax) jmax=j;    fclose(ficrespow);
           if (j <= jmin) jmin=j;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           sum=sum+j;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           /* if (j<10) printf("j=%d num=%d ",j,i); */    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));  /**** Computes Hessian and covariance matrix ***/
           k=k+1;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           if (j >= jmax) jmax=j;  {
           else if (j <= jmin)jmin=j;    double  **a,**y,*x,pd;
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    double **hess;
           sum=sum+j;    int i, j,jk;
         }    int *indx;
         jk= j/stepm;  
         jl= j -jk*stepm;    double hessii(double p[], double delta, int theta, double delti[]);
         ju= j -(jk+1)*stepm;    double hessij(double p[], double delti[], int i, int j);
         if(jl <= -ju)    void lubksb(double **a, int npar, int *indx, double b[]) ;
           dh[mi][i]=jk;    void ludcmp(double **a, int npar, int *indx, double *d) ;
         else  
           dh[mi][i]=jk+1;    hess=matrix(1,npar,1,npar);
         if(dh[mi][i]==0)  
           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++){
   }      printf("%d",i);fflush(stdout);
   jmean=sum/k;      fprintf(ficlog,"%d",i);fflush(ficlog);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      hess[i][i]=hessii(p,ftolhess,i,delti);
  }      /*printf(" %f ",p[i]);*/
 /*********** Tricode ****************************/      /*printf(" %lf ",hess[i][i]);*/
 void tricode(int *Tvar, int **nbcode, int imx)    }
 {    
   int Ndum[20],ij=1, k, j, i;    for (i=1;i<=npar;i++) {
   int cptcode=0;      for (j=1;j<=npar;j++)  {
   cptcoveff=0;        if (j>i) { 
            printf(".%d%d",i,j);fflush(stdout);
   for (k=0; k<19; k++) Ndum[k]=0;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   for (k=1; k<=7; k++) ncodemax[k]=0;          hess[i][j]=hessij(p,delti,i,j);
           hess[j][i]=hess[i][j];    
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          /*printf(" %lf ",hess[i][j]);*/
     for (i=1; i<=imx; i++) {        }
       ij=(int)(covar[Tvar[j]][i]);      }
       Ndum[ij]++;    }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    printf("\n");
       if (ij > cptcode) cptcode=ij;    fprintf(ficlog,"\n");
     }  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for (i=0; i<=cptcode; i++) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       if(Ndum[i]!=0) ncodemax[j]++;    
     }    a=matrix(1,npar,1,npar);
     ij=1;    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
     indx=ivector(1,npar);
     for (i=1; i<=ncodemax[j]; i++) {    for (i=1;i<=npar;i++)
       for (k=0; k<=19; k++) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         if (Ndum[k] != 0) {    ludcmp(a,npar,indx,&pd);
           nbcode[Tvar[j]][ij]=k;  
           ij++;    for (j=1;j<=npar;j++) {
         }      for (i=1;i<=npar;i++) x[i]=0;
         if (ij > ncodemax[j]) break;      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++) {    printf("\n#Hessian matrix#\n");
       ij=Tvar[i];    fprintf(ficlog,"\n#Hessian matrix#\n");
       Ndum[ij]++;    for (i=1;i<=npar;i++) { 
     }      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
  ij=1;        fprintf(ficlog,"%.3e ",hess[i][j]);
  for (i=1; i<=10; i++) {      }
    if((Ndum[i]!=0) && (i<=ncov)){      printf("\n");
      Tvaraff[ij]=i;      fprintf(ficlog,"\n");
      ij++;    }
    }  
  }    /* Recompute Inverse */
      for (i=1;i<=npar;i++)
     cptcoveff=ij-1;      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++) {
 {      for (i=1;i<=npar;i++) x[i]=0;
   /* Health expectancies */      x[j]=1;
   int i, j, nhstepm, hstepm, h;      lubksb(a,npar,indx,x);
   double age, agelim,hf;      for (i=1;i<=npar;i++){ 
   double ***p3mat;        y[i][j]=x[i];
          printf("%.3e ",y[i][j]);
   fprintf(ficreseij,"# Health expectancies\n");        fprintf(ficlog,"%.3e ",y[i][j]);
   fprintf(ficreseij,"# Age");      }
   for(i=1; i<=nlstate;i++)      printf("\n");
     for(j=1; j<=nlstate;j++)      fprintf(ficlog,"\n");
       fprintf(ficreseij," %1d-%1d",i,j);    }
   fprintf(ficreseij,"\n");    */
   
   hstepm=1*YEARM; /*  Every j years of age (in month) */    free_matrix(a,1,npar,1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
   agelim=AGESUP;    free_ivector(indx,1,npar);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    free_matrix(hess,1,npar,1,npar);
     /* nhstepm age range expressed in number of stepm */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years = 20*12/6=40 stepm */  }
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */  /*************** hessian matrix ****************/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  double hessii( double x[], double delta, int theta, double delti[])
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  {
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    int i;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      int l=1, lmax=20;
     double k1,k2;
     double p2[NPARMAX+1];
     for(i=1; i<=nlstate;i++)    double res;
       for(j=1; j<=nlstate;j++)    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    double fx;
           eij[i][j][(int)age] +=p3mat[i][j][h];    int k=0,kmax=10;
         }    double l1;
      
     hf=1;    fx=func(x);
     if (stepm >= YEARM) hf=stepm/YEARM;    for (i=1;i<=npar;i++) p2[i]=x[i];
     fprintf(ficreseij,"%.0f",age );    for(l=0 ; l <=lmax; l++){
     for(i=1; i<=nlstate;i++)      l1=pow(10,l);
       for(j=1; j<=nlstate;j++){      delts=delt;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);      for(k=1 ; k <kmax; k=k+1){
       }        delt = delta*(l1*k);
     fprintf(ficreseij,"\n");        p2[theta]=x[theta] +delt;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        k1=func(p2)-fx;
   }        p2[theta]=x[theta]-delt;
 }        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
 /************ Variance ******************/        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 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)        
 {  #ifdef DEBUG
   /* Variance of health expectancies */        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);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        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);
   double **newm;  #endif
   double **dnewm,**doldm;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   int i, j, nhstepm, hstepm, h;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   int k, cptcode;          k=kmax;
   double *xp;        }
   double **gp, **gm;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   double ***gradg, ***trgradg;          k=kmax; l=lmax*10.;
   double ***p3mat;        }
   double age,agelim;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   int theta;          delts=delt;
         }
    fprintf(ficresvij,"# Covariances of life expectancies\n");      }
   fprintf(ficresvij,"# Age");    }
   for(i=1; i<=nlstate;i++)    delti[theta]=delts;
     for(j=1; j<=nlstate;j++)    return res; 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    
   fprintf(ficresvij,"\n");  }
   
   xp=vector(1,npar);  double hessij( double x[], double delti[], int thetai,int thetaj)
   dnewm=matrix(1,nlstate,1,npar);  {
   doldm=matrix(1,nlstate,1,nlstate);    int i;
      int l=1, l1, lmax=20;
   hstepm=1*YEARM; /* Every year of age */    double k1,k2,k3,k4,res,fx;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double p2[NPARMAX+1];
   agelim = AGESUP;    int k;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fx=func(x);
     if (stepm >= YEARM) hstepm=1;    for (k=1; k<=2; k++) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (i=1;i<=npar;i++) p2[i]=x[i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p2[thetai]=x[thetai]+delti[thetai]/k;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     gp=matrix(0,nhstepm,1,nlstate);      k1=func(p2)-fx;
     gm=matrix(0,nhstepm,1,nlstate);    
       p2[thetai]=x[thetai]+delti[thetai]/k;
     for(theta=1; theta <=npar; theta++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(i=1; i<=npar; i++){ /* Computes gradient */      k2=func(p2)-fx;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    
       }      p2[thetai]=x[thetai]-delti[thetai]/k;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      k3=func(p2)-fx;
     
       if (popbased==1) {      p2[thetai]=x[thetai]-delti[thetai]/k;
         for(i=1; i<=nlstate;i++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           prlim[i][i]=probs[(int)age][i][ij];      k4=func(p2)-fx;
       }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    #ifdef DEBUG
       for(j=1; j<= nlstate; j++){      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);
         for(h=0; h<=nhstepm; h++){      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);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  #endif
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    }
         }    return res;
       }  }
      
       for(i=1; i<=npar; i++) /* Computes gradient */  /************** Inverse of matrix **************/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  void ludcmp(double **a, int n, int *indx, double *d) 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i,imax,j,k; 
      double big,dum,sum,temp; 
       if (popbased==1) {    double *vv; 
         for(i=1; i<=nlstate;i++)   
           prlim[i][i]=probs[(int)age][i][ij];    vv=vector(1,n); 
       }    *d=1.0; 
     for (i=1;i<=n;i++) { 
       for(j=1; j<= nlstate; j++){      big=0.0; 
         for(h=0; h<=nhstepm; h++){      for (j=1;j<=n;j++) 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         }      vv[i]=1.0/big; 
       }    } 
     for (j=1;j<=n;j++) { 
       for(j=1; j<= nlstate; j++)      for (i=1;i<j;i++) { 
         for(h=0; h<=nhstepm; h++){        sum=a[i][j]; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         }        a[i][j]=sum; 
     } /* End theta */      } 
       big=0.0; 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
     for(h=0; h<=nhstepm; h++)        for (k=1;k<j;k++) 
       for(j=1; j<=nlstate;j++)          sum -= a[i][k]*a[k][j]; 
         for(theta=1; theta <=npar; theta++)        a[i][j]=sum; 
           trgradg[h][j][theta]=gradg[h][theta][j];        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
     for(i=1;i<=nlstate;i++)          imax=i; 
       for(j=1;j<=nlstate;j++)        } 
         vareij[i][j][(int)age] =0.;      } 
     for(h=0;h<=nhstepm;h++){      if (j != imax) { 
       for(k=0;k<=nhstepm;k++){        for (k=1;k<=n;k++) { 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          dum=a[imax][k]; 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          a[imax][k]=a[j][k]; 
         for(i=1;i<=nlstate;i++)          a[j][k]=dum; 
           for(j=1;j<=nlstate;j++)        } 
             vareij[i][j][(int)age] += doldm[i][j];        *d = -(*d); 
       }        vv[imax]=vv[j]; 
     }      } 
     h=1;      indx[j]=imax; 
     if (stepm >= YEARM) h=stepm/YEARM;      if (a[j][j] == 0.0) a[j][j]=TINY; 
     fprintf(ficresvij,"%.0f ",age );      if (j != n) { 
     for(i=1; i<=nlstate;i++)        dum=1.0/(a[j][j]); 
       for(j=1; j<=nlstate;j++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      } 
       }    } 
     fprintf(ficresvij,"\n");    free_vector(vv,1,n);  /* Doesn't work */
     free_matrix(gp,0,nhstepm,1,nlstate);  ;
     free_matrix(gm,0,nhstepm,1,nlstate);  } 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  void lubksb(double **a, int n, int *indx, double b[]) 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  { 
   } /* End age */    int i,ii=0,ip,j; 
      double sum; 
   free_vector(xp,1,npar);   
   free_matrix(doldm,1,nlstate,1,npar);    for (i=1;i<=n;i++) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);      ip=indx[i]; 
       sum=b[ip]; 
 }      b[ip]=b[i]; 
       if (ii) 
 /************ Variance of prevlim ******************/        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[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)      else if (sum) ii=i; 
 {      b[i]=sum; 
   /* Variance of prevalence limit */    } 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (i=n;i>=1;i--) { 
   double **newm;      sum=b[i]; 
   double **dnewm,**doldm;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   int i, j, nhstepm, hstepm;      b[i]=sum/a[i][i]; 
   int k, cptcode;    } 
   double *xp;  } 
   double *gp, *gm;  
   double **gradg, **trgradg;  /************ Frequencies ********************/
   double age,agelim;  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)
   int theta;  {  /* Some frequencies */
        
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   fprintf(ficresvpl,"# Age");    int first;
   for(i=1; i<=nlstate;i++)    double ***freq; /* Frequencies */
       fprintf(ficresvpl," %1d-%1d",i,i);    double *pp, **prop;
   fprintf(ficresvpl,"\n");    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
   xp=vector(1,npar);    char fileresp[FILENAMELENGTH];
   dnewm=matrix(1,nlstate,1,npar);    
   doldm=matrix(1,nlstate,1,nlstate);    pp=vector(1,nlstate);
      prop=matrix(1,nlstate,iagemin,iagemax+3);
   hstepm=1*YEARM; /* Every year of age */    strcpy(fileresp,"p");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    strcat(fileresp,fileres);
   agelim = AGESUP;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      printf("Problem with prevalence resultfile: %s\n", fileresp);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     if (stepm >= YEARM) hstepm=1;      exit(0);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
     gradg=matrix(1,npar,1,nlstate);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     gp=vector(1,nlstate);    j1=0;
     gm=vector(1,nlstate);    
     j=cptcoveff;
     for(theta=1; theta <=npar; theta++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    first=1;
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for(k1=1; k1<=j;k1++){
       for(i=1;i<=nlstate;i++)      for(i1=1; i1<=ncodemax[k1];i1++){
         gp[i] = prlim[i][i];        j1++;
            /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       for(i=1; i<=npar; i++) /* Computes gradient */          scanf("%d", i);*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for (i=-1; i<=nlstate+ndeath; i++)  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       for(i=1;i<=nlstate;i++)            for(m=iagemin; m <= iagemax+3; m++)
         gm[i] = prlim[i][i];              freq[i][jk][m]=0;
   
       for(i=1;i<=nlstate;i++)      for (i=1; i<=nlstate; i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        for(m=iagemin; m <= iagemax+3; m++)
     } /* End theta */          prop[i][m]=0;
         
     trgradg =matrix(1,nlstate,1,npar);        dateintsum=0;
         k2cpt=0;
     for(j=1; j<=nlstate;j++)        for (i=1; i<=imx; i++) {
       for(theta=1; theta <=npar; theta++)          bool=1;
         trgradg[j][theta]=gradg[theta][j];          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
     for(i=1;i<=nlstate;i++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       varpl[i][(int)age] =0.;                bool=0;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          if (bool==1){
     for(i=1;i<=nlstate;i++)            for(m=firstpass; m<=lastpass; m++){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     fprintf(ficresvpl,"%.0f ",age );                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     for(i=1; i<=nlstate;i++)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     fprintf(ficresvpl,"\n");                if (m<lastpass) {
     free_vector(gp,1,nlstate);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     free_vector(gm,1,nlstate);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     free_matrix(gradg,1,npar,1,nlstate);                }
     free_matrix(trgradg,1,nlstate,1,npar);                
   } /* End age */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
   free_vector(xp,1,npar);                  k2cpt++;
   free_matrix(doldm,1,nlstate,1,npar);                }
   free_matrix(dnewm,1,nlstate,1,nlstate);                /*}*/
             }
 }          }
         }
 /************ Variance of one-step probabilities  ******************/         
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 {  
   int i, j;        if  (cptcovn>0) {
   int k=0, cptcode;          fprintf(ficresp, "\n#********** Variable "); 
   double **dnewm,**doldm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double *xp;          fprintf(ficresp, "**********\n#");
   double *gp, *gm;        }
   double **gradg, **trgradg;        for(i=1; i<=nlstate;i++) 
   double age,agelim, cov[NCOVMAX];          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   int theta;        fprintf(ficresp, "\n");
   char fileresprob[FILENAMELENGTH];        
         for(i=iagemin; i <= iagemax+3; i++){
   strcpy(fileresprob,"prob");          if(i==iagemax+3){
   strcat(fileresprob,fileres);            fprintf(ficlog,"Total");
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          }else{
     printf("Problem with resultfile: %s\n", fileresprob);            if(first==1){
   }              first=0;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);              printf("See log file for details...\n");
              }
             fprintf(ficlog,"Age %d", i);
   xp=vector(1,npar);          }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for(jk=1; jk <=nlstate ; jk++){
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                pp[jk] += freq[jk][m][i]; 
   cov[1]=1;          }
   for (age=bage; age<=fage; age ++){          for(jk=1; jk <=nlstate ; jk++){
     cov[2]=age;            for(m=-1, pos=0; m <=0 ; m++)
     gradg=matrix(1,npar,1,9);              pos += freq[jk][m][i];
     trgradg=matrix(1,9,1,npar);            if(pp[jk]>=1.e-10){
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              if(first==1){
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                  }
     for(theta=1; theta <=npar; theta++){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for(i=1; i<=npar; i++)            }else{
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              if(first==1)
                      printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                }
       k=0;          }
       for(i=1; i<= (nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){          for(jk=1; jk <=nlstate ; jk++){
            k=k+1;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           gp[k]=pmmij[i][j];              pp[jk] += freq[jk][m][i];
         }          }       
       }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
       for(i=1; i<=npar; i++)            posprop += prop[jk][i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }
              for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              if(first==1)
       k=0;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       for(i=1; i<=(nlstate+ndeath); i++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         for(j=1; j<=(nlstate+ndeath);j++){            }else{
           k=k+1;              if(first==1)
           gm[k]=pmmij[i][j];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       }            }
                  if( i <= iagemax){
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)              if(pos>=1.e-5){
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     }                /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)              }
       for(theta=1; theta <=npar; theta++)              else
       trgradg[j][theta]=gradg[theta][j];                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
              }
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
      pmij(pmmij,cov,ncovmodel,x,nlstate);            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
      k=0;              if(first==1)
      for(i=1; i<=(nlstate+ndeath); i++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
        for(j=1; j<=(nlstate+ndeath);j++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
          k=k+1;              }
          gm[k]=pmmij[i][j];          if(i <= iagemax)
         }            fprintf(ficresp,"\n");
      }          if(first==1)
                  printf("Others in log...\n");
      /*printf("\n%d ",(int)age);          fprintf(ficlog,"\n");
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        }
              }
     }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    dateintmean=dateintsum/k2cpt; 
      }*/   
     fclose(ficresp);
   fprintf(ficresprob,"\n%d ",(int)age);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    /* End of Freq */
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  }
   }  
   /************ Prevalence ********************/
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  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)
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  {  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       in each health status at the date of interview (if between dateprev1 and dateprev2).
 }       We still use firstpass and lastpass as another selection.
  free_vector(xp,1,npar);    */
 fclose(ficresprob);   
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
 }    double ***freq; /* Frequencies */
     double *pp, **prop;
 /******************* Printing html file ***********/    double pos,posprop; 
 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[] ){    double  y2; /* in fractional years */
   int jj1, k1, i1, cpt;    int iagemin, iagemax;
   FILE *fichtm;  
   /*char optionfilehtm[FILENAMELENGTH];*/    iagemin= (int) agemin;
     iagemax= (int) agemax;
   strcpy(optionfilehtm,optionfile);    /*pp=vector(1,nlstate);*/
   strcat(optionfilehtm,".htm");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     printf("Problem with %s \n",optionfilehtm), exit(0);    j1=0;
   }    
     j=cptcoveff;
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    
     for(k1=1; k1<=j;k1++){
 Total number of observations=%d <br>      for(i1=1; i1<=ncodemax[k1];i1++){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>        j1++;
 <hr  size=\"2\" color=\"#EC5E5E\">        
 <li>Outputs files<br><br>\n        for (i=1; i<=nlstate; i++)  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          for(m=iagemin; m <= iagemax+3; m++)
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>            prop[i][m]=0.0;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>       
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        for (i=1; i<=imx; i++) { /* Each individual */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          bool=1;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          if  (cptcovn>0) {
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>            for (z1=1; z1<=cptcoveff; z1++) 
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>                bool=0;
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>          } 
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);          if (bool==1) { 
              for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 fprintf(fichtm," <li>Graphs</li><p>");              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
  m=cptcoveff;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
  jj1=0;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
  for(k1=1; k1<=m;k1++){                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
    for(i1=1; i1<=ncodemax[k1];i1++){                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
        jj1++;                  prop[s[m][i]][iagemax+3] += weight[i]; 
        if (cptcovn > 0) {                } 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");              }
          for (cpt=1; cpt<=cptcoveff;cpt++)            } /* end selection of waves */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        }
        }        for(i=iagemin; i <= iagemax+3; i++){  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
        for(cpt=1; cpt<nlstate;cpt++){            posprop += prop[jk][i]; 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          } 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }          for(jk=1; jk <=nlstate ; jk++){     
     for(cpt=1; cpt<=nlstate;cpt++) {            if( i <=  iagemax){ 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              if(posprop>=1.e-5){ 
 interval) in state (%d): v%s%d%d.gif <br>                probs[i][jk][j1]= prop[jk][i]/posprop;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                } 
      }            } 
      for(cpt=1; cpt<=nlstate;cpt++) {          }/* end jk */ 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        }/* end i */ 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      } /* end i1 */
      }    } /* end k1 */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    
 health expectancies in states (1) and (2): e%s%d.gif<br>    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    /*free_vector(pp,1,nlstate);*/
 fprintf(fichtm,"\n</body>");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
    }  }  /* End of prevalence */
    }  
 fclose(fichtm);  /************* Waves Concatenation ***************/
 }  
   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)
 /******************* Gnuplot file **************/  {
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   strcpy(optionfilegnuplot,optionfilefiname);       and mw[mi+1][i]. dh depends on stepm.
   strcat(optionfilegnuplot,".plt");       */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);    int i, mi, m;
   }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
 #ifdef windows    int first;
     fprintf(ficgp,"cd \"%s\" \n",pathc);    int j, k=0,jk, ju, jl;
 #endif    double sum=0.;
 m=pow(2,cptcoveff);    first=0;
      jmin=1e+5;
  /* 1eme*/    jmax=-1;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    jmean=0.;
    for (k1=1; k1<= m ; k1 ++) {    for(i=1; i<=imx; i++){
       mi=0;
 #ifdef windows      m=firstpass;
     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);      while(s[m][i] <= nlstate){
 #endif        if(s[m][i]>=1)
 #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);        if(m >=lastpass)
 #endif          break;
         else
 for (i=1; i<= nlstate ; i ++) {          m++;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      }/* end while */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      if (s[m][i] > nlstate){
 }        mi++;     /* Death is another wave */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        /* if(mi==0)  never been interviewed correctly before death */
     for (i=1; i<= nlstate ; i ++) {           /* Only death is a correct wave */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        mw[mi][i]=m;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      wav[i]=mi;
      for (i=1; i<= nlstate ; i ++) {      if(mi==0){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if(first==0){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 }            first=1;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        }
 #ifdef unix        if(first==1){
 fprintf(ficgp,"\nset ter gif small size 400,300");          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
 #endif        }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      } /* end mi==0 */
    }    } /* End individuals */
   }  
   /*2 eme*/    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
   for (k1=1; k1<= m ; k1 ++) {        if (stepm <=0)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          dh[mi][i]=1;
            else{
     for (i=1; i<= nlstate+1 ; i ++) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       k=2*i;            if (agedc[i] < 2*AGESUP) {
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       for (j=1; j<= nlstate+1 ; j ++) {              if(j==0) j=1;  /* Survives at least one month after exam */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              else if(j<0){
   else fprintf(ficgp," \%%*lf (\%%*lf)");                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 */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                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);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                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(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                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 (j=1; j<= nlstate+1 ; j ++) {              }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              k=k+1;
         else fprintf(ficgp," \%%*lf (\%%*lf)");              if (j >= jmax) jmax=j;
 }                if (j <= jmin) jmin=j;
       fprintf(ficgp,"\" t\"\" w l 0,");              sum=sum+j;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       for (j=1; j<= nlstate+1 ; j ++) {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }            else{
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       else fprintf(ficgp,"\" t\"\" w l 0,");            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     }            k=k+1;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            if (j >= jmax) jmax=j;
   }            else if (j <= jmin)jmin=j;
              /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   /*3eme*/            /*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<0){
   for (k1=1; k1<= m ; k1 ++) {              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]);
     for (cpt=1; cpt<= nlstate ; cpt ++) {              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]);
       k=2+nlstate*(cpt-1);            }
       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);            sum=sum+j;
       for (i=1; i< nlstate ; i ++) {          }
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          jk= j/stepm;
       }          jl= j -jk*stepm;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          ju= j -(jk+1)*stepm;
     }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     }            if(jl==0){
                dh[mi][i]=jk;
   /* CV preval stat */              bh[mi][i]=0;
     for (k1=1; k1<= m ; k1 ++) {            }else{ /* We want a negative bias in order to only have interpolation ie
     for (cpt=1; cpt<nlstate ; cpt ++) {                    * at the price of an extra matrix product in likelihood */
       k=3;              dh[mi][i]=jk+1;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);              bh[mi][i]=ju;
             }
       for (i=1; i< nlstate ; i ++)          }else{
         fprintf(ficgp,"+$%d",k+i+1);            if(jl <= -ju){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              dh[mi][i]=jk;
                    bh[mi][i]=jl;       /* bias is positive if real duration
       l=3+(nlstate+ndeath)*cpt;                                   * is higher than the multiple of stepm and negative otherwise.
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                                   */
       for (i=1; i< nlstate ; i ++) {            }
         l=3+(nlstate+ndeath)*cpt;            else{
         fprintf(ficgp,"+$%d",l+i+1);              dh[mi][i]=jk+1;
       }              bh[mi][i]=ju;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            if(dh[mi][i]==0){
     }              dh[mi][i]=1; /* At least one step */
   }                bh[mi][i]=ju; /* At least one step */
                /*  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);*/
   /* proba elementaires */            }
    for(i=1,jk=1; i <=nlstate; i++){          } /* end if mle */
     for(k=1; k <=(nlstate+ndeath); k++){        }
       if (k != i) {      } /* end wave */
         for(j=1; j <=ncovmodel; j++){    }
            jmean=sum/k;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           jk++;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           fprintf(ficgp,"\n");   }
         }  
       }  /*********** Tricode ****************************/
     }  void tricode(int *Tvar, int **nbcode, int imx)
     }  {
     
     for(jk=1; jk <=m; jk++) {    int Ndum[20],ij=1, k, j, i, maxncov=19;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    int cptcode=0;
    i=1;    cptcoveff=0; 
    for(k2=1; k2<=nlstate; k2++) {   
      k3=i;    for (k=0; k<maxncov; k++) Ndum[k]=0;
      for(k=1; k<=(nlstate+ndeath); k++) {    for (k=1; k<=7; k++) ncodemax[k]=0;
        if (k != k2){  
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 ij=1;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         for(j=3; j <=ncovmodel; j++) {                                 modality*/ 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        Ndum[ij]++; /*store the modality */
             ij++;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
           else                                         Tvar[j]. If V=sex and male is 0 and 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                                         female is 1, then  cptcode=1.*/
         }      }
           fprintf(ficgp,")/(1");  
              for (i=0; i<=cptcode; i++) {
         for(k1=1; k1 <=nlstate; k1++){          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 */
           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++){      ij=1; 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for (i=1; i<=ncodemax[j]; i++) {
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for (k=0; k<= maxncov; k++) {
             ij++;          if (Ndum[k] != 0) {
           }            nbcode[Tvar[j]][ij]=k; 
           else            /* 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; */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            
           }            ij++;
           fprintf(ficgp,")");          }
         }          if (ij > ncodemax[j]) break; 
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        }  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      } 
         i=i+ncovmodel;    }  
        }  
      }   for (k=0; k< maxncov; k++) Ndum[k]=0;
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);   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.*/
         ij=Tvar[i];
   fclose(ficgp);     Ndum[ij]++;
 }  /* end gnuplot */   }
   
    ij=1;
 /*************** Moving average **************/   for (i=1; i<= maxncov; i++) {
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
   int i, cpt, cptcod;       ij++;
     for (agedeb=agemin; agedeb<=fage; agedeb++)     }
       for (i=1; i<=nlstate;i++)   }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)   
           mobaverage[(int)agedeb][i][cptcod]=0.;   cptcoveff=ij-1; /*Number of simple covariates*/
      }
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){  
       for (i=1; i<=nlstate;i++){  /*********** Health Expectancies ****************/
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){  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 )
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }  {
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    /* Health expectancies */
         }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       }    double age, agelim, hf;
     }    double ***p3mat,***varhe;
        double **dnewm,**doldm;
 }    double *xp;
     double **gp, **gm;
     double ***gradg, ***trgradg;
 /************** Forecasting ******************/    int theta;
 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){  
      varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    xp=vector(1,npar);
   int *popage;    dnewm=matrix(1,nlstate*nlstate,1,npar);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   double *popeffectif,*popcount;    
   double ***p3mat;    fprintf(ficreseij,"# Health expectancies\n");
   char fileresf[FILENAMELENGTH];    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
  agelim=AGESUP;      for(j=1; j<=nlstate;j++)
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
      fprintf(ficreseij,"\n");
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
     if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   strcpy(fileresf,"f");    }
   strcat(fileresf,fileres);    else  hstepm=estepm;   
   if((ficresf=fopen(fileresf,"w"))==NULL) {    /* We compute the life expectancy from trapezoids spaced every estepm months
     printf("Problem with forecast resultfile: %s\n", fileresf);     * This is mainly to measure the difference between two models: for example
   }     * if stepm=24 months pijx are given only every 2 years and by summing them
   printf("Computing forecasting: result on file '%s' \n", fileresf);     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   if (cptcoveff==0) ncodemax[cptcoveff]=1;     * 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
   if (mobilav==1) {     * to compare the new estimate of Life expectancy with the same linear 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * hypothesis. A more precise result, taking into account a more precise
     movingaverage(agedeb, fage, agemin, mobaverage);     * curvature will be obtained if estepm is as small as stepm. */
   }  
     /* For example we decided to compute the life expectancy with the smallest unit */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if (stepm<=12) stepsize=1;       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   agelim=AGESUP;       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like estepm months */
   hstepm=1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   hstepm=hstepm/stepm;       survival function given by stepm (the optimization length). Unfortunately it
   yp1=modf(dateintmean,&yp);       means that if the survival funtion is printed only each two years of age and if
   anprojmean=yp;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   yp2=modf((yp1*12),&yp);       results. So we changed our mind and took the option of the best precision.
   mprojmean=yp;    */
   yp1=modf((yp2*30.5),&yp);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;    agelim=AGESUP;
   if(mprojmean==0) jprojmean=1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        /* nhstepm age range expressed in number of stepm */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   for(cptcov=1;cptcov<=i2;cptcov++){      /* if (stepm >= YEARM) hstepm=1;*/
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       k=k+1;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficresf,"\n#******");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       for(j=1;j<=cptcoveff;j++) {      gp=matrix(0,nhstepm,1,nlstate*nlstate);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
       }  
       fprintf(ficresf,"******\n");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       fprintf(ficresf,"# StartingAge FinalAge");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
         
        
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        /* Computing Variances of health expectancies */
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){       for(theta=1; theta <=npar; theta++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(i=1; i<=npar; i++){ 
           nhstepm = nhstepm/hstepm;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                  }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           oldm=oldms;savm=savms;    
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          cptj=0;
                for(j=1; j<= nlstate; j++){
           for (h=0; h<=nhstepm; h++){          for(i=1; i<=nlstate; i++){
             if (h==(int) (calagedate+YEARM*cpt)) {            cptj=cptj+1;
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
             }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             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 {        for(i=1; i<=npar; i++) 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          xp[i] = x[i] - (i==theta ?delti[theta]:0);
                 }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                        
               }        cptj=0;
               if (h==(int)(calagedate+12*cpt)){        for(j=1; j<= nlstate; j++){
                 fprintf(ficresf," %.3f", kk1);          for(i=1;i<=nlstate;i++){
                                    cptj=cptj+1;
               }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
             }  
           }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
         }          }
       }        }
     }        for(j=1; j<= nlstate*nlstate; j++)
   }          for(h=0; h<=nhstepm-1; h++){
                    gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
        } 
   fclose(ficresf);     
 }  /* End theta */
 /************** Forecasting ******************/  
 populforecast(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){       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       for(h=0; h<=nhstepm-1; h++)
   int *popage;        for(j=1; j<=nlstate*nlstate;j++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          for(theta=1; theta <=npar; theta++)
   double *popeffectif,*popcount;            trgradg[h][j][theta]=gradg[h][theta][j];
   double ***p3mat,***tabpop,***tabpopprev;       
   char filerespop[FILENAMELENGTH];  
        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] =0.;
  agelim=AGESUP;  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;       printf("%d|",(int)age);fflush(stdout);
         fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   strcpy(filerespop,"pop");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   strcat(filerespop,fileres);          for(i=1;i<=nlstate*nlstate;i++)
   if((ficrespop=fopen(filerespop,"w"))==NULL) {            for(j=1;j<=nlstate*nlstate;j++)
     printf("Problem with forecast resultfile: %s\n", filerespop);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   }        }
   printf("Computing forecasting: result on file '%s' \n", filerespop);      }
       /* Computing expectancies */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   if (mobilav==1) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     movingaverage(agedeb, fage, agemin, mobaverage);            
   }  /* 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]);*/
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;          }
   if (stepm<=12) stepsize=1;  
        fprintf(ficreseij,"%3.0f",age );
   agelim=AGESUP;      cptj=0;
        for(i=1; i<=nlstate;i++)
   hstepm=1;        for(j=1; j<=nlstate;j++){
   hstepm=hstepm/stepm;          cptj++;
            fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   if (popforecast==1) {        }
     if((ficpop=fopen(popfile,"r"))==NULL) {      fprintf(ficreseij,"\n");
       printf("Problem with population file : %s\n",popfile);exit(0);     
     }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     popage=ivector(0,AGESUP);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     popeffectif=vector(0,AGESUP);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     popcount=vector(0,AGESUP);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     i=1;      }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    printf("\n");
        fprintf(ficlog,"\n");
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    free_vector(xp,1,npar);
   }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   for(cptcov=1;cptcov<=i2;cptcov++){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  }
       k=k+1;  
       fprintf(ficrespop,"\n#******");  /************ Variance ******************/
       for(j=1;j<=cptcoveff;j++) {  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)
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  {
       }    /* Variance of health expectancies */
       fprintf(ficrespop,"******\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       fprintf(ficrespop,"# StartingAge FinalAge");    /* double **newm;*/
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    double **dnewm,**doldm;
       if (popforecast==1)  fprintf(ficrespop," [Population]");    double **dnewmp,**doldmp;
          int i, j, nhstepm, hstepm, h, nstepm ;
       for (cpt=0; cpt<=0;cpt++) {    int k, cptcode;
         fprintf(ficrespop,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      double *xp;
            double **gp, **gm;  /* for var eij */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    double ***gradg, ***trgradg; /*for var eij */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double **gradgp, **trgradgp; /* for var p point j */
           nhstepm = nhstepm/hstepm;    double *gpp, *gmp; /* for var p point j */
              double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double ***p3mat;
           oldm=oldms;savm=savms;    double age,agelim, hf;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double ***mobaverage;
            int theta;
           for (h=0; h<=nhstepm; h++){    char digit[4];
             if (h==(int) (calagedate+YEARM*cpt)) {    char digitp[25];
               fprintf(ficrespop,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);  
             }    char fileresprobmorprev[FILENAMELENGTH];
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    if(popbased==1){
               for(i=1; i<=nlstate;i++) {                    if(mobilav!=0)
                 if (mobilav==1)        strcpy(digitp,"-populbased-mobilav-");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      else strcpy(digitp,"-populbased-nomobil-");
                 else {    }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    else 
                 }      strcpy(digitp,"-stablbased-");
               }  
               if (h==(int)(calagedate+12*cpt)){    if (mobilav!=0) {
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   /*fprintf(ficrespop," %.3f", kk1);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
               }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             }      }
             for(i=1; i<=nlstate;i++){    }
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){    strcpy(fileresprobmorprev,"prmorprev"); 
                   kk1= kk1+Tabpop[(int)(agedeb)][j][cptcod];    sprintf(digit,"%-d",ij);
                 }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    strcat(fileresprobmorprev,digit); /* Tvar to be done */
             }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
 if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) fprintf(ficrespop," %.3f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         }    }
       }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      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);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       for (cpt=1; cpt<=4;cpt++) {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficrespop,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        fprintf(ficresprobmorprev," p.%-d SE",j);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      for(i=1; i<=nlstate;i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           nhstepm = nhstepm/hstepm;    }  
              fprintf(ficresprobmorprev,"\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           oldm=oldms;savm=savms;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
           for (h=0; h<=nhstepm; h++){      exit(0);
             if (h==(int) (calagedate+YEARM*cpt)) {    }
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    else{
             }      fprintf(ficgp,"\n# Routine varevsij");
             for(j=1; j<=nlstate+ndeath;j++) {    }
               kk1=0.;kk2=0;  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
               for(i=1; i<=nlstate;i++) {                /*     printf("Problem with html file: %s\n", optionfilehtm); */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      /*     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); */
               }  /*     exit(0); */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %.3f", kk1);    /*   } */
             }  /*   else{ */
           }    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
         }  /*   } */
       }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    }  
   }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
      fprintf(ficresvij,"# Age");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
   if (popforecast==1) {        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     free_ivector(popage,0,AGESUP);    fprintf(ficresvij,"\n");
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);    xp=vector(1,npar);
   }    dnewm=matrix(1,nlstate,1,npar);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    doldm=matrix(1,nlstate,1,nlstate);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   fclose(ficrespop);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 }  
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
 /***********************************************/    gpp=vector(nlstate+1,nlstate+ndeath);
 /**************** Main Program *****************/    gmp=vector(nlstate+1,nlstate+ndeath);
 /***********************************************/    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
 int main(int argc, char *argv[])    if(estepm < stepm){
 {      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    else  hstepm=estepm;   
   double agedeb, agefin,hf;    /* For example we decided to compute the life expectancy with the smallest unit */
   double agemin=1.e20, agemax=-1.e20;    /* 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 
   double fret;       nstepm is the number of stepm from age to agelin. 
   double **xi,tmp,delta;       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
   double dum; /* Dummy variable */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double ***p3mat;       survival function given by stepm (the optimization length). Unfortunately it
   int *indx;       means that if the survival funtion is printed every two years of age and if
   char line[MAXLINE], linepar[MAXLINE];       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   char title[MAXLINE];       results. So we changed our mind and took the option of the best precision.
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      agelim = AGESUP;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   char filerest[FILENAMELENGTH];      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   char fileregp[FILENAMELENGTH];      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   char popfile[FILENAMELENGTH];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      gp=matrix(0,nhstepm,1,nlstate);
   int firstobs=1, lastobs=10;      gm=matrix(0,nhstepm,1,nlstate);
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;  
   int ju,jl, mi;      for(theta=1; theta <=npar; theta++){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   int mobilav=0,popforecast=0;        }
   int hstepm, nhstepm;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
   double bage, fage, age, agelim, agebase;        if (popbased==1) {
   double ftolpl=FTOL;          if(mobilav ==0){
   double **prlim;            for(i=1; i<=nlstate;i++)
   double *severity;              prlim[i][i]=probs[(int)age][i][ij];
   double ***param; /* Matrix of parameters */          }else{ /* mobilav */ 
   double  *p;            for(i=1; i<=nlstate;i++)
   double **matcov; /* Matrix of covariance */              prlim[i][i]=mobaverage[(int)age][i][ij];
   double ***delti3; /* Scale */          }
   double *delti; /* Scale */        }
   double ***eij, ***vareij;    
   double **varpl; /* Variances of prevalence limits by age */        for(j=1; j<= nlstate; j++){
   double *epj, vepp;          for(h=0; h<=nhstepm; h++){
   double kk1, kk2;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
         }
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";        /* This for computing probability of death (h=1 means
   char *alph[]={"a","a","b","c","d","e"}, str[4];           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
   char z[1]="c", occ;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 #include <sys/time.h>          for(i=1,gpp[j]=0.; i<= nlstate; i++)
 #include <time.h>            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        }    
          /* end probability of death */
   /* long total_usecs;  
   struct timeval start_time, end_time;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   printf("\n%s",version);        if (popbased==1) {
   if(argc <=1){          if(mobilav ==0){
     printf("\nEnter the parameter file name: ");            for(i=1; i<=nlstate;i++)
     scanf("%s",pathtot);              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
   else{            for(i=1; i<=nlstate;i++)
     strcpy(pathtot,argv[1]);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        }
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        for(j=1; j<= nlstate; j++){
   /* cutv(path,optionfile,pathtot,'\\');*/          for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          }
   chdir(path);        }
   replace(pathc,path);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
 /*-------- arguments in the command line --------*/           as a weighted average of prlim.
         */
   strcpy(fileres,"r");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   strcat(fileres, optionfilefiname);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   strcat(fileres,".txt");    /* Other files have txt extension */           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   /*---------arguments file --------*/        /* end probability of death */
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        for(j=1; j<= nlstate; j++) /* vareij */
     printf("Problem with optionfile %s\n",optionfile);          for(h=0; h<=nhstepm; h++){
     goto end;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
   
   strcpy(filereso,"o");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   strcat(filereso,fileres);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   if((ficparo=fopen(filereso,"w"))==NULL) {        }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }      } /* End theta */
   
   /* Reads comments: lines beginning with '#' */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      for(h=0; h<=nhstepm; h++) /* veij */
     fgets(line, MAXLINE, ficpar);        for(j=1; j<=nlstate;j++)
     puts(line);          for(theta=1; theta <=npar; theta++)
     fputs(line,ficparo);            trgradg[h][j][theta]=gradg[h][theta][j];
   }  
   ungetc(c,ficpar);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
   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);          trgradgp[j][theta]=gradgp[theta][j];
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    
   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);  
 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);
              matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   covar=matrix(0,NCOVMAX,1,n);          for(i=1;i<=nlstate;i++)
   cptcovn=0;            for(j=1;j<=nlstate;j++)
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   ncovmodel=2+cptcovn;      }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    
        /* pptj */
   /* Read guess parameters */      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   /* Reads comments: lines beginning with '#' */      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   while((c=getc(ficpar))=='#' && c!= EOF){      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     ungetc(c,ficpar);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     fgets(line, MAXLINE, ficpar);          varppt[j][i]=doldmp[j][i];
     puts(line);      /* end ppptj */
     fputs(line,ficparo);      /*  x centered again */
   }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   ungetc(c,ficpar);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      if (popbased==1) {
     for(i=1; i <=nlstate; i++)        if(mobilav ==0){
     for(j=1; j <=nlstate+ndeath-1; j++){          for(i=1; i<=nlstate;i++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);            prlim[i][i]=probs[(int)age][i][ij];
       fprintf(ficparo,"%1d%1d",i1,j1);        }else{ /* mobilav */ 
       printf("%1d%1d",i,j);          for(i=1; i<=nlstate;i++)
       for(k=1; k<=ncovmodel;k++){            prlim[i][i]=mobaverage[(int)age][i][ij];
         fscanf(ficpar," %lf",&param[i][j][k]);        }
         printf(" %lf",param[i][j][k]);      }
         fprintf(ficparo," %lf",param[i][j][k]);               
       }      /* This for computing probability of death (h=1 means
       fscanf(ficpar,"\n");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       printf("\n");         as a weighted average of prlim.
       fprintf(ficparo,"\n");      */
     }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
   p=param[1][1];      /* end probability of death */
    
   /* Reads comments: lines beginning with '#' */      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   while((c=getc(ficpar))=='#' && c!= EOF){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     ungetc(c,ficpar);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     fgets(line, MAXLINE, ficpar);        for(i=1; i<=nlstate;i++){
     puts(line);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     fputs(line,ficparo);        }
   }      } 
   ungetc(c,ficpar);      fprintf(ficresprobmorprev,"\n");
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      fprintf(ficresvij,"%.0f ",age );
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      for(i=1; i<=nlstate;i++)
   for(i=1; i <=nlstate; i++){        for(j=1; j<=nlstate;j++){
     for(j=1; j <=nlstate+ndeath-1; j++){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       fscanf(ficpar,"%1d%1d",&i1,&j1);        }
       printf("%1d%1d",i,j);      fprintf(ficresvij,"\n");
       fprintf(ficparo,"%1d%1d",i1,j1);      free_matrix(gp,0,nhstepm,1,nlstate);
       for(k=1; k<=ncovmodel;k++){      free_matrix(gm,0,nhstepm,1,nlstate);
         fscanf(ficpar,"%le",&delti3[i][j][k]);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         printf(" %le",delti3[i][j][k]);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
         fprintf(ficparo," %le",delti3[i][j][k]);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    } /* End age */
       fscanf(ficpar,"\n");    free_vector(gpp,nlstate+1,nlstate+ndeath);
       printf("\n");    free_vector(gmp,nlstate+1,nlstate+ndeath);
       fprintf(ficparo,"\n");    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   delti=delti3[1][1];    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /* Reads comments: lines beginning with '#' */  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   while((c=getc(ficpar))=='#' && c!= EOF){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     ungetc(c,ficpar);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fgets(line, MAXLINE, ficpar);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
     puts(line);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
     fputs(line,ficparo);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
   }    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   ungetc(c,ficpar);    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);
   matcov=matrix(1,npar,1,npar);  */
   for(i=1; i <=npar; i++){    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
     fscanf(ficpar,"%s",&str);  
     printf("%s",str);    free_vector(xp,1,npar);
     fprintf(ficparo,"%s",str);    free_matrix(doldm,1,nlstate,1,nlstate);
     for(j=1; j <=i; j++){    free_matrix(dnewm,1,nlstate,1,npar);
       fscanf(ficpar," %le",&matcov[i][j]);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       printf(" %.5le",matcov[i][j]);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       fprintf(ficparo," %.5le",matcov[i][j]);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fscanf(ficpar,"\n");    fclose(ficresprobmorprev);
     printf("\n");    fclose(ficgp);
     fprintf(ficparo,"\n");  /*   fclose(fichtm); */
   }  }  /* end varevsij */
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)  /************ Variance of prevlim ******************/
       matcov[i][j]=matcov[j][i];  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)
      {
   printf("\n");    /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     /*-------- data file ----------*/    double **dnewm,**doldm;
     if((ficres =fopen(fileres,"w"))==NULL) {    int i, j, nhstepm, hstepm;
       printf("Problem with resultfile: %s\n", fileres);goto end;    int k, cptcode;
     }    double *xp;
     fprintf(ficres,"#%s\n",version);    double *gp, *gm;
        double **gradg, **trgradg;
     if((fic=fopen(datafile,"r"))==NULL)    {    double age,agelim;
       printf("Problem with datafile: %s\n", datafile);goto end;    int theta;
     }     
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     n= lastobs;    fprintf(ficresvpl,"# Age");
     severity = vector(1,maxwav);    for(i=1; i<=nlstate;i++)
     outcome=imatrix(1,maxwav+1,1,n);        fprintf(ficresvpl," %1d-%1d",i,i);
     num=ivector(1,n);    fprintf(ficresvpl,"\n");
     moisnais=vector(1,n);  
     annais=vector(1,n);    xp=vector(1,npar);
     moisdc=vector(1,n);    dnewm=matrix(1,nlstate,1,npar);
     andc=vector(1,n);    doldm=matrix(1,nlstate,1,nlstate);
     agedc=vector(1,n);    
     cod=ivector(1,n);    hstepm=1*YEARM; /* Every year of age */
     weight=vector(1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    agelim = AGESUP;
     mint=matrix(1,maxwav,1,n);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     anint=matrix(1,maxwav,1,n);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     s=imatrix(1,maxwav+1,1,n);      if (stepm >= YEARM) hstepm=1;
     adl=imatrix(1,maxwav+1,1,n);          nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     tab=ivector(1,NCOVMAX);      gradg=matrix(1,npar,1,nlstate);
     ncodemax=ivector(1,8);      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {      for(theta=1; theta <=npar; theta++){
       if ((i >= firstobs) && (i <=lastobs)) {        for(i=1; i<=npar; i++){ /* Computes gradient */
                  xp[i] = x[i] + (i==theta ?delti[theta]:0);
         for (j=maxwav;j>=1;j--){        }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           strcpy(line,stra);        for(i=1;i<=nlstate;i++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          gp[i] = prlim[i][i];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      
         }        for(i=1; i<=npar; i++) /* Computes gradient */
                  xp[i] = x[i] - (i==theta ?delti[theta]:0);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      } /* End theta */
         for (j=ncov;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      trgradg =matrix(1,nlstate,1,npar);
         }  
         num[i]=atol(stra);      for(j=1; j<=nlstate;j++)
                for(theta=1; theta <=npar; theta++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          trgradg[j][theta]=gradg[theta][j];
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  
       for(i=1;i<=nlstate;i++)
         i=i+1;        varpl[i][(int)age] =0.;
       }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     /* printf("ii=%d", ij);      for(i=1;i<=nlstate;i++)
        scanf("%d",i);*/        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   imx=i-1; /* Number of individuals */  
       fprintf(ficresvpl,"%.0f ",age );
   /* for (i=1; i<=imx; i++){      for(i=1; i<=nlstate;i++)
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      fprintf(ficresvpl,"\n");
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      free_vector(gp,1,nlstate);
     }      free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
     for (i=1; i<=imx; i++)      free_matrix(trgradg,1,nlstate,1,npar);
     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]));*/    } /* End age */
   
   /* Calculation of the number of parameter from char model*/    free_vector(xp,1,npar);
   Tvar=ivector(1,15);    free_matrix(doldm,1,nlstate,1,npar);
   Tprod=ivector(1,15);    free_matrix(dnewm,1,nlstate,1,nlstate);
   Tvaraff=ivector(1,15);  
   Tvard=imatrix(1,15,1,2);  }
   Tage=ivector(1,15);        
      /************ Variance of one-step probabilities  ******************/
   if (strlen(model) >1){  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
     j=0, j1=0, k1=1, k2=1;  {
     j=nbocc(model,'+');    int i, j=0,  i1, k1, l1, t, tj;
     j1=nbocc(model,'*');    int k2, l2, j1,  z1;
     cptcovn=j+1;    int k=0,l, cptcode;
     cptcovprod=j1;    int first=1, first1;
        double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
        double **dnewm,**doldm;
     strcpy(modelsav,model);    double *xp;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    double *gp, *gm;
       printf("Error. Non available option model=%s ",model);    double **gradg, **trgradg;
       goto end;    double **mu;
     }    double age,agelim, cov[NCOVMAX];
        double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     for(i=(j+1); i>=1;i--){    int theta;
       cutv(stra,strb,modelsav,'+');    char fileresprob[FILENAMELENGTH];
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    char fileresprobcov[FILENAMELENGTH];
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    char fileresprobcor[FILENAMELENGTH];
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {    double ***varpij;
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {    strcpy(fileresprob,"prob"); 
           cptcovprod--;    strcat(fileresprob,fileres);
           cutv(strb,stre,strd,'V');    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           Tvar[i]=atoi(stre);      printf("Problem with resultfile: %s\n", fileresprob);
           cptcovage++;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
             Tage[cptcovage]=i;    }
             /*printf("stre=%s ", stre);*/    strcpy(fileresprobcov,"probcov"); 
         }    strcat(fileresprobcov,fileres);
         else if (strcmp(strd,"age")==0) {    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
           cptcovprod--;      printf("Problem with resultfile: %s\n", fileresprobcov);
           cutv(strb,stre,strc,'V');      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
           Tvar[i]=atoi(stre);    }
           cptcovage++;    strcpy(fileresprobcor,"probcor"); 
           Tage[cptcovage]=i;    strcat(fileresprobcor,fileres);
         }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         else {      printf("Problem with resultfile: %s\n", fileresprobcor);
           cutv(strb,stre,strc,'V');      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
           Tvar[i]=ncov+k1;    }
           cutv(strb,strc,strd,'V');    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           Tprod[k1]=i;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           Tvard[k1][1]=atoi(strc);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           Tvard[k1][2]=atoi(stre);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           Tvar[cptcovn+k2]=Tvard[k1][1];    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           for (k=1; k<=lastobs;k++)    
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           k1++;    fprintf(ficresprob,"# Age");
           k2=k2+2;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
         }    fprintf(ficresprobcov,"# Age");
       }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       else {    fprintf(ficresprobcov,"# Age");
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');    for(i=1; i<=nlstate;i++)
       Tvar[i]=atoi(strc);      for(j=1; j<=(nlstate+ndeath);j++){
       }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       strcpy(modelsav,stra);          fprintf(ficresprobcov," p%1d-%1d ",i,j);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
         scanf("%d",i);*/      }  
     }   /* fprintf(ficresprob,"\n");
 }    fprintf(ficresprobcov,"\n");
      fprintf(ficresprobcor,"\n");
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);   */
   printf("cptcovprod=%d ", cptcovprod);   xp=vector(1,npar);
   scanf("%d ",i);*/    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     fclose(fic);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     /*  if(mle==1){*/    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     if (weightopt != 1) { /* Maximisation without weights*/    first=1;
       for(i=1;i<=n;i++) weight[i]=1.0;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     /*-calculation of age at interview from date of interview and age at death -*/      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     agev=matrix(1,maxwav,1,imx);      exit(0);
     }
    for (i=1; i<=imx; i++)    else{
      for(m=2; (m<= maxwav); m++)      fprintf(ficgp,"\n# Routine varprob");
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    }
          anint[m][i]=9999;  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
          s[m][i]=-1;  /*     printf("Problem with html file: %s\n", optionfilehtm); */
        }  /*     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); */
      /*     exit(0); */
     for (i=1; i<=imx; i++)  {  /*   } */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  /*   else{ */
       for(m=1; (m<= maxwav); m++){      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         if(s[m][i] >0){      fprintf(fichtm,"\n");
           if (s[m][i] == nlstate+1) {  
             if(agedc[i]>0)      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
               if(moisdc[i]!=99 && andc[i]!=9999)      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[m][i]=agedc[i];      fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
             else {  
               if (andc[i]!=9999){  /*   } */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;    cov[1]=1;
               }    tj=cptcoveff;
             }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
           }    j1=0;
           else if(s[m][i] !=9){ /* Should no more exist */    for(t=1; t<=tj;t++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      for(i1=1; i1<=ncodemax[t];i1++){ 
             if(mint[m][i]==99 || anint[m][i]==9999)        j1++;
               agev[m][i]=1;        if  (cptcovn>0) {
             else if(agev[m][i] <agemin){          fprintf(ficresprob, "\n#********** Variable "); 
               agemin=agev[m][i];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "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(ficresprob, "**********\n#\n");
             }          fprintf(ficresprobcov, "\n#********** Variable "); 
             else if(agev[m][i] >agemax){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               agemax=agev[m][i];          fprintf(ficresprobcov, "**********\n#\n");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          
             }          fprintf(ficgp, "\n#********** Variable "); 
             /*agev[m][i]=anint[m][i]-annais[i];*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             /*   agev[m][i] = age[i]+2*m;*/          fprintf(ficgp, "**********\n#\n");
           }          
           else { /* =9 */          
             agev[m][i]=1;          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
             s[m][i]=-1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         }          
         else /*= 0 Unknown */          fprintf(ficresprobcor, "\n#********** Variable ");    
           agev[m][i]=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresprobcor, "**********\n#");    
            }
     }        
     for (i=1; i<=imx; i++)  {        for (age=bage; age<=fage; age ++){ 
       for(m=1; (m<= maxwav); m++){          cov[2]=age;
         if (s[m][i] > (nlstate+ndeath)) {          for (k=1; k<=cptcovn;k++) {
           printf("Error: Wrong value in nlstate or ndeath\n");              cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           goto end;          }
         }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       }          for (k=1; k<=cptcovprod;k++)
     }            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(severity,1,maxwav);          gp=vector(1,(nlstate)*(nlstate+ndeath));
     free_imatrix(outcome,1,maxwav+1,1,n);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     free_vector(moisnais,1,n);      
     free_vector(annais,1,n);          for(theta=1; theta <=npar; theta++){
     /* free_matrix(mint,1,maxwav,1,n);            for(i=1; i<=npar; i++)
        free_matrix(anint,1,maxwav,1,n);*/              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     free_vector(moisdc,1,n);            
     free_vector(andc,1,n);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
                k=0;
     wav=ivector(1,imx);            for(i=1; i<= (nlstate); i++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              for(j=1; j<=(nlstate+ndeath);j++){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                k=k+1;
                    gp[k]=pmmij[i][j];
     /* Concatenates waves */              }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            }
             
             for(i=1; i<=npar; i++)
       Tcode=ivector(1,100);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      
       ncodemax[1]=1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            k=0;
                  for(i=1; i<=(nlstate); i++){
    codtab=imatrix(1,100,1,10);              for(j=1; j<=(nlstate+ndeath);j++){
    h=0;                k=k+1;
    m=pow(2,cptcoveff);                gm[k]=pmmij[i][j];
                }
    for(k=1;k<=cptcoveff; k++){            }
      for(i=1; i <=(m/pow(2,k));i++){       
        for(j=1; j <= ncodemax[k]; j++){            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
            h++;          }
            if (h>m) h=1;codtab[h][k]=j;  
          }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
        }            for(theta=1; theta <=npar; theta++)
      }              trgradg[j][theta]=gradg[theta][j];
    }          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
    /*for(i=1; i <=m ;i++){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
      for(k=1; k <=cptcovn; k++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
      }          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
      printf("\n");  
    }          pmij(pmmij,cov,ncovmodel,x,nlstate);
    scanf("%d",i);*/          
              k=0;
    /* Calculates basic frequencies. Computes observed prevalence at single age          for(i=1; i<=(nlstate); i++){
        and prints on file fileres'p'. */            for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
                  mu[k][(int) age]=pmmij[i][j];
                }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          }
     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 */            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              varpij[i][j][(int)age] = doldm[i][j];
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
                /*printf("\n%d ",(int)age);
     /* For Powell, parameters are in a vector p[] starting at p[1]            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          fprintf(ficresprob,"\n%d ",(int)age);
     }          fprintf(ficresprobcov,"\n%d ",(int)age);
              fprintf(ficresprobcor,"\n%d ",(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=%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)*(nlstate+ndeath);i++)
              fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
    jk=1;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
    fprintf(ficres,"# Parameters\n");            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
    printf("# Parameters\n");          }
    for(i=1,jk=1; i <=nlstate; i++){          i=0;
      for(k=1; k <=(nlstate+ndeath); k++){          for (k=1; k<=(nlstate);k++){
        if (k != i)            for (l=1; l<=(nlstate+ndeath);l++){ 
          {              i=i++;
            printf("%d%d ",i,k);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
            fprintf(ficres,"%1d%1d ",i,k);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
            for(j=1; j <=ncovmodel; j++){              for (j=1; j<=i;j++){
              printf("%f ",p[jk]);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
              fprintf(ficres,"%f ",p[jk]);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
              jk++;              }
            }            }
            printf("\n");          }/* end of loop for state */
            fprintf(ficres,"\n");        } /* end of loop for age */
          }  
      }        /* Confidence intervalle of pij  */
    }        /*
  if(mle==1){          fprintf(ficgp,"\nset noparametric;unset label");
     /* Computing hessian and covariance matrix */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     ftolhess=ftol; /* Usually correct */          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     hesscov(matcov, p, npar, delti, ftolhess, func);          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
  }          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     fprintf(ficres,"# Scales\n");          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     printf("# Scales\n");          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
      for(i=1,jk=1; i <=nlstate; i++){        */
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           fprintf(ficres,"%1d%1d",i,j);        first1=1;
           printf("%1d%1d",i,j);        for (k2=1; k2<=(nlstate);k2++){
           for(k=1; k<=ncovmodel;k++){          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             printf(" %.5e",delti[jk]);            if(l2==k2) continue;
             fprintf(ficres," %.5e",delti[jk]);            j=(k2-1)*(nlstate+ndeath)+l2;
             jk++;            for (k1=1; k1<=(nlstate);k1++){
           }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
           printf("\n");                if(l1==k1) continue;
           fprintf(ficres,"\n");                i=(k1-1)*(nlstate+ndeath)+l1;
         }                if(i<=j) continue;
       }                for (age=bage; age<=fage; age ++){ 
      }                  if ((int)age %5==0){
                        v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     k=1;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     fprintf(ficres,"# Covariance\n");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     printf("# Covariance\n");                    mu1=mu[i][(int) age]/stepm*YEARM ;
     for(i=1;i<=npar;i++){                    mu2=mu[j][(int) age]/stepm*YEARM;
       /*  if (k>nlstate) k=1;                    c12=cv12/sqrt(v1*v2);
       i1=(i-1)/(ncovmodel*nlstate)+1;                    /* Computing eigen value of matrix of covariance */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       printf("%s%d%d",alph[k],i1,tab[i]);*/                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       fprintf(ficres,"%3d",i);                    /* Eigen vectors */
       printf("%3d",i);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       for(j=1; j<=i;j++){                    /*v21=sqrt(1.-v11*v11); *//* error */
         fprintf(ficres," %.5e",matcov[i][j]);                    v21=(lc1-v1)/cv12*v11;
         printf(" %.5e",matcov[i][j]);                    v12=-v21;
       }                    v22=v11;
       fprintf(ficres,"\n");                    tnalp=v21/v11;
       printf("\n");                    if(first1==1){
       k++;                      first1=0;
     }                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                        }
     while((c=getc(ficpar))=='#' && c!= EOF){                    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);
       ungetc(c,ficpar);                    /*printf(fignu*/
       fgets(line, MAXLINE, ficpar);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       puts(line);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       fputs(line,ficparo);                    if(first==1){
     }                      first=0;
     ungetc(c,ficpar);                      fprintf(ficgp,"\nset parametric;unset label");
                        fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                          fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
     if (fage <= 2) {                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
       bage = agemin;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       fage = agemax;                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
     }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                          fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                      }else{
     while((c=getc(ficpar))=='#' && c!= EOF){                      first=0;
     ungetc(c,ficpar);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
     fgets(line, MAXLINE, ficpar);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     puts(line);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     fputs(line,ficparo);                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   ungetc(c,ficpar);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                      }/* if first */
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                  } /* age mod 5 */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                } /* end loop age */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                      first=1;
   while((c=getc(ficpar))=='#' && c!= EOF){              } /*l12 */
     ungetc(c,ficpar);            } /* k12 */
     fgets(line, MAXLINE, ficpar);          } /*l1 */
     puts(line);        }/* k1 */
     fputs(line,ficparo);      } /* loop covariates */
   }    }
   ungetc(c,ficpar);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    fclose(ficresprob);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    fclose(ficresprobcov);
     fclose(ficresprobcor);
   fscanf(ficpar,"pop_based=%d\n",&popbased);    fclose(ficgp);
    fprintf(ficparo,"pop_based=%d\n",popbased);    }
    fprintf(ficres,"pop_based=%d\n",popbased);    
   
   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){
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);    int jj1, k1, i1, cpt;
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    /*char optionfilehtm[FILENAMELENGTH];*/
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   /*   } */
 /*------------ gnuplot -------------*/  
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);     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 \
 /*------------ free_vector  -------------*/   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
  chdir(path);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
     - Life expectancies by age and initial health status (estepm=%2d months): \
  free_ivector(wav,1,imx);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
  free_ivector(num,1,n);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
  free_vector(agedc,1,n);  
  /*free_matrix(covar,1,NCOVMAX,1,n);*/   m=cptcoveff;
  fclose(ficparo);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
  fclose(ficres);  
     jj1=0;
   /* Reads comments: lines beginning with '#' */   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,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       /* Pij */
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);       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(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
 /*--------- index.htm --------*/       /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> \
   <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
           /* Stable prevalence in each health state */
   /*--------------- Prevalence limit --------------*/         for(cpt=1; cpt<nlstate;cpt++){
             fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   strcpy(filerespl,"pl");  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   strcat(filerespl,fileres);         }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       for(cpt=1; cpt<=nlstate;cpt++) {
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
   }  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);       }
   fprintf(ficrespl,"#Prevalence limit\n");       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   fprintf(ficrespl,"#Age ");  health expectancies in states (1) and (2): e%s%d.png<br>\
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   fprintf(ficrespl,"\n");     } /* end i1 */
     }/* End k1 */
   prlim=matrix(1,nlstate,1,nlstate);   fprintf(fichtm,"</ul>");
   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 */   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
   k=0;   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
   agebase=agemin;   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
   agelim=agemax;   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
   ftolpl=1.e-10;   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
   i1=cptcoveff;   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   if (cptcovn < 1){i1=1;}  
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   for(cptcov=1;cptcov<=i1;cptcov++){  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
         k=k+1;  /*      <br>",fileres,fileres,fileres,fileres); */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  /*  else  */
         fprintf(ficrespl,"\n#******");  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
         for(j=1;j<=cptcoveff;j++)  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");   m=cptcoveff;
           if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         for (age=agebase; age<=agelim; age++){  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   jj1=0;
           fprintf(ficrespl,"%.0f",age );   for(k1=1; k1<=m;k1++){
           for(i=1; i<=nlstate;i++)     for(i1=1; i1<=ncodemax[k1];i1++){
           fprintf(ficrespl," %.5f", prlim[i][i]);       jj1++;
           fprintf(ficrespl,"\n");       if (cptcovn > 0) {
         }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       }         for (cpt=1; cpt<=cptcoveff;cpt++) 
     }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   fclose(ficrespl);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   /*------------- h Pij x at various ages ------------*/       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  interval) in state (%d): v%s%d%d.png <br>\
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;       }
   }     } /* end i1 */
   printf("Computing pij: result on file '%s' \n", filerespij);   }/* End k1 */
     fprintf(fichtm,"</ul>");
   stepsize=(int) (stepm+YEARM-1)/YEARM;   fflush(fichtm);
   /*if (stepm<=24) stepsize=2;*/  }
   
   agelim=AGESUP;  /******************* Gnuplot file **************/
   hstepm=stepsize*YEARM; /* Every year of age */  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
      int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   k=0;    int ng;
   for(cptcov=1;cptcov<=i1;cptcov++){    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf("Problem with file %s",optionfilegnuplot);
       k=k+1;      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
         fprintf(ficrespij,"\n#****** ");    }
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*#ifdef windows */
         fprintf(ficrespij,"******\n");      fprintf(ficgp,"cd \"%s\" \n",pathc);
              /*#endif */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  m=pow(2,cptcoveff);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   /* 1eme*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (cpt=1; cpt<= nlstate ; cpt ++) {
           oldm=oldms;savm=savms;     for (k1=1; k1<= m ; k1 ++) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           fprintf(ficrespij,"# 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);
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)       for (i=1; i<= nlstate ; i ++) {
               fprintf(ficrespij," %1d-%1d",i,j);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           fprintf(ficrespij,"\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
           for (h=0; h<=nhstepm; h++){       }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
             for(i=1; i<=nlstate;i++)       for (i=1; i<= nlstate ; i ++) {
               for(j=1; j<=nlstate+ndeath;j++)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);         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*$3) \"\%%lf",fileres,k1-1,k1-1); 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       for (i=1; i<= nlstate ; i ++) {
           fprintf(ficrespij,"\n");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         }         else fprintf(ficgp," \%%*lf (\%%*lf)");
     }       }  
   }       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      }
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    }
     /*2 eme*/
   fclose(ficrespij);    
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
   /*---------- Forecasting ------------------*/      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   if(stepm == 1) {      
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      for (i=1; i<= nlstate+1 ; i ++) {
 populforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);        k=2*i;
     free_matrix(mint,1,maxwav,1,n);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        for (j=1; j<= nlstate+1 ; j ++) {
     free_vector(weight,1,n);}          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   else{          else fprintf(ficgp," \%%*lf (\%%*lf)");
     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);        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 ++) {
   /*---------- Health expectancies and variances ------------*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   strcpy(filerest,"t");        }   
   strcat(filerest,fileres);        fprintf(ficgp,"\" t\"\" w l 0,");
   if((ficrest=fopen(filerest,"w"))==NULL) {        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        for (j=1; j<= nlstate+1 ; j ++) {
   }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   strcpy(filerese,"e");        else fprintf(ficgp,"\" t\"\" w l 0,");
   strcat(filerese,fileres);      }
   if((ficreseij=fopen(filerese,"w"))==NULL) {    }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    
   }    /*3eme*/
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    
     for (k1=1; k1<= m ; k1 ++) { 
  strcpy(fileresv,"v");      for (cpt=1; cpt<= nlstate ; cpt ++) {
   strcat(fileresv,fileres);        k=2+nlstate*(2*cpt-2);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
   }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   k=0;          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   for(cptcov=1;cptcov<=i1;cptcov++){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       k=k+1;          
       fprintf(ficrest,"\n#****** ");        */
       for(j=1;j<=cptcoveff;j++)        for (i=1; i< nlstate ; i ++) {
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          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);
       fprintf(ficrest,"******\n");          
         } 
       fprintf(ficreseij,"\n#****** ");      }
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    
       fprintf(ficreseij,"******\n");    /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficresvij,"\n#****** ");      for (cpt=1; cpt<=nlstate ; cpt ++) {
       for(j=1;j<=cptcoveff;j++)        k=3;
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       fprintf(ficresvij,"******\n");        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);
         
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        for (i=1; i< nlstate ; i ++)
       oldm=oldms;savm=savms;          fprintf(ficgp,"+$%d",k+i+1);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        
       oldm=oldms;savm=savms;        l=3+(nlstate+ndeath)*cpt;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
            for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
            fprintf(ficgp,"+$%d",l+i+1);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       fprintf(ficrest,"\n");      } 
     }  
       hf=1;    
       if (stepm >= YEARM) hf=stepm/YEARM;    /* proba elementaires */
       epj=vector(1,nlstate+1);    for(i=1,jk=1; i <=nlstate; i++){
       for(age=bage; age <=fage ;age++){      for(k=1; k <=(nlstate+ndeath); k++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        if (k != i) {
         if (popbased==1) {          for(j=1; j <=ncovmodel; j++){
           for(i=1; i<=nlstate;i++)            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             prlim[i][i]=probs[(int)age][i][k];            jk++; 
         }            fprintf(ficgp,"\n");
                  }
         fprintf(ficrest," %.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]*hf*eij[i][j][(int)age];  
           }     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
           epj[nlstate+1] +=epj[j];       for(jk=1; jk <=m; jk++) {
         }         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
         for(i=1, vepp=0.;i <=nlstate;i++)         if (ng==2)
           for(j=1;j <=nlstate;j++)           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
             vepp += vareij[i][j][(int)age];         else
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));           fprintf(ficgp,"\nset title \"Probability\"\n");
         for(j=1;j <=nlstate;j++){         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));         i=1;
         }         for(k2=1; k2<=nlstate; k2++) {
         fprintf(ficrest,"\n");           k3=i;
       }           for(k=1; k<=(nlstate+ndeath); k++) {
     }             if (k != k2){
   }               if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   fclose(ficreseij);               else
   fclose(ficresvij);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   fclose(ficrest);               ij=1;
   fclose(ficpar);               for(j=3; j <=ncovmodel; j++) {
   free_vector(epj,1,nlstate+1);                 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]]]);
   /*------- Variance limit prevalence------*/                     ij++;
                  }
   strcpy(fileresvpl,"vpl");                 else
   strcat(fileresvpl,fileres);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {               }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);               fprintf(ficgp,")/(1");
     exit(0);               
   }               for(k1=1; k1 <=nlstate; k1++){   
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
   k=0;                 for(j=3; j <=ncovmodel; j++){
   for(cptcov=1;cptcov<=i1;cptcov++){                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       k=k+1;                     ij++;
       fprintf(ficresvpl,"\n#****** ");                   }
       for(j=1;j<=cptcoveff;j++)                   else
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       fprintf(ficresvpl,"******\n");                 }
                       fprintf(ficgp,")");
       varpl=matrix(1,nlstate,(int) bage, (int) fage);               }
       oldm=oldms;savm=savms;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     }               i=i+ncovmodel;
  }             }
            } /* end k */
   fclose(ficresvpl);         } /* end k2 */
        } /* end jk */
   /*---------- End : free ----------------*/     } /* end ng */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);     fclose(ficgp); 
    }  /* end gnuplot */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
    /*************** Moving average **************/
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    int i, cpt, cptcod;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    int modcovmax =1;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    int mobilavrange, mob;
      double age;
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   free_matrix(agev,1,maxwav,1,imx);                             a covariate has 2 modalities */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   if(erreur >0)    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     printf("End of Imach with error %d\n",erreur);      if(mobilav==1) mobilavrange=5; /* default */
   else   printf("End of Imach\n");      else mobilavrange=mobilav;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      for (age=bage; age<=fage; age++)
          for (i=1; i<=nlstate;i++)
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   /*------ End -----------*/      /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
  end:      */ 
 #ifdef windows      for (mob=3;mob <=mobilavrange;mob=mob+2){
   /* chdir(pathcd);*/        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
 #endif          for (i=1; i<=nlstate;i++){
  /*system("wgnuplot graph.plt");*/            for (cptcod=1;cptcod<=modcovmax;cptcod++){
  /*system("../gp37mgw/wgnuplot graph.plt");*/              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
  /*system("cd ../gp37mgw");*/                for (cpt=1;cpt<=(mob-1)/2;cpt++){
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
  strcpy(plotcmd,GNUPLOTPROGRAM);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
  strcat(plotcmd," ");                }
  strcat(plotcmd,optionfilegnuplot);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
  system(plotcmd);            }
           }
 #ifdef windows        }/* end age */
   while (z[0] != 'q') {      }/* end mob */
     chdir(path);    }else return -1;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    return 0;
     scanf("%s",z);  }/* End movingaverage */
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') {  
       chdir(path);  /************** Forecasting ******************/
       system(optionfilehtm);  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     }    /* proj1, year, month, day of starting projection 
     else if (z[0] == 'q') exit(0);       agemin, agemax range of age
   }       dateprev1 dateprev2 range of dates during which prevalence is computed
 #endif       anproj2 year of en of projection (same day and month as proj1).
 }    */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            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.1.27  
changed lines
  Added in v.1.87


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