Diff for /imach/src/imach.c between versions 1.41.2.2 and 1.88

version 1.41.2.2, 2003/06/13 07:45:28 version 1.88, 2003/06/23 17:54:56
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.88  2003/06/23 17:54:56  brouard
      * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.87  2003/06/18 12:26:01  brouard
   first survey ("cross") where individuals from different ages are    Version 0.96
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.86  2003/06/17 20:04:08  brouard
   second wave of interviews ("longitudinal") which measure each change    (Module): Change position of html and gnuplot routines and added
   (if any) in individual health status.  Health expectancies are    routine fileappend.
   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    Revision 1.85  2003/06/17 13:12:43  brouard
   Maximum Likelihood of the parameters involved in the model.  The    * imach.c (Repository): Check when date of death was earlier that
   simplest model is the multinomial logistic model where pij is the    current date of interview. It may happen when the death was just
   probability to be observed in state j at the second wave    prior to the death. In this case, dh was negative and likelihood
   conditional to be observed in state i at the first wave. Therefore    was wrong (infinity). We still send an "Error" but patch by
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    assuming that the date of death was just one stepm after the
   'age' is age and 'sex' is a covariate. If you want to have a more    interview.
   complex model than "constant and age", you should modify the program    (Repository): Because some people have very long ID (first column)
   where the markup *Covariates have to be included here again* invites    we changed int to long in num[] and we added a new lvector for
   you to do it.  More covariates you add, slower the    memory allocation. But we also truncated to 8 characters (left
   convergence.    truncation)
     (Repository): No more line truncation errors.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.84  2003/06/13 21:44:43  brouard
   identical for each individual. Also, if a individual missed an    * imach.c (Repository): Replace "freqsummary" at a correct
   intermediate interview, the information is lost, but taken into    place. It differs from routine "prevalence" which may be called
   account using an interpolation or extrapolation.      many times. Probs is memory consuming and must be used with
     parcimony.
   hPijx is the probability to be observed in state i at age x+h    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   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 1.83  2003/06/10 13:39:11  lievre
   states. This elementary transition (by month or quarter trimester,    *** empty log message ***
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.82  2003/06/05 15:57:20  brouard
   and the contribution of each individual to the likelihood is simply    Add log in  imach.c and  fullversion number is now printed.
   hPijx.  
   */
   Also this programme outputs the covariance matrix of the parameters but also  /*
   of the life expectancies. It also computes the prevalence limits.     Interpolated Markov Chain
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Short summary of the programme:
            Institut national d'études démographiques, Paris.    
   This software have been partly granted by Euro-REVES, a concerted action    This program computes Healthy Life Expectancies from
   from the European Union.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   It is copyrighted identically to a GNU software product, ie programme and    first survey ("cross") where individuals from different ages are
   software can be distributed freely for non commercial use. Latest version    interviewed on their health status or degree of disability (in the
   can be accessed at http://euroreves.ined.fr/imach .    case of a health survey which is our main interest) -2- at least a
   **********************************************************************/    second wave of interviews ("longitudinal") which measure each change
      (if any) in individual health status.  Health expectancies are
 #include <math.h>    computed from the time spent in each health state according to a
 #include <stdio.h>    model. More health states you consider, more time is necessary to reach the
 #include <stdlib.h>    Maximum Likelihood of the parameters involved in the model.  The
 #include <unistd.h>    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 #define MAXLINE 256    conditional to be observed in state i at the first wave. Therefore
 #define GNUPLOTPROGRAM "wgnuplot"    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    'age' is age and 'sex' is a covariate. If you want to have a more
 #define FILENAMELENGTH 80    complex model than "constant and age", you should modify the program
 /*#define DEBUG*/    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 /*#define windows*/    convergence.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    identical for each individual. Also, if a individual missed an
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    hPijx is the probability to be observed in state i at age x+h
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    conditional to the observed state i at age x. The delay 'h' can be
 #define NCOVMAX 8 /* Maximum number of covariates */    split into an exact number (nh*stepm) of unobserved intermediate
 #define MAXN 20000    states. This elementary transition (by month, quarter,
 #define YEARM 12. /* Number of months per year */    semester or year) is modelled as a multinomial logistic.  The hPx
 #define AGESUP 130    matrix is simply the matrix product of nh*stepm elementary matrices
 #define AGEBASE 40    and the contribution of each individual to the likelihood is simply
     hPijx.
   
 int erreur; /* Error number */    Also this programme outputs the covariance matrix of the parameters but also
 int nvar;    of the life expectancies. It also computes the stable prevalence. 
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    
 int npar=NPARMAX;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int nlstate=2; /* Number of live states */             Institut national d'études démographiques, Paris.
 int ndeath=1; /* Number of dead states */    This software have been partly granted by Euro-REVES, a concerted action
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    from the European Union.
 int popbased=0;    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 int *wav; /* Number of waves for this individuual 0 is possible */    can be accessed at http://euroreves.ined.fr/imach .
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int mle, weightopt;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 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 */  /*
 double **oldm, **newm, **savm; /* Working pointers to matrices */    main
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    read parameterfile
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    read datafile
 FILE *ficgp,*ficresprob,*ficpop;    concatwav
 FILE *ficreseij;    freqsummary
   char filerese[FILENAMELENGTH];    if (mle >= 1)
  FILE  *ficresvij;      mlikeli
   char fileresv[FILENAMELENGTH];    print results files
  FILE  *ficresvpl;    if mle==1 
   char fileresvpl[FILENAMELENGTH];       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 #define NR_END 1        begin-prev-date,...
 #define FREE_ARG char*    open gnuplot file
 #define FTOL 1.0e-10    open html file
     stable prevalence
 #define NRANSI     for age prevalim()
 #define ITMAX 200    h Pij x
     variance of p varprob
 #define TOL 2.0e-4    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 #define CGOLD 0.3819660    Variance-covariance of DFLE
 #define ZEPS 1.0e-10    prevalence()
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);     movingaverage()
     varevsij() 
 #define GOLD 1.618034    if popbased==1 varevsij(,popbased)
 #define GLIMIT 100.0    total life expectancies
 #define TINY 1.0e-20    Variance of stable prevalence
    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))   
 #define rint(a) floor(a+0.5)  #include <math.h>
   #include <stdio.h>
 static double sqrarg;  #include <stdlib.h>
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #include <unistd.h>
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   #include <sys/time.h>
 int imx;  #include <time.h>
 int stepm;  #include "timeval.h"
 /* Stepm, step in month: minimum step interpolation*/  
   #define MAXLINE 256
 int estepm;  #define GNUPLOTPROGRAM "gnuplot"
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 int m,nb;  /*#define DEBUG*/
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  /*#define windows*/
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 double **pmmij, ***probs, ***mobaverage;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 double dateintmean=0;  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 double *weight;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 int **s; /* Status */  
 double *agedc, **covar, idx;  #define NINTERVMAX 8
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define NCOVMAX 8 /* Maximum number of covariates */
 double ftolhess; /* Tolerance for computing hessian */  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 /**************** split *************************/  #define AGESUP 130
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define AGEBASE 40
 {  #ifdef unix
    char *s;                             /* pointer */  #define DIRSEPARATOR '/'
    int  l1, l2;                         /* length counters */  #define ODIRSEPARATOR '\\'
   #else
    l1 = strlen( path );                 /* length of path */  #define DIRSEPARATOR '\\'
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define ODIRSEPARATOR '/'
 #ifdef windows  #endif
    s = strrchr( path, '\\' );           /* find last / */  
 #else  /* $Id$ */
    s = strrchr( path, '/' );            /* find last / */  /* $State$ */
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
 #if     defined(__bsd__)                /* get current working directory */  char fullversion[]="$Revision$ $Date$"; 
       extern char       *getwd( );  int erreur; /* Error number */
   int nvar;
       if ( getwd( dirc ) == NULL ) {  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #else  int npar=NPARMAX;
       extern char       *getcwd( );  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #endif  int popbased=0;
          return( GLOCK_ERROR_GETCWD );  
       }  int *wav; /* Number of waves for this individuual 0 is possible */
       strcpy( name, path );             /* we've got it */  int maxwav; /* Maxim number of waves */
    } else {                             /* strip direcotry from path */  int jmin, jmax; /* min, max spacing between 2 waves */
       s++;                              /* after this, the filename */  int gipmx, gsw; /* Global variables on the number of contributions 
       l2 = strlen( s );                 /* length of filename */                     to the likelihood and the sum of weights (done by funcone)*/
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int mle, weightopt;
       strcpy( name, s );                /* save file name */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       dirc[l1-l2] = 0;                  /* add zero */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
    }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
    l1 = strlen( dirc );                 /* length of directory */  double jmean; /* Mean space between 2 waves */
 #ifdef windows  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 */
 #else  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  FILE *ficlog, *ficrespow;
 #endif  int globpr; /* Global variable for printing or not */
    s = strrchr( name, '.' );            /* find last / */  double fretone; /* Only one call to likelihood */
    s++;  long ipmx; /* Number of contributions */
    strcpy(ext,s);                       /* save extension */  double sw; /* Sum of weights */
    l1= strlen( name);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
    l2= strlen( s)+1;  FILE *ficresilk;
    strncpy( finame, name, l1-l2);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    finame[l1-l2]= 0;  FILE *ficresprobmorprev;
    return( 0 );                         /* we're done */  FILE *fichtm; /* Html File */
 }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 /******************************************/  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 void replace(char *s, char*t)  char fileresvpl[FILENAMELENGTH];
 {  char title[MAXLINE];
   int i;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   int lg=20;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   i=0;  char tmpout[FILENAMELENGTH]; 
   lg=strlen(t);  char command[FILENAMELENGTH];
   for(i=0; i<= lg; i++) {  int  outcmd=0;
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   }  char lfileres[FILENAMELENGTH];
 }  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 int nbocc(char *s, char occ)  char fileregp[FILENAMELENGTH];
 {  char popfile[FILENAMELENGTH];
   int i,j=0;  
   int lg=20;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   i=0;  
   lg=strlen(s);  #define NR_END 1
   for(i=0; i<= lg; i++) {  #define FREE_ARG char*
   if  (s[i] == occ ) j++;  #define FTOL 1.0e-10
   }  
   return j;  #define NRANSI 
 }  #define ITMAX 200 
   
 void cutv(char *u,char *v, char*t, char occ)  #define TOL 2.0e-4 
 {  
   int i,lg,j,p=0;  #define CGOLD 0.3819660 
   i=0;  #define ZEPS 1.0e-10 
   for(j=0; j<=strlen(t)-1; j++) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  #define GOLD 1.618034 
   #define GLIMIT 100.0 
   lg=strlen(t);  #define TINY 1.0e-20 
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  static double maxarg1,maxarg2;
   }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
      u[p]='\0';  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
    for(j=0; j<= lg; j++) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define rint(a) floor(a+0.5)
   }  
 }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /********************** nrerror ********************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
 void nrerror(char error_text[])  int imx; 
 {  int stepm;
   fprintf(stderr,"ERREUR ...\n");  /* Stepm, step in month: minimum step interpolation*/
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  int estepm;
 }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  int m,nb;
 {  long *num;
   double *v;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   if (!v) nrerror("allocation failure in vector");  double **pmmij, ***probs;
   return v-nl+NR_END;  double dateintmean=0;
 }  
   double *weight;
 /************************ free vector ******************/  int **s; /* Status */
 void free_vector(double*v, int nl, int nh)  double *agedc, **covar, idx;
 {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   free((FREE_ARG)(v+nl-NR_END));  
 }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  /**************** split *************************/
 {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   int *v;  {
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    char  *ss;                            /* pointer */
   if (!v) nrerror("allocation failure in ivector");    int   l1, l2;                         /* length counters */
   return v-nl+NR_END;  
 }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 /******************free ivector **************************/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 void free_ivector(int *v, long nl, long nh)    if ( ss == NULL ) {                   /* no directory, so use current */
 {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   free((FREE_ARG)(v+nl-NR_END));        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 }      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 /******************* imatrix *******************************/      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 int **imatrix(long nrl, long nrh, long ncl, long nch)        return( GLOCK_ERROR_GETCWD );
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */      }
 {      strcpy( name, path );               /* we've got it */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    } else {                              /* strip direcotry from path */
   int **m;      ss++;                               /* after this, the filename */
        l2 = strlen( ss );                  /* length of filename */
   /* allocate pointers to rows */      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));      strcpy( name, ss );         /* save file name */
   if (!m) nrerror("allocation failure 1 in matrix()");      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   m += NR_END;      dirc[l1-l2] = 0;                    /* add zero */
   m -= nrl;    }
      l1 = strlen( dirc );                  /* length of directory */
      /*#ifdef windows
   /* 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)));  #else
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   m[nrl] += NR_END;  #endif
   m[nrl] -= ncl;    */
      ss = strrchr( name, '.' );            /* find last / */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    ss++;
      strcpy(ext,ss);                       /* save extension */
   /* return pointer to array of pointers to rows */    l1= strlen( name);
   return m;    l2= strlen(ss)+1;
 }    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 /****************** free_imatrix *************************/    return( 0 );                          /* we're done */
 void free_imatrix(m,nrl,nrh,ncl,nch)  }
       int **m;  
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  /******************************************/
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  void replace(char *s, char*t)
   free((FREE_ARG) (m+nrl-NR_END));  {
 }    int i;
     int lg=20;
 /******************* matrix *******************************/    i=0;
 double **matrix(long nrl, long nrh, long ncl, long nch)    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;      (s[i] = t[i]);
   double **m;      if (t[i]== '\\') s[i]='/';
     }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  int nbocc(char *s, char occ)
   m -= nrl;  {
     int i,j=0;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    int lg=20;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    i=0;
   m[nrl] += NR_END;    lg=strlen(s);
   m[nrl] -= ncl;    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    }
   return m;    return j;
 }  }
   
 /*************************free matrix ************************/  void cutv(char *u,char *v, char*t, char occ)
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  {
 {    /* cuts string t into u and v where u is ended by char occ excluding it
   free((FREE_ARG)(m[nrl]+ncl-NR_END));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   free((FREE_ARG)(m+nrl-NR_END));       gives u="abcedf" and v="ghi2j" */
 }    int i,lg,j,p=0;
     i=0;
 /******************* ma3x *******************************/    for(j=0; j<=strlen(t)-1; j++) {
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 {    }
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    lg=strlen(t);
     for(j=0; j<p; j++) {
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      (u[j] = t[j]);
   if (!m) nrerror("allocation failure 1 in matrix()");    }
   m += NR_END;       u[p]='\0';
   m -= nrl;  
      for(j=0; j<= lg; j++) {
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));      if (j>=(p+1))(v[j-p-1] = t[j]);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    }
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
   /********************** nrerror ********************/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   void nrerror(char error_text[])
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  {
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    fprintf(stderr,"ERREUR ...\n");
   m[nrl][ncl] += NR_END;    fprintf(stderr,"%s\n",error_text);
   m[nrl][ncl] -= nll;    exit(EXIT_FAILURE);
   for (j=ncl+1; j<=nch; j++)  }
     m[nrl][j]=m[nrl][j-1]+nlay;  /*********************** vector *******************/
    double *vector(int nl, int nh)
   for (i=nrl+1; i<=nrh; i++) {  {
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    double *v;
     for (j=ncl+1; j<=nch; j++)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       m[i][j]=m[i][j-1]+nlay;    if (!v) nrerror("allocation failure in vector");
   }    return v-nl+NR_END;
   return m;  }
 }  
   /************************ free vector ******************/
 /*************************free ma3x ************************/  void free_vector(double*v, int nl, int nh)
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  {
 {    free((FREE_ARG)(v+nl-NR_END));
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  /************************ivector *******************************/
 }  int *ivector(long nl,long nh)
   {
 /***************** f1dim *************************/    int *v;
 extern int ncom;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 extern double *pcom,*xicom;    if (!v) nrerror("allocation failure in ivector");
 extern double (*nrfunc)(double []);    return v-nl+NR_END;
    }
 double f1dim(double x)  
 {  /******************free ivector **************************/
   int j;  void free_ivector(int *v, long nl, long nh)
   double f;  {
   double *xt;    free((FREE_ARG)(v+nl-NR_END));
    }
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /************************lvector *******************************/
   f=(*nrfunc)(xt);  long *lvector(long nl,long nh)
   free_vector(xt,1,ncom);  {
   return f;    long *v;
 }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
 /*****************brent *************************/    return v-nl+NR_END;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  }
 {  
   int iter;  /******************free lvector **************************/
   double a,b,d,etemp;  void free_lvector(long *v, long nl, long nh)
   double fu,fv,fw,fx;  {
   double ftemp;    free((FREE_ARG)(v+nl-NR_END));
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    /******************* imatrix *******************************/
   a=(ax < cx ? ax : cx);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   b=(ax > cx ? ax : cx);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   x=w=v=bx;  { 
   fw=fv=fx=(*f)(x);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   for (iter=1;iter<=ITMAX;iter++) {    int **m; 
     xm=0.5*(a+b);    
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    /* allocate pointers to rows */ 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     printf(".");fflush(stdout);    if (!m) nrerror("allocation failure 1 in matrix()"); 
 #ifdef DEBUG    m += NR_END; 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    m -= nrl; 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    
 #endif    
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    /* allocate rows and set pointers to them */ 
       *xmin=x;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       return fx;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     }    m[nrl] += NR_END; 
     ftemp=fu;    m[nrl] -= ncl; 
     if (fabs(e) > tol1) {    
       r=(x-w)*(fx-fv);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       q=(x-v)*(fx-fw);    
       p=(x-v)*q-(x-w)*r;    /* return pointer to array of pointers to rows */ 
       q=2.0*(q-r);    return m; 
       if (q > 0.0) p = -p;  } 
       q=fabs(q);  
       etemp=e;  /****************** free_imatrix *************************/
       e=d;  void free_imatrix(m,nrl,nrh,ncl,nch)
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))        int **m;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));        long nch,ncl,nrh,nrl; 
       else {       /* free an int matrix allocated by imatrix() */ 
         d=p/q;  { 
         u=x+d;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         if (u-a < tol2 || b-u < tol2)    free((FREE_ARG) (m+nrl-NR_END)); 
           d=SIGN(tol1,xm-x);  } 
       }  
     } else {  /******************* matrix *******************************/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  double **matrix(long nrl, long nrh, long ncl, long nch)
     }  {
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     fu=(*f)(u);    double **m;
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       SHFT(v,w,x,u)    if (!m) nrerror("allocation failure 1 in matrix()");
         SHFT(fv,fw,fx,fu)    m += NR_END;
         } else {    m -= nrl;
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
             v=w;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
             w=u;    m[nrl] += NR_END;
             fv=fw;    m[nrl] -= ncl;
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
             v=u;    return m;
             fv=fu;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
           }     */
         }  }
   }  
   nrerror("Too many iterations in brent");  /*************************free matrix ************************/
   *xmin=x;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   return fx;  {
 }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 /****************** mnbrak ***********************/  }
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /******************* ma3x *******************************/
             double (*func)(double))  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 {  {
   double ulim,u,r,q, dum;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   double fu;    double ***m;
    
   *fa=(*func)(*ax);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   *fb=(*func)(*bx);    if (!m) nrerror("allocation failure 1 in matrix()");
   if (*fb > *fa) {    m += NR_END;
     SHFT(dum,*ax,*bx,dum)    m -= nrl;
       SHFT(dum,*fb,*fa,dum)  
       }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   *cx=(*bx)+GOLD*(*bx-*ax);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   *fc=(*func)(*cx);    m[nrl] += NR_END;
   while (*fb > *fc) {    m[nrl] -= ncl;
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     ulim=(*bx)+GLIMIT*(*cx-*bx);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     if ((*bx-u)*(u-*cx) > 0.0) {    m[nrl][ncl] += NR_END;
       fu=(*func)(u);    m[nrl][ncl] -= nll;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    for (j=ncl+1; j<=nch; j++) 
       fu=(*func)(u);      m[nrl][j]=m[nrl][j-1]+nlay;
       if (fu < *fc) {    
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    for (i=nrl+1; i<=nrh; i++) {
           SHFT(*fb,*fc,fu,(*func)(u))      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
           }      for (j=ncl+1; j<=nch; j++) 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {        m[i][j]=m[i][j-1]+nlay;
       u=ulim;    }
       fu=(*func)(u);    return m; 
     } else {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       u=(*cx)+GOLD*(*cx-*bx);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       fu=(*func)(u);    */
     }  }
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  /*************************free ma3x ************************/
       }  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));
 /*************** linmin ************************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 int ncom;  }
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  /***************** f1dim *************************/
    extern int ncom; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  extern double *pcom,*xicom;
 {  extern double (*nrfunc)(double []); 
   double brent(double ax, double bx, double cx,   
                double (*f)(double), double tol, double *xmin);  double f1dim(double x) 
   double f1dim(double x);  { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    int j; 
               double *fc, double (*func)(double));    double f;
   int j;    double *xt; 
   double xx,xmin,bx,ax;   
   double fx,fb,fa;    xt=vector(1,ncom); 
      for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   ncom=n;    f=(*nrfunc)(xt); 
   pcom=vector(1,n);    free_vector(xt,1,ncom); 
   xicom=vector(1,n);    return f; 
   nrfunc=func;  } 
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  /*****************brent *************************/
     xicom[j]=xi[j];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   }  { 
   ax=0.0;    int iter; 
   xx=1.0;    double a,b,d,etemp;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double fu,fv,fw,fx;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    double ftemp;
 #ifdef DEBUG    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    double e=0.0; 
 #endif   
   for (j=1;j<=n;j++) {    a=(ax < cx ? ax : cx); 
     xi[j] *= xmin;    b=(ax > cx ? ax : cx); 
     p[j] += xi[j];    x=w=v=bx; 
   }    fw=fv=fx=(*f)(x); 
   free_vector(xicom,1,n);    for (iter=1;iter<=ITMAX;iter++) { 
   free_vector(pcom,1,n);      xm=0.5*(a+b); 
 }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 /*************** powell ************************/      printf(".");fflush(stdout);
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      fprintf(ficlog,".");fflush(ficlog);
             double (*func)(double []))  #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);
   void linmin(double p[], double xi[], int n, double *fret,      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);
               double (*func)(double []));      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   int i,ibig,j;  #endif
   double del,t,*pt,*ptt,*xit;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double fp,fptt;        *xmin=x; 
   double *xits;        return fx; 
   pt=vector(1,n);      } 
   ptt=vector(1,n);      ftemp=fu;
   xit=vector(1,n);      if (fabs(e) > tol1) { 
   xits=vector(1,n);        r=(x-w)*(fx-fv); 
   *fret=(*func)(p);        q=(x-v)*(fx-fw); 
   for (j=1;j<=n;j++) pt[j]=p[j];        p=(x-v)*q-(x-w)*r; 
   for (*iter=1;;++(*iter)) {        q=2.0*(q-r); 
     fp=(*fret);        if (q > 0.0) p = -p; 
     ibig=0;        q=fabs(q); 
     del=0.0;        etemp=e; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);        e=d; 
     for (i=1;i<=n;i++)        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       printf(" %d %.12f",i, p[i]);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     printf("\n");        else { 
     for (i=1;i<=n;i++) {          d=p/q; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];          u=x+d; 
       fptt=(*fret);          if (u-a < tol2 || b-u < tol2) 
 #ifdef DEBUG            d=SIGN(tol1,xm-x); 
       printf("fret=%lf \n",*fret);        } 
 #endif      } else { 
       printf("%d",i);fflush(stdout);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       linmin(p,xit,n,fret,func);      } 
       if (fabs(fptt-(*fret)) > del) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         del=fabs(fptt-(*fret));      fu=(*f)(u); 
         ibig=i;      if (fu <= fx) { 
       }        if (u >= x) a=x; else b=x; 
 #ifdef DEBUG        SHFT(v,w,x,u) 
       printf("%d %.12e",i,(*fret));          SHFT(fv,fw,fx,fu) 
       for (j=1;j<=n;j++) {          } else { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);            if (u < x) a=u; else b=u; 
         printf(" x(%d)=%.12e",j,xit[j]);            if (fu <= fw || w == x) { 
       }              v=w; 
       for(j=1;j<=n;j++)              w=u; 
         printf(" p=%.12e",p[j]);              fv=fw; 
       printf("\n");              fw=fu; 
 #endif            } else if (fu <= fv || v == x || v == w) { 
     }              v=u; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {              fv=fu; 
 #ifdef DEBUG            } 
       int k[2],l;          } 
       k[0]=1;    } 
       k[1]=-1;    nrerror("Too many iterations in brent"); 
       printf("Max: %.12e",(*func)(p));    *xmin=x; 
       for (j=1;j<=n;j++)    return fx; 
         printf(" %.12e",p[j]);  } 
       printf("\n");  
       for(l=0;l<=1;l++) {  /****************** mnbrak ***********************/
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);              double (*func)(double)) 
         }  { 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double ulim,u,r,q, dum;
       }    double fu; 
 #endif   
     *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
       free_vector(xit,1,n);    if (*fb > *fa) { 
       free_vector(xits,1,n);      SHFT(dum,*ax,*bx,dum) 
       free_vector(ptt,1,n);        SHFT(dum,*fb,*fa,dum) 
       free_vector(pt,1,n);        } 
       return;    *cx=(*bx)+GOLD*(*bx-*ax); 
     }    *fc=(*func)(*cx); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    while (*fb > *fc) { 
     for (j=1;j<=n;j++) {      r=(*bx-*ax)*(*fb-*fc); 
       ptt[j]=2.0*p[j]-pt[j];      q=(*bx-*cx)*(*fb-*fa); 
       xit[j]=p[j]-pt[j];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       pt[j]=p[j];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     fptt=(*func)(ptt);      if ((*bx-u)*(u-*cx) > 0.0) { 
     if (fptt < fp) {        fu=(*func)(u); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       if (t < 0.0) {        fu=(*func)(u); 
         linmin(p,xit,n,fret,func);        if (fu < *fc) { 
         for (j=1;j<=n;j++) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
           xi[j][ibig]=xi[j][n];            SHFT(*fb,*fc,fu,(*func)(u)) 
           xi[j][n]=xit[j];            } 
         }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 #ifdef DEBUG        u=ulim; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        fu=(*func)(u); 
         for(j=1;j<=n;j++)      } else { 
           printf(" %.12e",xit[j]);        u=(*cx)+GOLD*(*cx-*bx); 
         printf("\n");        fu=(*func)(u); 
 #endif      } 
       }      SHFT(*ax,*bx,*cx,u) 
     }        SHFT(*fa,*fb,*fc,fu) 
   }        } 
 }  } 
   
 /**** Prevalence limit ****************/  /*************** linmin ************************/
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  int ncom; 
 {  double *pcom,*xicom;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  double (*nrfunc)(double []); 
      matrix by transitions matrix until convergence is reached */   
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   int i, ii,j,k;  { 
   double min, max, maxmin, maxmax,sumnew=0.;    double brent(double ax, double bx, double cx, 
   double **matprod2();                 double (*f)(double), double tol, double *xmin); 
   double **out, cov[NCOVMAX], **pmij();    double f1dim(double x); 
   double **newm;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   double agefin, delaymax=50 ; /* Max number of years to converge */                double *fc, double (*func)(double)); 
     int j; 
   for (ii=1;ii<=nlstate+ndeath;ii++)    double xx,xmin,bx,ax; 
     for (j=1;j<=nlstate+ndeath;j++){    double fx,fb,fa;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);   
     }    ncom=n; 
     pcom=vector(1,n); 
    cov[1]=1.;    xicom=vector(1,n); 
      nrfunc=func; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for (j=1;j<=n;j++) { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      pcom[j]=p[j]; 
     newm=savm;      xicom[j]=xi[j]; 
     /* Covariates have to be included here again */    } 
      cov[2]=agefin;    ax=0.0; 
      xx=1.0; 
       for (k=1; k<=cptcovn;k++) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         /*      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]]);*/  #ifdef DEBUG
       }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (k=1; k<=cptcovprod;k++)  #endif
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      p[j] += xi[j]; 
       /*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]);*/    free_vector(xicom,1,n); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    free_vector(pcom,1,n); 
   } 
     savm=oldm;  
     oldm=newm;  /*************** powell ************************/
     maxmax=0.;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     for(j=1;j<=nlstate;j++){              double (*func)(double [])) 
       min=1.;  { 
       max=0.;    void linmin(double p[], double xi[], int n, double *fret, 
       for(i=1; i<=nlstate; i++) {                double (*func)(double [])); 
         sumnew=0;    int i,ibig,j; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    double del,t,*pt,*ptt,*xit;
         prlim[i][j]= newm[i][j]/(1-sumnew);    double fp,fptt;
         max=FMAX(max,prlim[i][j]);    double *xits;
         min=FMIN(min,prlim[i][j]);    pt=vector(1,n); 
       }    ptt=vector(1,n); 
       maxmin=max-min;    xit=vector(1,n); 
       maxmax=FMAX(maxmax,maxmin);    xits=vector(1,n); 
     }    *fret=(*func)(p); 
     if(maxmax < ftolpl){    for (j=1;j<=n;j++) pt[j]=p[j]; 
       return prlim;    for (*iter=1;;++(*iter)) { 
     }      fp=(*fret); 
   }      ibig=0; 
 }      del=0.0; 
       printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 /*************** transition probabilities ***************/      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       fprintf(ficrespow,"%d %.12f",*iter,*fret);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      for (i=1;i<=n;i++) {
 {        printf(" %d %.12f",i, p[i]);
   double s1, s2;        fprintf(ficlog," %d %.12lf",i, p[i]);
   /*double t34;*/        fprintf(ficrespow," %.12lf", p[i]);
   int i,j,j1, nc, ii, jj;      }
       printf("\n");
     for(i=1; i<= nlstate; i++){      fprintf(ficlog,"\n");
     for(j=1; j<i;j++){      fprintf(ficrespow,"\n");
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      for (i=1;i<=n;i++) { 
         /*s2 += param[i][j][nc]*cov[nc];*/        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        fptt=(*fret); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  #ifdef DEBUG
       }        printf("fret=%lf \n",*fret);
       ps[i][j]=s2;        fprintf(ficlog,"fret=%lf \n",*fret);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  #endif
     }        printf("%d",i);fflush(stdout);
     for(j=i+1; j<=nlstate+ndeath;j++){        fprintf(ficlog,"%d",i);fflush(ficlog);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        linmin(p,xit,n,fret,func); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        if (fabs(fptt-(*fret)) > del) { 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          del=fabs(fptt-(*fret)); 
       }          ibig=i; 
       ps[i][j]=s2;        } 
     }  #ifdef DEBUG
   }        printf("%d %.12e",i,(*fret));
     /*ps[3][2]=1;*/        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   for(i=1; i<= nlstate; i++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
      s1=0;          printf(" x(%d)=%.12e",j,xit[j]);
     for(j=1; j<i; j++)          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       s1+=exp(ps[i][j]);        }
     for(j=i+1; j<=nlstate+ndeath; j++)        for(j=1;j<=n;j++) {
       s1+=exp(ps[i][j]);          printf(" p=%.12e",p[j]);
     ps[i][i]=1./(s1+1.);          fprintf(ficlog," p=%.12e",p[j]);
     for(j=1; j<i; j++)        }
       ps[i][j]= exp(ps[i][j])*ps[i][i];        printf("\n");
     for(j=i+1; j<=nlstate+ndeath; j++)        fprintf(ficlog,"\n");
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #endif
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      } 
   } /* end i */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        int k[2],l;
     for(jj=1; jj<= nlstate+ndeath; jj++){        k[0]=1;
       ps[ii][jj]=0;        k[1]=-1;
       ps[ii][ii]=1;        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
   }        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        }
     for(jj=1; jj<= nlstate+ndeath; jj++){        printf("\n");
      printf("%lf ",ps[ii][jj]);        fprintf(ficlog,"\n");
    }        for(l=0;l<=1;l++) {
     printf("\n ");          for (j=1;j<=n;j++) {
     }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     printf("\n ");printf("%lf ",cov[2]);*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 /*            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          }
   goto end;*/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     return ps;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 }        }
   #endif
 /**************** Product of 2 matrices ******************/  
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        free_vector(xit,1,n); 
 {        free_vector(xits,1,n); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        free_vector(ptt,1,n); 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        free_vector(pt,1,n); 
   /* in, b, out are matrice of pointers which should have been initialized        return; 
      before: only the contents of out is modified. The function returns      } 
      a pointer to pointers identical to out */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   long i, j, k;      for (j=1;j<=n;j++) { 
   for(i=nrl; i<= nrh; i++)        ptt[j]=2.0*p[j]-pt[j]; 
     for(k=ncolol; k<=ncoloh; k++)        xit[j]=p[j]-pt[j]; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        pt[j]=p[j]; 
         out[i][k] +=in[i][j]*b[j][k];      } 
       fptt=(*func)(ptt); 
   return out;      if (fptt < fp) { 
 }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
 /************* Higher Matrix Product ***************/          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            xi[j][n]=xit[j]; 
 {          }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  #ifdef DEBUG
      duration (i.e. until          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          for(j=1;j<=n;j++){
      (typically every 2 years instead of every month which is too big).            printf(" %.12e",xit[j]);
      Model is determined by parameters x and covariates have to be            fprintf(ficlog," %.12e",xit[j]);
      included manually here.          }
           printf("\n");
      */          fprintf(ficlog,"\n");
   #endif
   int i, j, d, h, k;        }
   double **out, cov[NCOVMAX];      } 
   double **newm;    } 
   } 
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  /**** Prevalence limit (stable prevalence)  ****************/
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       po[i][j][0]=(i==j ? 1.0 : 0.0);  {
     }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */       matrix by transitions matrix until convergence is reached */
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){    int i, ii,j,k;
       newm=savm;    double min, max, maxmin, maxmax,sumnew=0.;
       /* Covariates have to be included here again */    double **matprod2();
       cov[1]=1.;    double **out, cov[NCOVMAX], **pmij();
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    double **newm;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    double agefin, delaymax=50 ; /* Max number of years to converge */
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (k=1; k<=cptcovprod;k++)      for (j=1;j<=nlstate+ndeath;j++){
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/     cov[1]=1.;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/   
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       savm=oldm;      newm=savm;
       oldm=newm;      /* Covariates have to be included here again */
     }       cov[2]=agefin;
     for(i=1; i<=nlstate+ndeath; i++)    
       for(j=1;j<=nlstate+ndeath;j++) {        for (k=1; k<=cptcovn;k++) {
         po[i][j][h]=newm[i][j];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          /*      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 (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   } /* end h */        for (k=1; k<=cptcovprod;k++)
   return po;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 }  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 /*************** log-likelihood *************/        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 double func( double *x)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
 {  
   int i, ii, j, k, mi, d, kk;      savm=oldm;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      oldm=newm;
   double **out;      maxmax=0.;
   double sw; /* Sum of weights */      for(j=1;j<=nlstate;j++){
   double lli; /* Individual log likelihood */        min=1.;
   int s1, s2;        max=0.;
   long ipmx;        for(i=1; i<=nlstate; i++) {
   /*extern weight */          sumnew=0;
   /* We are differentiating ll according to initial status */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          prlim[i][j]= newm[i][j]/(1-sumnew);
   /*for(i=1;i<imx;i++)          max=FMAX(max,prlim[i][j]);
     printf(" %d\n",s[4][i]);          min=FMIN(min,prlim[i][j]);
   */        }
   cov[1]=1.;        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
   for(k=1; k<=nlstate; k++) ll[k]=0.;      }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      if(maxmax < ftolpl){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        return prlim;
     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);  
           savm[ii][j]=(ii==j ? 1.0 : 0.0);  /*************** transition probabilities ***************/ 
         }  
       for(d=0; d<dh[mi][i]; d++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         newm=savm;  {
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    double s1, s2;
         for (kk=1; kk<=cptcovage;kk++) {    /*double t34;*/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    int i,j,j1, nc, ii, jj;
         }  
              for(i=1; i<= nlstate; i++){
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      for(j=1; j<i;j++){
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         savm=oldm;          /*s2 += param[i][j][nc]*cov[nc];*/
         oldm=newm;          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;
              /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       s1=s[mw[mi][i]][i];      }
       s2=s[mw[mi+1][i]][i];      for(j=i+1; j<=nlstate+ndeath;j++){
       if( s2 > nlstate){        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         /* i.e. if s2 is a death state and if the date of death is known then the contribution          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
            to the likelihood is the probability to die between last step unit time and current          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
            step unit time, which is also the differences between probability to die before dh        }
            and probability to die before dh-stepm .        ps[i][j]=s2;
            In version up to 0.92 likelihood was computed      }
            as if date of death was unknown. Death was treated as any other    }
            health state: the date of the interview describes the actual state      /*ps[3][2]=1;*/
            and not the date of a change in health state. The former idea was  
            to consider that at each interview the state was recorded    for(i=1; i<= nlstate; i++){
            (healthy, disable or death) and IMaCh was corrected; but when we       s1=0;
            introduced the exact date of death then we should have modified      for(j=1; j<i; j++)
            the contribution of an exact death to the likelihood. This new        s1+=exp(ps[i][j]);
            contribution is smaller and very dependent of the step unit      for(j=i+1; j<=nlstate+ndeath; j++)
            stepm. It is no more the probability to die between last interview        s1+=exp(ps[i][j]);
            and month of death but the probability to survive from last      ps[i][i]=1./(s1+1.);
            interview up to one month before death multiplied by the      for(j=1; j<i; j++)
            probability to die within a month. Thanks to Chris        ps[i][j]= exp(ps[i][j])*ps[i][i];
            Jackson for correcting this bug.  Former versions increased      for(j=i+1; j<=nlstate+ndeath; j++)
            mortality artificially. The bad side is that we add another loop        ps[i][j]= exp(ps[i][j])*ps[i][i];
            which slows down the processing. The difference can be up to 10%      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
            lower mortality.    } /* end i */
         */  
         lli=log(out[s1][s2] - savm[s1][s2]);    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       }else{      for(jj=1; jj<= nlstate+ndeath; jj++){
         lli=log(out[s1][s2]); /* or     lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); */        ps[ii][jj]=0;
         /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        ps[ii][ii]=1;
       }      }
       ipmx +=1;    }
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d lli=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],lli,weight[i],out[s1][s2],savm[s1][s2]);*/    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     } /* end of wave */      for(jj=1; jj<= nlstate+ndeath; jj++){
   } /* end of individual */       printf("%lf ",ps[ii][jj]);
      }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      printf("\n ");
   /* 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 */      printf("\n ");printf("%lf ",cov[2]);*/
   /*exit(0);*/  /*
   return -l;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
 }    goto end;*/
       return ps;
   }
 /*********** Maximum Likelihood Estimation ***************/  
   /**************** Product of 2 matrices ******************/
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   int i,j, iter;  {
   double **xi,*delti;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double fret;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   xi=matrix(1,npar,1,npar);    /* in, b, out are matrice of pointers which should have been initialized 
   for (i=1;i<=npar;i++)       before: only the contents of out is modified. The function returns
     for (j=1;j<=npar;j++)       a pointer to pointers identical to out */
       xi[i][j]=(i==j ? 1.0 : 0.0);    long i, j, k;
   printf("Powell\n");    for(i=nrl; i<= nrh; i++)
   powell(p,xi,npar,ftol,&iter,&fret,func);      for(k=ncolol; k<=ncoloh; k++)
         for(j=ncl,out[i][k]=0.; j<=nch; j++)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          out[i][k] +=in[i][j]*b[j][k];
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  
     return out;
 }  }
   
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /************* Higher Matrix Product ***************/
 {  
   double  **a,**y,*x,pd;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   double **hess;  {
   int i, j,jk;    /* Computes the transition matrix starting at age 'age' over 
   int *indx;       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   double hessii(double p[], double delta, int theta, double delti[]);       nhstepm*hstepm matrices. 
   double hessij(double p[], double delti[], int i, int j);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   void lubksb(double **a, int npar, int *indx, double b[]) ;       (typically every 2 years instead of every month which is too big 
   void ludcmp(double **a, int npar, int *indx, double *d) ;       for the memory).
        Model is determined by parameters x and covariates have to be 
   hess=matrix(1,npar,1,npar);       included manually here. 
   
   printf("\nCalculation of the hessian matrix. Wait...\n");       */
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);    int i, j, d, h, k;
     hess[i][i]=hessii(p,ftolhess,i,delti);    double **out, cov[NCOVMAX];
     /*printf(" %f ",p[i]);*/    double **newm;
     /*printf(" %lf ",hess[i][i]);*/  
   }    /* Hstepm could be zero and should return the unit matrix */
      for (i=1;i<=nlstate+ndeath;i++)
   for (i=1;i<=npar;i++) {      for (j=1;j<=nlstate+ndeath;j++){
     for (j=1;j<=npar;j++)  {        oldm[i][j]=(i==j ? 1.0 : 0.0);
       if (j>i) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
         printf(".%d%d",i,j);fflush(stdout);      }
         hess[i][j]=hessij(p,delti,i,j);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         hess[j][i]=hess[i][j];        for(h=1; h <=nhstepm; h++){
         /*printf(" %lf ",hess[i][j]);*/      for(d=1; d <=hstepm; d++){
       }        newm=savm;
     }        /* Covariates have to be included here again */
   }        cov[1]=1.;
   printf("\n");        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        for (k=1; k<=cptcovage;k++)
            cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   a=matrix(1,npar,1,npar);        for (k=1; k<=cptcovprod;k++)
   y=matrix(1,npar,1,npar);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   x=vector(1,npar);  
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   ludcmp(a,npar,indx,&pd);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (j=1;j<=npar;j++) {        savm=oldm;
     for (i=1;i<=npar;i++) x[i]=0;        oldm=newm;
     x[j]=1;      }
     lubksb(a,npar,indx,x);      for(i=1; i<=nlstate+ndeath; i++)
     for (i=1;i<=npar;i++){        for(j=1;j<=nlstate+ndeath;j++) {
       matcov[i][j]=x[i];          po[i][j][h]=newm[i][j];
     }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   }           */
         }
   printf("\n#Hessian matrix#\n");    } /* end h */
   for (i=1;i<=npar;i++) {    return po;
     for (j=1;j<=npar;j++) {  }
       printf("%.3e ",hess[i][j]);  
     }  
     printf("\n");  /*************** log-likelihood *************/
   }  double func( double *x)
   {
   /* Recompute Inverse */    int i, ii, j, k, mi, d, kk;
   for (i=1;i<=npar;i++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    double **out;
   ludcmp(a,npar,indx,&pd);    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
   /*  printf("\n#Hessian matrix recomputed#\n");    int s1, s2;
     double bbh, survp;
   for (j=1;j<=npar;j++) {    long ipmx;
     for (i=1;i<=npar;i++) x[i]=0;    /*extern weight */
     x[j]=1;    /* We are differentiating ll according to initial status */
     lubksb(a,npar,indx,x);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for (i=1;i<=npar;i++){    /*for(i=1;i<imx;i++) 
       y[i][j]=x[i];      printf(" %d\n",s[4][i]);
       printf("%.3e ",y[i][j]);    */
     }    cov[1]=1.;
     printf("\n");  
   }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   */  
     if(mle==1){
   free_matrix(a,1,npar,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_matrix(y,1,npar,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_vector(x,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   free_ivector(indx,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_matrix(hess,1,npar,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<dh[mi][i]; d++){
 /*************** hessian matrix ****************/            newm=savm;
 double hessii( double x[], double delta, int theta, double delti[])            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
   int i;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int l=1, lmax=20;            }
   double k1,k2;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double p2[NPARMAX+1];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double res;            savm=oldm;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            oldm=newm;
   double fx;          } /* end mult */
   int k=0,kmax=10;        
   double l1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias and large stepm.
   fx=func(x);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   for (i=1;i<=npar;i++) p2[i]=x[i];           * (in months) between two waves is not a multiple of stepm, we rounded to 
   for(l=0 ; l <=lmax; l++){           * the nearest (and in case of equal distance, to the lowest) interval but now
     l1=pow(10,l);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     delts=delt;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     for(k=1 ; k <kmax; k=k+1){           * probability in order to take into account the bias as a fraction of the way
       delt = delta*(l1*k);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       p2[theta]=x[theta] +delt;           * -stepm/2 to stepm/2 .
       k1=func(p2)-fx;           * For stepm=1 the results are the same as for previous versions of Imach.
       p2[theta]=x[theta]-delt;           * For stepm > 1 the results are less biased than in previous versions. 
       k2=func(p2)-fx;           */
       /*res= (k1-2.0*fx+k2)/delt/delt; */          s1=s[mw[mi][i]][i];
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          s2=s[mw[mi+1][i]][i];
                bbh=(double)bh[mi][i]/(double)stepm; 
 #ifdef DEBUG          /* bias is positive if real duration
       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);           * is higher than the multiple of stepm and negative otherwise.
 #endif           */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          if( s2 > nlstate){ 
         k=kmax;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       }               to the likelihood is the probability to die between last step unit time and current 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */               step unit time, which is also the differences between probability to die before dh 
         k=kmax; l=lmax*10.;               and probability to die before dh-stepm . 
       }               In version up to 0.92 likelihood was computed
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          as if date of death was unknown. Death was treated as any other
         delts=delt;          health state: the date of the interview describes the actual state
       }          and not the date of a change in health state. The former idea was
     }          to consider that at each interview the state was recorded
   }          (healthy, disable or death) and IMaCh was corrected; but when we
   delti[theta]=delts;          introduced the exact date of death then we should have modified
   return res;          the contribution of an exact death to the likelihood. This new
            contribution is smaller and very dependent of the step unit
 }          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
 double hessij( double x[], double delti[], int thetai,int thetaj)          interview up to one month before death multiplied by the
 {          probability to die within a month. Thanks to Chris
   int i;          Jackson for correcting this bug.  Former versions increased
   int l=1, l1, lmax=20;          mortality artificially. The bad side is that we add another loop
   double k1,k2,k3,k4,res,fx;          which slows down the processing. The difference can be up to 10%
   double p2[NPARMAX+1];          lower mortality.
   int k;            */
             lli=log(out[s1][s2] - savm[s1][s2]);
   fx=func(x);          }else{
   for (k=1; k<=2; k++) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for (i=1;i<=npar;i++) p2[i]=x[i];            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     p2[thetai]=x[thetai]+delti[thetai]/k;          } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     k1=func(p2)-fx;          /*if(lli ==000.0)*/
            /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     p2[thetai]=x[thetai]+delti[thetai]/k;          ipmx +=1;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          sw += weight[i];
     k2=func(p2)-fx;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
     p2[thetai]=x[thetai]-delti[thetai]/k;      } /* end of individual */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    }  else if(mle==2){
     k3=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetai]=x[thetai]-delti[thetai]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
     k4=func(p2)-fx;            for (j=1;j<=nlstate+ndeath;j++){
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef DEBUG              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);            }
 #endif          for(d=0; d<=dh[mi][i]; d++){
   }            newm=savm;
   return res;            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];
 /************** Inverse of matrix **************/            }
 void ludcmp(double **a, int n, int *indx, double *d)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i,imax,j,k;            savm=oldm;
   double big,dum,sum,temp;            oldm=newm;
   double *vv;          } /* end mult */
          
   vv=vector(1,n);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   *d=1.0;          /* But now since version 0.9 we anticipate for bias and large stepm.
   for (i=1;i<=n;i++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     big=0.0;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     for (j=1;j<=n;j++)           * the nearest (and in case of equal distance, to the lowest) interval but now
       if ((temp=fabs(a[i][j])) > big) big=temp;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     vv[i]=1.0/big;           * probability in order to take into account the bias as a fraction of the way
   }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for (j=1;j<=n;j++) {           * -stepm/2 to stepm/2 .
     for (i=1;i<j;i++) {           * For stepm=1 the results are the same as for previous versions of Imach.
       sum=a[i][j];           * For stepm > 1 the results are less biased than in previous versions. 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];           */
       a[i][j]=sum;          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
     big=0.0;          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=j;i<=n;i++) {          /* bias is positive if real duration
       sum=a[i][j];           * is higher than the multiple of stepm and negative otherwise.
       for (k=1;k<j;k++)           */
         sum -= a[i][k]*a[k][j];          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       a[i][j]=sum;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       if ( (dum=vv[i]*fabs(sum)) >= big) {          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
         big=dum;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         imax=i;          /*if(lli ==000.0)*/
       }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     }          ipmx +=1;
     if (j != imax) {          sw += weight[i];
       for (k=1;k<=n;k++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         dum=a[imax][k];        } /* end of wave */
         a[imax][k]=a[j][k];      } /* end of individual */
         a[j][k]=dum;    }  else if(mle==3){  /* exponential inter-extrapolation */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       *d = -(*d);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       vv[imax]=vv[j];        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
     indx[j]=imax;            for (j=1;j<=nlstate+ndeath;j++){
     if (a[j][j] == 0.0) a[j][j]=TINY;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (j != n) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       dum=1.0/(a[j][j]);            }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_vector(vv,1,n);  /* Doesn't work */            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,
 void lubksb(double **a, int n, int *indx, double b[])                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {            savm=oldm;
   int i,ii=0,ip,j;            oldm=newm;
   double sum;          } /* end mult */
          
   for (i=1;i<=n;i++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     ip=indx[i];          /* But now since version 0.9 we anticipate for bias and large stepm.
     sum=b[ip];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     b[ip]=b[i];           * (in months) between two waves is not a multiple of stepm, we rounded to 
     if (ii)           * the nearest (and in case of equal distance, to the lowest) interval but now
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     else if (sum) ii=i;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     b[i]=sum;           * probability in order to take into account the bias as a fraction of the way
   }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for (i=n;i>=1;i--) {           * -stepm/2 to stepm/2 .
     sum=b[i];           * For stepm=1 the results are the same as for previous versions of Imach.
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];           * For stepm > 1 the results are less biased than in previous versions. 
     b[i]=sum/a[i][i];           */
   }          s1=s[mw[mi][i]][i];
 }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
 /************ Frequencies ********************/          /* bias is positive if real duration
 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)           * is higher than the multiple of stepm and negative otherwise.
 {  /* Some frequencies */           */
            /* 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 */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   double ***freq; /* Frequencies */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double *pp;          /*if(lli ==000.0)*/
   double pos, k2, dateintsum=0,k2cpt=0;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   FILE *ficresp;          ipmx +=1;
   char fileresp[FILENAMELENGTH];          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   pp=vector(1,nlstate);        } /* end of wave */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      } /* end of individual */
   strcpy(fileresp,"p");    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   strcat(fileresp,fileres);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if((ficresp=fopen(fileresp,"w"))==NULL) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for(mi=1; mi<= wav[i]-1; mi++){
     exit(0);          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++;            }
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          
         scanf("%d", i);*/            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 */
              
       dateintsum=0;          s1=s[mw[mi][i]][i];
       k2cpt=0;          s2=s[mw[mi+1][i]][i];
       for (i=1; i<=imx; i++) {          if( s2 > nlstate){ 
         bool=1;            lli=log(out[s1][s2] - savm[s1][s2]);
         if  (cptcovn>0) {          }else{
           for (z1=1; z1<=cptcoveff; z1++)            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          }
               bool=0;          ipmx +=1;
         }          sw += weight[i];
         if (bool==1) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(m=firstpass; m<=lastpass; 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]); */
             k2=anint[m][i]+(mint[m][i]/12.);        } /* end of wave */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      } /* end of individual */
               if(agev[m][i]==0) agev[m][i]=agemax+1;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
               if(agev[m][i]==1) agev[m][i]=agemax+2;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               if (m<lastpass) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for(mi=1; mi<= wav[i]-1; mi++){
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
               }            for (j=1;j<=nlstate+ndeath;j++){
                            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                 dateintsum=dateintsum+k2;            }
                 k2cpt++;          for(d=0; d<dh[mi][i]; d++){
               }            newm=savm;
             }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
                  
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if  (cptcovn>0) {            savm=oldm;
         fprintf(ficresp, "\n#********** Variable ");            oldm=newm;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          } /* end mult */
         fprintf(ficresp, "**********\n#");        
       }          s1=s[mw[mi][i]][i];
       for(i=1; i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       fprintf(ficresp, "\n");          ipmx +=1;
                sw += weight[i];
       for(i=(int)agemin; i <= (int)agemax+3; i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if(i==(int)agemax+3)          /*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("Total");        } /* end of wave */
         else      } /* end of individual */
           printf("Age %d", i);    } /* End of if */
         for(jk=1; jk <=nlstate ; jk++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
             pp[jk] += freq[jk][m][i];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         }    return -l;
         for(jk=1; jk <=nlstate ; jk++){  }
           for(m=-1, pos=0; m <=0 ; m++)  
             pos += freq[jk][m][i];  /*************** log-likelihood *************/
           if(pp[jk]>=1.e-10)  double funcone( double *x)
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  {
           else    /* Same as likeli but slower because of a lot of printf and if */
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    int i, ii, j, k, mi, d, kk;
         }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
         for(jk=1; jk <=nlstate ; jk++){    double lli; /* Individual log likelihood */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double llt;
             pp[jk] += freq[jk][m][i];    int s1, s2;
         }    double bbh, survp;
     /*extern weight */
         for(jk=1,pos=0; jk <=nlstate ; jk++)    /* We are differentiating ll according to initial status */
           pos += pp[jk];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         for(jk=1; jk <=nlstate ; jk++){    /*for(i=1;i<imx;i++) 
           if(pos>=1.e-5)      printf(" %d\n",s[4][i]);
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    */
           else    cov[1]=1.;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  
           if( i <= (int) agemax){    for(k=1; k<=nlstate; k++) ll[k]=0.;
             if(pos>=1.e-5){  
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               probs[i][jk][j1]= pp[jk]/pos;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               /*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(mi=1; mi<= wav[i]-1; mi++){
             }        for (ii=1;ii<=nlstate+ndeath;ii++)
             else          for (j=1;j<=nlstate+ndeath;j++){
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }          }
                for(d=0; d<dh[mi][i]; d++){
         for(jk=-1; jk <=nlstate+ndeath; jk++)          newm=savm;
           for(m=-1; m <=nlstate+ndeath; m++)          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          for (kk=1; kk<=cptcovage;kk++) {
         if(i <= (int) agemax)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           fprintf(ficresp,"\n");          }
         printf("\n");          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }          savm=oldm;
   }          oldm=newm;
   dateintmean=dateintsum/k2cpt;        } /* end mult */
          
   fclose(ficresp);        s1=s[mw[mi][i]][i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        s2=s[mw[mi+1][i]][i];
   free_vector(pp,1,nlstate);        bbh=(double)bh[mi][i]/(double)stepm; 
          /* bias is positive if real duration
   /* End of Freq */         * is higher than the multiple of stepm and negative otherwise.
 }         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
 /************ Prevalence ********************/          lli=log(out[s1][s2] - savm[s1][s2]);
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        } else if (mle==1){
 {  /* Some frequencies */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          } else if(mle==2){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   double ***freq; /* Frequencies */        } else if(mle==3){  /* exponential inter-extrapolation */
   double *pp;          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 */
   double pos, k2;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
   pp=vector(1,nlstate);        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          lli=log(out[s1][s2]); /* Original formula */
          } /* End of if */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        ipmx +=1;
   j1=0;        sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   j=cptcoveff;  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        if(globpr){
            fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
  for(k1=1; k1<=j;k1++){   %10.6f %10.6f %10.6f ", \
     for(i1=1; i1<=ncodemax[k1];i1++){                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       j1++;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
            for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       for (i=-1; i<=nlstate+ndeath; i++)              llt +=ll[k]*gipmx/gsw;
         for (jk=-1; jk<=nlstate+ndeath; jk++)              fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           for(m=agemin; m <= agemax+3; m++)          }
             freq[i][jk][m]=0;          fprintf(ficresilk," %10.6f\n", -llt);
              }
       for (i=1; i<=imx; i++) {      } /* end of wave */
         bool=1;    } /* end of individual */
         if  (cptcovn>0) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           for (z1=1; z1<=cptcoveff; z1++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
               bool=0;    if(globpr==0){ /* First time we count the contributions and weights */
         }      gipmx=ipmx;
         if (bool==1) {      gsw=sw;
           for(m=firstpass; m<=lastpass; m++){    }
             k2=anint[m][i]+(mint[m][i]/12.);    return -l;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  }
               if(agev[m][i]==0) agev[m][i]=agemax+1;  
               if(agev[m][i]==1) agev[m][i]=agemax+2;  char *subdirf(char fileres[])
               if (m<lastpass)  {
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    
               else    strcpy(tmpout,optionfilefiname);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    strcat(tmpout,"/"); /* Add to the right */
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    strcat(tmpout,fileres);
             }    return tmpout;
           }  }
         }  
       }  char *subdirf2(char fileres[], char *preop)
         for(i=(int)agemin; i <= (int)agemax+3; i++){  {
           for(jk=1; jk <=nlstate ; jk++){    
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    strcpy(tmpout,optionfilefiname);
               pp[jk] += freq[jk][m][i];    strcat(tmpout,"/");
           }    strcat(tmpout,preop);
           for(jk=1; jk <=nlstate ; jk++){    strcat(tmpout,fileres);
             for(m=-1, pos=0; m <=0 ; m++)    return tmpout;
             pos += freq[jk][m][i];  }
         }  char *subdirf3(char fileres[], char *preop, char *preop2)
          {
          for(jk=1; jk <=nlstate ; jk++){    
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    strcpy(tmpout,optionfilefiname);
              pp[jk] += freq[jk][m][i];    strcat(tmpout,"/");
          }    strcat(tmpout,preop);
              strcat(tmpout,preop2);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    strcat(tmpout,fileres);
     return tmpout;
          for(jk=1; jk <=nlstate ; jk++){            }
            if( i <= (int) agemax){  
              if(pos>=1.e-5){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
                probs[i][jk][j1]= pp[jk]/pos;  {
              }    /* This routine should help understanding what is done with 
            }       the selection of individuals/waves and
          }       to check the exact contribution to the likelihood.
                 Plotting could be done.
         }     */
     }    int k;
   }  
     if(*globpri !=0){ /* Just counts and sums, no printings */
        strcpy(fileresilk,"ilk"); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      strcat(fileresilk,fileres);
   free_vector(pp,1,nlstate);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresilk);
 }  /* End of Freq */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
 /************* Waves Concatenation ***************/      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 2wlli out sav ");
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
 {      for(k=1; k<=nlstate; k++) 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
      Death is a valid wave (if date is known).      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    }
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  
      and mw[mi+1][i]. dh depends on stepm.    *fretone=(*funcone)(p);
      */    if(*globpri !=0){
       fclose(ficresilk);
   int i, mi, m;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      fflush(fichtm); 
      double sum=0., jmean=0.;*/    } 
     return;
   int j, k=0,jk, ju, jl;  }
   double sum=0.;  
   jmin=1e+5;  
   jmax=-1;  /*********** Maximum Likelihood Estimation ***************/
   jmean=0.;  
   for(i=1; i<=imx; i++){  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     mi=0;  {
     m=firstpass;    int i,j, iter;
     while(s[m][i] <= nlstate){    double **xi;
       if(s[m][i]>=1)    double fret;
         mw[++mi][i]=m;    double fretone; /* Only one call to likelihood */
       if(m >=lastpass)    char filerespow[FILENAMELENGTH];
         break;    xi=matrix(1,npar,1,npar);
       else    for (i=1;i<=npar;i++)
         m++;      for (j=1;j<=npar;j++)
     }/* end while */        xi[i][j]=(i==j ? 1.0 : 0.0);
     if (s[m][i] > nlstate){    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       mi++;     /* Death is another wave */    strcpy(filerespow,"pow"); 
       /* if(mi==0)  never been interviewed correctly before death */    strcat(filerespow,fileres);
          /* Only death is a correct wave */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       mw[mi][i]=m;      printf("Problem with resultfile: %s\n", filerespow);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     wav[i]=mi;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     if(mi==0)    for (i=1;i<=nlstate;i++)
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      for(j=1;j<=nlstate+ndeath;j++)
   }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){    powell(p,xi,npar,ftol,&iter,&fret,func);
       if (stepm <=0)  
         dh[mi][i]=1;    fclose(ficrespow);
       else{    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         if (s[mw[mi+1][i]][i] > nlstate) {    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           if (agedc[i] < 2*AGESUP) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */  }
           k=k+1;  
           if (j >= jmax) jmax=j;  /**** Computes Hessian and covariance matrix ***/
           if (j <= jmin) jmin=j;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           sum=sum+j;  {
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    double  **a,**y,*x,pd;
           }    double **hess;
         }    int i, j,jk;
         else{    int *indx;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;    double hessii(double p[], double delta, int theta, double delti[]);
           if (j >= jmax) jmax=j;    double hessij(double p[], double delti[], int i, int j);
           else if (j <= jmin)jmin=j;    void lubksb(double **a, int npar, int *indx, double b[]) ;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    void ludcmp(double **a, int npar, int *indx, double *d) ;
           sum=sum+j;  
         }    hess=matrix(1,npar,1,npar);
         jk= j/stepm;  
         jl= j -jk*stepm;    printf("\nCalculation of the hessian matrix. Wait...\n");
         ju= j -(jk+1)*stepm;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         if(jl <= -ju)    for (i=1;i<=npar;i++){
           dh[mi][i]=jk;      printf("%d",i);fflush(stdout);
         else      fprintf(ficlog,"%d",i);fflush(ficlog);
           dh[mi][i]=jk+1;      hess[i][i]=hessii(p,ftolhess,i,delti);
         if(dh[mi][i]==0)      /*printf(" %f ",p[i]);*/
           dh[mi][i]=1; /* At least one step */      /*printf(" %lf ",hess[i][i]);*/
       }    }
     }    
   }    for (i=1;i<=npar;i++) {
   jmean=sum/k;      for (j=1;j<=npar;j++)  {
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        if (j>i) { 
  }          printf(".%d%d",i,j);fflush(stdout);
 /*********** Tricode ****************************/          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 void tricode(int *Tvar, int **nbcode, int imx)          hess[i][j]=hessij(p,delti,i,j);
 {          hess[j][i]=hess[i][j];    
   int Ndum[20],ij=1, k, j, i;          /*printf(" %lf ",hess[i][j]);*/
   int cptcode=0;        }
   cptcoveff=0;      }
      }
   for (k=0; k<19; k++) Ndum[k]=0;    printf("\n");
   for (k=1; k<=7; k++) ncodemax[k]=0;    fprintf(ficlog,"\n");
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for (i=1; i<=imx; i++) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       ij=(int)(covar[Tvar[j]][i]);    
       Ndum[ij]++;    a=matrix(1,npar,1,npar);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    y=matrix(1,npar,1,npar);
       if (ij > cptcode) cptcode=ij;    x=vector(1,npar);
     }    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
     for (i=0; i<=cptcode; i++) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       if(Ndum[i]!=0) ncodemax[j]++;    ludcmp(a,npar,indx,&pd);
     }  
     ij=1;    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
     for (i=1; i<=ncodemax[j]; i++) {      lubksb(a,npar,indx,x);
       for (k=0; k<=19; k++) {      for (i=1;i<=npar;i++){ 
         if (Ndum[k] != 0) {        matcov[i][j]=x[i];
           nbcode[Tvar[j]][ij]=k;      }
              }
           ij++;  
         }    printf("\n#Hessian matrix#\n");
         if (ij > ncodemax[j]) break;    fprintf(ficlog,"\n#Hessian matrix#\n");
       }      for (i=1;i<=npar;i++) { 
     }      for (j=1;j<=npar;j++) { 
   }          printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
  for (k=0; k<19; k++) Ndum[k]=0;      }
       printf("\n");
  for (i=1; i<=ncovmodel-2; i++) {      fprintf(ficlog,"\n");
       ij=Tvar[i];    }
       Ndum[ij]++;  
     }    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
  ij=1;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
  for (i=1; i<=10; i++) {    ludcmp(a,npar,indx,&pd);
    if((Ndum[i]!=0) && (i<=ncovcol)){  
      Tvaraff[ij]=i;    /*  printf("\n#Hessian matrix recomputed#\n");
      ij++;  
    }    for (j=1;j<=npar;j++) {
  }      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
     cptcoveff=ij-1;      lubksb(a,npar,indx,x);
 }      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
 /*********** Health Expectancies ****************/        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )      }
       printf("\n");
 {      fprintf(ficlog,"\n");
   /* Health expectancies */    }
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    */
   double age, agelim, hf;  
   double ***p3mat,***varhe;    free_matrix(a,1,npar,1,npar);
   double **dnewm,**doldm;    free_matrix(y,1,npar,1,npar);
   double *xp;    free_vector(x,1,npar);
   double **gp, **gm;    free_ivector(indx,1,npar);
   double ***gradg, ***trgradg;    free_matrix(hess,1,npar,1,npar);
   int theta;  
   
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);  }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate*2,1,npar);  /*************** hessian matrix ****************/
   doldm=matrix(1,nlstate*2,1,nlstate*2);  double hessii( double x[], double delta, int theta, double delti[])
    {
   fprintf(ficreseij,"# Health expectancies\n");    int i;
   fprintf(ficreseij,"# Age");    int l=1, lmax=20;
   for(i=1; i<=nlstate;i++)    double k1,k2;
     for(j=1; j<=nlstate;j++)    double p2[NPARMAX+1];
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    double res;
   fprintf(ficreseij,"\n");    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
   if(estepm < stepm){    int k=0,kmax=10;
     printf ("Problem %d lower than %d\n",estepm, stepm);    double l1;
   }  
   else  hstepm=estepm;      fx=func(x);
   /* We compute the life expectancy from trapezoids spaced every estepm months    for (i=1;i<=npar;i++) p2[i]=x[i];
    * This is mainly to measure the difference between two models: for example    for(l=0 ; l <=lmax; l++){
    * if stepm=24 months pijx are given only every 2 years and by summing them      l1=pow(10,l);
    * we are calculating an estimate of the Life Expectancy assuming a linear      delts=delt;
    * progression inbetween and thus overestimating or underestimating according      for(k=1 ; k <kmax; k=k+1){
    * to the curvature of the survival function. If, for the same date, we        delt = delta*(l1*k);
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        p2[theta]=x[theta] +delt;
    * to compare the new estimate of Life expectancy with the same linear        k1=func(p2)-fx;
    * hypothesis. A more precise result, taking into account a more precise        p2[theta]=x[theta]-delt;
    * curvature will be obtained if estepm is as small as stepm. */        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
   /* For example we decided to compute the life expectancy with the smallest unit */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   /* 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  #ifdef DEBUG
      nstepm is the number of stepm from age to agelin.        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);
      Look at hpijx to understand the reason of that which relies in memory size        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);
      and note for a fixed period like estepm months */  #endif
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
      survival function given by stepm (the optimization length). Unfortunately it        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
      means that if the survival funtion is printed only each two years of age and if          k=kmax;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        }
      results. So we changed our mind and took the option of the best precision.        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   */          k=kmax; l=lmax*10.;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   agelim=AGESUP;          delts=delt;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        }
     /* nhstepm age range expressed in number of stepm */      }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    delti[theta]=delts;
     /* if (stepm >= YEARM) hstepm=1;*/    return res; 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);  
     gp=matrix(0,nhstepm,1,nlstate*2);  double hessij( double x[], double delti[], int thetai,int thetaj)
     gm=matrix(0,nhstepm,1,nlstate*2);  {
     int i;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    int l=1, l1, lmax=20;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    double k1,k2,k3,k4,res,fx;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      double p2[NPARMAX+1];
      int k;
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    fx=func(x);
     for (k=1; k<=2; k++) {
     /* Computing Variances of health expectancies */      for (i=1;i<=npar;i++) p2[i]=x[i];
       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++){      k1=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;
        k2=func(p2)-fx;
       cptj=0;    
       for(j=1; j<= nlstate; j++){      p2[thetai]=x[thetai]-delti[thetai]/k;
         for(i=1; i<=nlstate; i++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           cptj=cptj+1;      k3=func(p2)-fx;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      p2[thetai]=x[thetai]-delti[thetai]/k;
           }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         }      k4=func(p2)-fx;
       }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
        #ifdef DEBUG
            printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       for(i=1; i<=npar; i++)      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);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  #endif
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }
          return res;
       cptj=0;  }
       for(j=1; j<= nlstate; j++){  
         for(i=1;i<=nlstate;i++){  /************** Inverse of matrix **************/
           cptj=cptj+1;  void ludcmp(double **a, int n, int *indx, double *d) 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  { 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    int i,imax,j,k; 
           }    double big,dum,sum,temp; 
         }    double *vv; 
       }   
          vv=vector(1,n); 
        *d=1.0; 
     for (i=1;i<=n;i++) { 
       for(j=1; j<= nlstate*2; j++)      big=0.0; 
         for(h=0; h<=nhstepm-1; h++){      for (j=1;j<=n;j++) 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        if ((temp=fabs(a[i][j])) > big) big=temp; 
         }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
      }    } 
        for (j=1;j<=n;j++) { 
 /* End theta */      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
      for(h=0; h<=nhstepm-1; h++)      } 
       for(j=1; j<=nlstate*2;j++)      big=0.0; 
         for(theta=1; theta <=npar; theta++)      for (i=j;i<=n;i++) { 
         trgradg[h][j][theta]=gradg[h][theta][j];        sum=a[i][j]; 
         for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
      for(i=1;i<=nlstate*2;i++)        a[i][j]=sum; 
       for(j=1;j<=nlstate*2;j++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         varhe[i][j][(int)age] =0.;          big=dum; 
           imax=i; 
     for(h=0;h<=nhstepm-1;h++){        } 
       for(k=0;k<=nhstepm-1;k++){      } 
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);      if (j != imax) { 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);        for (k=1;k<=n;k++) { 
         for(i=1;i<=nlstate*2;i++)          dum=a[imax][k]; 
           for(j=1;j<=nlstate*2;j++)          a[imax][k]=a[j][k]; 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          a[j][k]=dum; 
       }        } 
     }        *d = -(*d); 
         vv[imax]=vv[j]; 
            } 
     /* Computing expectancies */      indx[j]=imax; 
     for(i=1; i<=nlstate;i++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
       for(j=1; j<=nlstate;j++)      if (j != n) { 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        dum=1.0/(a[j][j]); 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
                } 
 /* 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]);*/    } 
     free_vector(vv,1,n);  /* Doesn't work */
         }  ;
   } 
     fprintf(ficreseij,"%3.0f",age );  
     cptj=0;  void lubksb(double **a, int n, int *indx, double b[]) 
     for(i=1; i<=nlstate;i++)  { 
       for(j=1; j<=nlstate;j++){    int i,ii=0,ip,j; 
         cptj++;    double sum; 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );   
       }    for (i=1;i<=n;i++) { 
     fprintf(ficreseij,"\n");      ip=indx[i]; 
          sum=b[ip]; 
     free_matrix(gm,0,nhstepm,1,nlstate*2);      b[ip]=b[i]; 
     free_matrix(gp,0,nhstepm,1,nlstate*2);      if (ii) 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      else if (sum) ii=i; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      b[i]=sum; 
   }    } 
   free_vector(xp,1,npar);    for (i=n;i>=1;i--) { 
   free_matrix(dnewm,1,nlstate*2,1,npar);      sum=b[i]; 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);      b[i]=sum/a[i][i]; 
 }    } 
   } 
 /************ Variance ******************/  
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)  /************ Frequencies ********************/
 {  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)
   /* Variance of health expectancies */  {  /* Some frequencies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    
   double **newm;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   double **dnewm,**doldm;    int first;
   int i, j, nhstepm, hstepm, h, nstepm ;    double ***freq; /* Frequencies */
   int k, cptcode;    double *pp, **prop;
   double *xp;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   double **gp, **gm;    FILE *ficresp;
   double ***gradg, ***trgradg;    char fileresp[FILENAMELENGTH];
   double ***p3mat;    
   double age,agelim, hf;    pp=vector(1,nlstate);
   int theta;    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
    fprintf(ficresvij,"# Covariances of life expectancies\n");    strcat(fileresp,fileres);
   fprintf(ficresvij,"# Age");    if((ficresp=fopen(fileresp,"w"))==NULL) {
   for(i=1; i<=nlstate;i++)      printf("Problem with prevalence resultfile: %s\n", fileresp);
     for(j=1; j<=nlstate;j++)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      exit(0);
   fprintf(ficresvij,"\n");    }
     freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   xp=vector(1,npar);    j1=0;
   dnewm=matrix(1,nlstate,1,npar);    
   doldm=matrix(1,nlstate,1,nlstate);    j=cptcoveff;
      if (cptcovn<1) {j=1;ncodemax[1]=1;}
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);    first=1;
   }  
   else  hstepm=estepm;      for(k1=1; k1<=j;k1++){
   /* For example we decided to compute the life expectancy with the smallest unit */      for(i1=1; i1<=ncodemax[k1];i1++){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        j1++;
      nhstepm is the number of hstepm from age to agelim        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
      nstepm is the number of stepm from age to agelin.          scanf("%d", i);*/
      Look at hpijx to understand the reason of that which relies in memory size        for (i=-1; i<=nlstate+ndeath; i++)  
      and note for a fixed period like k years */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            for(m=iagemin; m <= iagemax+3; m++)
      survival function given by stepm (the optimization length). Unfortunately it              freq[i][jk][m]=0;
      means that if the survival funtion is printed only each two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      for (i=1; i<=nlstate; i++)  
      results. So we changed our mind and took the option of the best precision.        for(m=iagemin; m <= iagemax+3; m++)
   */          prop[i][m]=0;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        
   agelim = AGESUP;        dateintsum=0;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        k2cpt=0;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for (i=1; i<=imx; i++) {
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          bool=1;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if  (cptcovn>0) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            for (z1=1; z1<=cptcoveff; z1++) 
     gp=matrix(0,nhstepm,1,nlstate);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     gm=matrix(0,nhstepm,1,nlstate);                bool=0;
           }
     for(theta=1; theta <=npar; theta++){          if (bool==1){
       for(i=1; i<=npar; i++){ /* Computes gradient */            for(m=firstpass; m<=lastpass; m++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              k2=anint[m][i]+(mint[m][i]/12.);
       }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  if(agev[m][i]==0) agev[m][i]=iagemax+1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       if (popbased==1) {                if (m<lastpass) {
         for(i=1; i<=nlstate;i++)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           prlim[i][i]=probs[(int)age][i][ij];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       }                }
                  
       for(j=1; j<= nlstate; j++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
         for(h=0; h<=nhstepm; h++){                  dateintsum=dateintsum+k2;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)                  k2cpt++;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];                }
         }                /*}*/
       }            }
              }
       for(i=1; i<=npar; i++) /* Computes gradient */        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);         
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
          if  (cptcovn>0) {
       if (popbased==1) {          fprintf(ficresp, "\n#********** Variable "); 
         for(i=1; i<=nlstate;i++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           prlim[i][i]=probs[(int)age][i][ij];          fprintf(ficresp, "**********\n#");
       }        }
         for(i=1; i<=nlstate;i++) 
       for(j=1; j<= nlstate; j++){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         for(h=0; h<=nhstepm; h++){        fprintf(ficresp, "\n");
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        for(i=iagemin; i <= iagemax+3; i++){
         }          if(i==iagemax+3){
       }            fprintf(ficlog,"Total");
           }else{
       for(j=1; j<= nlstate; j++)            if(first==1){
         for(h=0; h<=nhstepm; h++){              first=0;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              printf("See log file for details...\n");
         }            }
     } /* End theta */            fprintf(ficlog,"Age %d", i);
           }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for(h=0; h<=nhstepm; h++)              pp[jk] += freq[jk][m][i]; 
       for(j=1; j<=nlstate;j++)          }
         for(theta=1; theta <=npar; theta++)          for(jk=1; jk <=nlstate ; jk++){
           trgradg[h][j][theta]=gradg[h][theta][j];            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            if(pp[jk]>=1.e-10){
     for(i=1;i<=nlstate;i++)              if(first==1){
       for(j=1;j<=nlstate;j++)              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         vareij[i][j][(int)age] =0.;              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     for(h=0;h<=nhstepm;h++){            }else{
       for(k=0;k<=nhstepm;k++){              if(first==1)
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         for(i=1;i<=nlstate;i++)            }
           for(j=1;j<=nlstate;j++)          }
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }          for(jk=1; jk <=nlstate ; jk++){
     }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
     fprintf(ficresvij,"%.0f ",age );          }       
     for(i=1; i<=nlstate;i++)          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       for(j=1; j<=nlstate;j++){            pos += pp[jk];
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            posprop += prop[jk][i];
       }          }
     fprintf(ficresvij,"\n");          for(jk=1; jk <=nlstate ; jk++){
     free_matrix(gp,0,nhstepm,1,nlstate);            if(pos>=1.e-5){
     free_matrix(gm,0,nhstepm,1,nlstate);              if(first==1)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }else{
   } /* End age */              if(first==1)
                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   free_vector(xp,1,npar);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   free_matrix(doldm,1,nlstate,1,npar);            }
   free_matrix(dnewm,1,nlstate,1,nlstate);            if( i <= iagemax){
               if(pos>=1.e-5){
 }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
 /************ Variance of prevlim ******************/                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 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
   /* Variance of prevalence limit */                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            }
   double **newm;          }
   double **dnewm,**doldm;          
   int i, j, nhstepm, hstepm;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   int k, cptcode;            for(m=-1; m <=nlstate+ndeath; m++)
   double *xp;              if(freq[jk][m][i] !=0 ) {
   double *gp, *gm;              if(first==1)
   double **gradg, **trgradg;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double age,agelim;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   int theta;              }
              if(i <= iagemax)
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            fprintf(ficresp,"\n");
   fprintf(ficresvpl,"# Age");          if(first==1)
   for(i=1; i<=nlstate;i++)            printf("Others in log...\n");
       fprintf(ficresvpl," %1d-%1d",i,i);          fprintf(ficlog,"\n");
   fprintf(ficresvpl,"\n");        }
       }
   xp=vector(1,npar);    }
   dnewm=matrix(1,nlstate,1,npar);    dateintmean=dateintsum/k2cpt; 
   doldm=matrix(1,nlstate,1,nlstate);   
      fclose(ficresp);
   hstepm=1*YEARM; /* Every year of age */    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    free_vector(pp,1,nlstate);
   agelim = AGESUP;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* End of Freq */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  }
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  /************ Prevalence ********************/
     gradg=matrix(1,npar,1,nlstate);  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)
     gp=vector(1,nlstate);  {  
     gm=vector(1,nlstate);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
     for(theta=1; theta <=npar; theta++){       We still use firstpass and lastpass as another selection.
       for(i=1; i<=npar; i++){ /* Computes gradient */    */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);   
       }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double ***freq; /* Frequencies */
       for(i=1;i<=nlstate;i++)    double *pp, **prop;
         gp[i] = prlim[i][i];    double pos,posprop; 
        double  y2; /* in fractional years */
       for(i=1; i<=npar; i++) /* Computes gradient */    int iagemin, iagemax;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    iagemin= (int) agemin;
       for(i=1;i<=nlstate;i++)    iagemax= (int) agemax;
         gm[i] = prlim[i][i];    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
       for(i=1;i<=nlstate;i++)    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    j1=0;
     } /* End theta */    
     j=cptcoveff;
     trgradg =matrix(1,nlstate,1,npar);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
     for(j=1; j<=nlstate;j++)    for(k1=1; k1<=j;k1++){
       for(theta=1; theta <=npar; theta++)      for(i1=1; i1<=ncodemax[k1];i1++){
         trgradg[j][theta]=gradg[theta][j];        j1++;
         
     for(i=1;i<=nlstate;i++)        for (i=1; i<=nlstate; i++)  
       varpl[i][(int)age] =0.;          for(m=iagemin; m <= iagemax+3; m++)
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            prop[i][m]=0.0;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);       
     for(i=1;i<=nlstate;i++)        for (i=1; i<=imx; i++) { /* Each individual */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          bool=1;
           if  (cptcovn>0) {
     fprintf(ficresvpl,"%.0f ",age );            for (z1=1; z1<=cptcoveff; z1++) 
     for(i=1; i<=nlstate;i++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));                bool=0;
     fprintf(ficresvpl,"\n");          } 
     free_vector(gp,1,nlstate);          if (bool==1) { 
     free_vector(gm,1,nlstate);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     free_matrix(gradg,1,npar,1,nlstate);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     free_matrix(trgradg,1,nlstate,1,npar);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   } /* End age */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
   free_vector(xp,1,npar);                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); 
   free_matrix(doldm,1,nlstate,1,npar);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);                  /*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]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
 }                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
 /************ Variance of one-step probabilities  ******************/              }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)            } /* end selection of waves */
 {          }
   int i, j, i1, k1, j1, z1;        }
   int k=0, cptcode;        for(i=iagemin; i <= iagemax+3; i++){  
   double **dnewm,**doldm;          
   double *xp;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   double *gp, *gm;            posprop += prop[jk][i]; 
   double **gradg, **trgradg;          } 
   double age,agelim, cov[NCOVMAX];  
   int theta;          for(jk=1; jk <=nlstate ; jk++){     
   char fileresprob[FILENAMELENGTH];            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
   strcpy(fileresprob,"prob");                probs[i][jk][j1]= prop[jk][i]/posprop;
   strcat(fileresprob,fileres);              } 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            } 
     printf("Problem with resultfile: %s\n", fileresprob);          }/* end jk */ 
   }        }/* end i */ 
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      } /* end i1 */
      } /* end k1 */
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");    
   fprintf(ficresprob,"# Age");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   for(i=1; i<=nlstate;i++)    /*free_vector(pp,1,nlstate);*/
     for(j=1; j<=(nlstate+ndeath);j++)    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  }  /* End of prevalence */
   
   /************* Waves Concatenation ***************/
   fprintf(ficresprob,"\n");  
   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)
   {
   xp=vector(1,npar);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       Death is a valid wave (if date is known).
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));       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]
   cov[1]=1;       and mw[mi+1][i]. dh depends on stepm.
   j=cptcoveff;       */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   j1=0;    int i, mi, m;
   for(k1=1; k1<=1;k1++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for(i1=1; i1<=ncodemax[k1];i1++){       double sum=0., jmean=0.;*/
     j1++;    int first;
     int j, k=0,jk, ju, jl;
     if  (cptcovn>0) {    double sum=0.;
       fprintf(ficresprob, "\n#********** Variable ");    first=0;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    jmin=1e+5;
       fprintf(ficresprob, "**********\n#");    jmax=-1;
     }    jmean=0.;
        for(i=1; i<=imx; i++){
       for (age=bage; age<=fage; age ++){      mi=0;
         cov[2]=age;      m=firstpass;
         for (k=1; k<=cptcovn;k++) {      while(s[m][i] <= nlstate){
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];        if(s[m][i]>=1)
                    mw[++mi][i]=m;
         }        if(m >=lastpass)
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          break;
         for (k=1; k<=cptcovprod;k++)        else
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          m++;
              }/* end while */
         gradg=matrix(1,npar,1,9);      if (s[m][i] > nlstate){
         trgradg=matrix(1,9,1,npar);        mi++;     /* Death is another wave */
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        /* if(mi==0)  never been interviewed correctly before death */
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));           /* Only death is a correct wave */
            mw[mi][i]=m;
         for(theta=1; theta <=npar; theta++){      }
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      wav[i]=mi;
                if(mi==0){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        if(first==0){
                    printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           k=0;          first=1;
           for(i=1; i<= (nlstate+ndeath); i++){        }
             for(j=1; j<=(nlstate+ndeath);j++){        if(first==1){
               k=k+1;          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
               gp[k]=pmmij[i][j];        }
             }      } /* end mi==0 */
           }    } /* End individuals */
            
           for(i=1; i<=npar; i++)    for(i=1; i<=imx; i++){
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      for(mi=1; mi<wav[i];mi++){
            if (stepm <=0)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          dh[mi][i]=1;
           k=0;        else{
           for(i=1; i<=(nlstate+ndeath); i++){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             for(j=1; j<=(nlstate+ndeath);j++){            if (agedc[i] < 2*AGESUP) {
               k=k+1;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               gm[k]=pmmij[i][j];              if(j==0) j=1;  /* Survives at least one month after exam */
             }              else if(j<0){
           }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                      j=1; /* Careful Patch */
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)                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);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                  printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
               }
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)              k=k+1;
           for(theta=1; theta <=npar; theta++)              if (j >= jmax) jmax=j;
             trgradg[j][theta]=gradg[theta][j];              if (j <= jmin) jmin=j;
                      sum=sum+j;
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                    }
         pmij(pmmij,cov,ncovmodel,x,nlstate);          }
                  else{
         k=0;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         for(i=1; i<=(nlstate+ndeath); i++){            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           for(j=1; j<=(nlstate+ndeath);j++){            k=k+1;
             k=k+1;            if (j >= jmax) jmax=j;
             gm[k]=pmmij[i][j];            else if (j <= jmin)jmin=j;
           }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         }            /*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){
      /*printf("\n%d ",(int)age);              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 (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            }
      }*/            sum=sum+j;
           }
         fprintf(ficresprob,"\n%d ",(int)age);          jk= j/stepm;
           jl= j -jk*stepm;
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)          ju= j -(jk+1)*stepm;
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
              if(jl==0){
       }              dh[mi][i]=jk;
     }              bh[mi][i]=0;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            }else{ /* We want a negative bias in order to only have interpolation ie
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));                    * at the price of an extra matrix product in likelihood */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              dh[mi][i]=jk+1;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              bh[mi][i]=ju;
   }            }
   free_vector(xp,1,npar);          }else{
   fclose(ficresprob);            if(jl <= -ju){
                dh[mi][i]=jk;
 }              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
 /******************* Printing html file ***********/                                   */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \            }
  int lastpass, int stepm, int weightopt, char model[],\            else{
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \              dh[mi][i]=jk+1;
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\              bh[mi][i]=ju;
  char version[], int popforecast, int estepm ){            }
   int jj1, k1, i1, cpt;            if(dh[mi][i]==0){
   FILE *fichtm;              dh[mi][i]=1; /* At least one step */
   /*char optionfilehtm[FILENAMELENGTH];*/              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);*/
   strcpy(optionfilehtm,optionfile);            }
   strcat(optionfilehtm,".htm");          } /* end if mle */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        }
     printf("Problem with %s \n",optionfilehtm), exit(0);      } /* end wave */
   }    }
     jmean=sum/k;
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 \n   }
 Total number of observations=%d <br>\n  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  /*********** Tricode ****************************/
 <hr  size=\"2\" color=\"#EC5E5E\">  void tricode(int *Tvar, int **nbcode, int imx)
  <ul><li>Outputs files<br>\n  {
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    int Ndum[20],ij=1, k, j, i, maxncov=19;
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    int cptcode=0;
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    cptcoveff=0; 
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n   
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
  fprintf(fichtm,"\n  
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n                                 modality*/ 
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);        Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
  if(popforecast==1) fprintf(fichtm,"\n        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n                                         Tvar[j]. If V=sex and male is 0 and 
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n                                         female is 1, then  cptcode=1.*/
         <br>",fileres,fileres,fileres,fileres);      }
  else  
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);      for (i=0; i<=cptcode; i++) {
 fprintf(fichtm," <li>Graphs</li><p>");        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 */
       }
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
  jj1=0;        for (k=0; k<= maxncov; k++) {
  for(k1=1; k1<=m;k1++){          if (Ndum[k] != 0) {
    for(i1=1; i1<=ncodemax[k1];i1++){            nbcode[Tvar[j]][ij]=k; 
        jj1++;            /* 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; */
        if (cptcovn > 0) {            
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            ij++;
          for (cpt=1; cpt<=cptcoveff;cpt++)          }
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          if (ij > ncodemax[j]) break; 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        }  
        }      } 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    }  
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      
        for(cpt=1; cpt<nlstate;cpt++){   for (k=0; k< maxncov; k++) Ndum[k]=0;
          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 (i=1; i<=ncovmodel-2; i++) { 
        }     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     for(cpt=1; cpt<=nlstate;cpt++) {     ij=Tvar[i];
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident     Ndum[ij]++;
 interval) in state (%d): v%s%d%d.gif <br>   }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
      }   ij=1;
      for(cpt=1; cpt<=nlstate;cpt++) {   for (i=1; i<= maxncov; i++) {
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>     if((Ndum[i]!=0) && (i<=ncovcol)){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);       Tvaraff[ij]=i; /*For printing */
      }       ij++;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and     }
 health expectancies in states (1) and (2): e%s%d.gif<br>   }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);   
 fprintf(fichtm,"\n</body>");   cptcoveff=ij-1; /*Number of simple covariates*/
    }  }
    }  
 fclose(fichtm);  /*********** Health Expectancies ****************/
 }  
   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 )
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  {
     /* Health expectancies */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
   strcpy(optionfilegnuplot,optionfilefiname);    double ***p3mat,***varhe;
   strcat(optionfilegnuplot,".gp.txt");    double **dnewm,**doldm;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    double *xp;
     printf("Problem with file %s",optionfilegnuplot);    double **gp, **gm;
   }    double ***gradg, ***trgradg;
     int theta;
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 #endif    xp=vector(1,npar);
 m=pow(2,cptcoveff);    dnewm=matrix(1,nlstate*nlstate,1,npar);
      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  /* 1eme*/    
   for (cpt=1; cpt<= nlstate ; cpt ++) {    fprintf(ficreseij,"# Health expectancies\n");
    for (k1=1; k1<= m ; k1 ++) {    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
      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",ageminpar,fage,fileres,k1-1,k1-1);      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
 for (i=1; i<= nlstate ; i ++) {    fprintf(ficreseij,"\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    if(estepm < stepm){
 }      printf ("Problem %d lower than %d\n",estepm, stepm);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    }
     for (i=1; i<= nlstate ; i ++) {    else  hstepm=estepm;   
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* We compute the life expectancy from trapezoids spaced every estepm months
   else fprintf(ficgp," \%%*lf (\%%*lf)");     * 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
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);     * we are calculating an estimate of the Life Expectancy assuming a linear 
      for (i=1; i<= nlstate ; i ++) {     * progression in between and thus overestimating or underestimating according
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");     * to the curvature of the survival function. If, for the same date, we 
   else fprintf(ficgp," \%%*lf (\%%*lf)");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
 }       * to compare the new estimate of Life expectancy with the same linear 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }    /* For example we decided to compute the life expectancy with the smallest unit */
   }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   /*2 eme*/       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   for (k1=1; k1<= m ; k1 ++) {       Look at hpijx to understand the reason of that which relies in memory size
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);       and note for a fixed period like estepm months */
        /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     for (i=1; i<= nlstate+1 ; i ++) {       survival function given by stepm (the optimization length). Unfortunately it
       k=2*i;       means that if the survival funtion is printed only each two years of age and if
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for (j=1; j<= nlstate+1 ; j ++) {       results. So we changed our mind and took the option of the best precision.
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    agelim=AGESUP;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      /* nhstepm age range expressed in number of stepm */
       for (j=1; j<= nlstate+1 ; j ++) {      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         else fprintf(ficgp," \%%*lf (\%%*lf)");      /* if (stepm >= YEARM) hstepm=1;*/
 }        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fprintf(ficgp,"\" t\"\" w l 0,");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        /* Computed by stepm unit matrices, product of hstepm matrices, stored
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       else fprintf(ficgp,"\" t\"\" w l 0,");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     }   
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  
   }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    
   /*3eme*/      /* Computing Variances of health expectancies */
   
   for (k1=1; k1<= m ; k1 ++) {       for(theta=1; theta <=npar; theta++){
     for (cpt=1; cpt<= nlstate ; cpt ++) {        for(i=1; i<=npar; i++){ 
       k=2+nlstate*(2*cpt-2);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       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",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);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        cptj=0;
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        for(j=1; j<= nlstate; j++){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for(i=1; i<=nlstate; i++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            cptj=cptj+1;
             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 (i=1; i< nlstate ; i ++) {            }
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);          }
         }
       }       
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       
     }        for(i=1; i<=npar; i++) 
     }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /* CV preval stat */        
     for (k1=1; k1<= m ; k1 ++) {        cptj=0;
     for (cpt=1; cpt<nlstate ; cpt ++) {        for(j=1; j<= nlstate; j++){
       k=3;          for(i=1;i<=nlstate;i++){
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            }
                }
       l=3+(nlstate+ndeath)*cpt;        }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        for(j=1; j<= nlstate*nlstate; j++)
       for (i=1; i< nlstate ; i ++) {          for(h=0; h<=nhstepm-1; h++){
         l=3+(nlstate+ndeath)*cpt;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         fprintf(ficgp,"+$%d",l+i+1);          }
       }       } 
       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);  /* End theta */
     }  
   }         trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
    
   /* proba elementaires */       for(h=0; h<=nhstepm-1; h++)
    for(i=1,jk=1; i <=nlstate; i++){        for(j=1; j<=nlstate*nlstate;j++)
     for(k=1; k <=(nlstate+ndeath); k++){          for(theta=1; theta <=npar; theta++)
       if (k != i) {            trgradg[h][j][theta]=gradg[h][theta][j];
         for(j=1; j <=ncovmodel; j++){       
          
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);       for(i=1;i<=nlstate*nlstate;i++)
           jk++;        for(j=1;j<=nlstate*nlstate;j++)
           fprintf(ficgp,"\n");          varhe[i][j][(int)age] =0.;
         }  
       }       printf("%d|",(int)age);fflush(stdout);
     }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     }       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
     for(jk=1; jk <=m; jk++) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
    i=1;          for(i=1;i<=nlstate*nlstate;i++)
    for(k2=1; k2<=nlstate; k2++) {            for(j=1;j<=nlstate*nlstate;j++)
      k3=i;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
      for(k=1; k<=(nlstate+ndeath); k++) {        }
        if (k != k2){      }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      /* Computing expectancies */
 ij=1;      for(i=1; i<=nlstate;i++)
         for(j=3; j <=ncovmodel; j++) {        for(j=1; j<=nlstate;j++)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             ij++;            
           }  /* 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]);*/
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }
         }  
           fprintf(ficgp,")/(1");      fprintf(ficreseij,"%3.0f",age );
              cptj=0;
         for(k1=1; k1 <=nlstate; k1++){        for(i=1; i<=nlstate;i++)
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        for(j=1; j<=nlstate;j++){
 ij=1;          cptj++;
           for(j=3; j <=ncovmodel; j++){          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        }
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      fprintf(ficreseij,"\n");
             ij++;     
           }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           else      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
           fprintf(ficgp,")");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    printf("\n");
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    fprintf(ficlog,"\n");
         i=i+ncovmodel;  
        }    free_vector(xp,1,npar);
      }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    }  }
      
   fclose(ficgp);  /************ Variance ******************/
 }  /* end gnuplot */  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)
   {
     /* Variance of health expectancies */
 /*************** Moving average **************/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    /* double **newm;*/
     double **dnewm,**doldm;
   int i, cpt, cptcod;    double **dnewmp,**doldmp;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    int i, j, nhstepm, hstepm, h, nstepm ;
       for (i=1; i<=nlstate;i++)    int k, cptcode;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    double *xp;
           mobaverage[(int)agedeb][i][cptcod]=0.;    double **gp, **gm;  /* for var eij */
        double ***gradg, ***trgradg; /*for var eij */
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    double **gradgp, **trgradgp; /* for var p point j */
       for (i=1; i<=nlstate;i++){    double *gpp, *gmp; /* for var p point j */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           for (cpt=0;cpt<=4;cpt++){    double ***p3mat;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    double age,agelim, hf;
           }    double ***mobaverage;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    int theta;
         }    char digit[4];
       }    char digitp[25];
     }  
        char fileresprobmorprev[FILENAMELENGTH];
 }  
     if(popbased==1){
       if(mobilav!=0)
 /************** Forecasting ******************/        strcpy(digitp,"-populbased-mobilav-");
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){      else strcpy(digitp,"-populbased-nomobil-");
      }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    else 
   int *popage;      strcpy(digitp,"-stablbased-");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;    if (mobilav!=0) {
   double ***p3mat;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   char fileresf[FILENAMELENGTH];      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  agelim=AGESUP;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      }
     }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
      strcpy(fileresprobmorprev,"prmorprev"); 
      sprintf(digit,"%-d",ij);
   strcpy(fileresf,"f");    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   strcat(fileresf,fileres);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   if((ficresf=fopen(fileresf,"w"))==NULL) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     printf("Problem with forecast resultfile: %s\n", fileresf);    strcat(fileresprobmorprev,fileres);
   }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   printf("Computing forecasting: result on file '%s' \n", fileresf);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   if (mobilav==1) {    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    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);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      for(i=1; i<=nlstate;i++)
   if (stepm<=12) stepsize=1;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
   agelim=AGESUP;    fprintf(ficresprobmorprev,"\n");
      fprintf(ficgp,"\n# Routine varevsij");
   hstepm=1;    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");
   hstepm=hstepm/stepm;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   yp1=modf(dateintmean,&yp);  /*   } */
   anprojmean=yp;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;    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");
   yp1=modf((yp2*30.5),&yp);    fprintf(ficresvij,"# Age");
   jprojmean=yp;    for(i=1; i<=nlstate;i++)
   if(jprojmean==0) jprojmean=1;      for(j=1; j<=nlstate;j++)
   if(mprojmean==0) jprojmean=1;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
      fprintf(ficresvij,"\n");
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
      xp=vector(1,npar);
   for(cptcov=1;cptcov<=i2;cptcov++){    dnewm=matrix(1,nlstate,1,npar);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    doldm=matrix(1,nlstate,1,nlstate);
       k=k+1;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       fprintf(ficresf,"\n#******");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       }    gpp=vector(nlstate+1,nlstate+ndeath);
       fprintf(ficresf,"******\n");    gmp=vector(nlstate+1,nlstate+ndeath);
       fprintf(ficresf,"# StartingAge FinalAge");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    
          if(estepm < stepm){
            printf ("Problem %d lower than %d\n",estepm, stepm);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    }
         fprintf(ficresf,"\n");    else  hstepm=estepm;   
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       nhstepm is the number of hstepm from age to agelim 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       nstepm is the number of stepm from age to agelin. 
           nhstepm = nhstepm/hstepm;       Look at hpijx to understand the reason of that which relies in memory size
                 and note for a fixed period like k years */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           oldm=oldms;savm=savms;       survival function given by stepm (the optimization length). Unfortunately it
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         means that if the survival funtion is printed every two years of age and if
               you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           for (h=0; h<=nhstepm; h++){       results. So we changed our mind and took the option of the best precision.
             if (h==(int) (calagedate+YEARM*cpt)) {    */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             }    agelim = AGESUP;
             for(j=1; j<=nlstate+ndeath;j++) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
               kk1=0.;kk2=0;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
               for(i=1; i<=nlstate;i++) {                    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                 if (mobilav==1)      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                 else {      gp=matrix(0,nhstepm,1,nlstate);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      gm=matrix(0,nhstepm,1,nlstate);
                 }  
                  
               }      for(theta=1; theta <=npar; theta++){
               if (h==(int)(calagedate+12*cpt)){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                 fprintf(ficresf," %.3f", kk1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                                }
               }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if (popbased==1) {
         }          if(mobilav ==0){
       }            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
                    for(i=1; i<=nlstate;i++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   fclose(ficresf);        }
 }    
 /************** Forecasting ******************/        for(j=1; j<= nlstate; j++){
 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){          for(h=0; h<=nhstepm; h++){
              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   int *popage;          }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        }
   double *popeffectif,*popcount;        /* This for computing probability of death (h=1 means
   double ***p3mat,***tabpop,***tabpopprev;           computed over hstepm matrices product = hstepm*stepm months) 
   char filerespop[FILENAMELENGTH];           as a weighted average of prlim.
         */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   agelim=AGESUP;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        }    
          /* end probability of death */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   strcpy(filerespop,"pop");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   strcat(filerespop,fileres);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {   
     printf("Problem with forecast resultfile: %s\n", filerespop);        if (popbased==1) {
   }          if(mobilav ==0){
   printf("Computing forecasting: result on file '%s' \n", filerespop);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   if (mobilav==1) {              prlim[i][i]=mobaverage[(int)age][i][ij];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
     movingaverage(agedeb, fage, ageminpar, mobaverage);        }
   }  
         for(j=1; j<= nlstate; j++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(h=0; h<=nhstepm; h++){
   if (stepm<=12) stepsize=1;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   agelim=AGESUP;          }
          }
   hstepm=1;        /* This for computing probability of death (h=1 means
   hstepm=hstepm/stepm;           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
   if (popforecast==1) {        */
     if((ficpop=fopen(popfile,"r"))==NULL) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       printf("Problem with population file : %s\n",popfile);exit(0);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     popage=ivector(0,AGESUP);        }    
     popeffectif=vector(0,AGESUP);        /* end probability of death */
     popcount=vector(0,AGESUP);  
            for(j=1; j<= nlstate; j++) /* vareij */
     i=1;            for(h=0; h<=nhstepm; h++){
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
              }
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      } /* End theta */
       k=k+1;  
       fprintf(ficrespop,"\n#******");      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(h=0; h<=nhstepm; h++) /* veij */
       }        for(j=1; j<=nlstate;j++)
       fprintf(ficrespop,"******\n");          for(theta=1; theta <=npar; theta++)
       fprintf(ficrespop,"# Age");            trgradg[h][j][theta]=gradg[h][theta][j];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
              for(theta=1; theta <=npar; theta++)
       for (cpt=0; cpt<=0;cpt++) {          trgradgp[j][theta]=gradgp[theta][j];
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(i=1;i<=nlstate;i++)
           nhstepm = nhstepm/hstepm;        for(j=1;j<=nlstate;j++)
                    vareij[i][j][(int)age] =0.;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      for(h=0;h<=nhstepm;h++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(k=0;k<=nhstepm;k++){
                  matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           for (h=0; h<=nhstepm; h++){          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
             if (h==(int) (calagedate+YEARM*cpt)) {          for(i=1;i<=nlstate;i++)
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            for(j=1;j<=nlstate;j++)
             }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;      }
               for(i=1; i<=nlstate;i++) {                  
                 if (mobilav==1)      /* pptj */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
                 else {      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for(j=nlstate+1;j<=nlstate+ndeath;j++)
                 }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
               }          varppt[j][i]=doldmp[j][i];
               if (h==(int)(calagedate+12*cpt)){      /* end ppptj */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      /*  x centered again */
                   /*fprintf(ficrespop," %.3f", kk1);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
               }   
             }      if (popbased==1) {
             for(i=1; i<=nlstate;i++){        if(mobilav ==0){
               kk1=0.;          for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate;j++){            prlim[i][i]=probs[(int)age][i][ij];
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        }else{ /* mobilav */ 
                 }          for(i=1; i<=nlstate;i++)
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];            prlim[i][i]=mobaverage[(int)age][i][ij];
             }        }
       }
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)               
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      /* This for computing probability of death (h=1 means
           }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         as a weighted average of prlim.
         }      */
       }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   /******/          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      /* end probability of death */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           nhstepm = nhstepm/hstepm;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
                  for(i=1; i<=nlstate;i++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           oldm=oldms;savm=savms;        }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        } 
           for (h=0; h<=nhstepm; h++){      fprintf(ficresprobmorprev,"\n");
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      fprintf(ficresvij,"%.0f ",age );
             }      for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++) {        for(j=1; j<=nlstate;j++){
               kk1=0.;kk2=0;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
               for(i=1; i<=nlstate;i++) {                      }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          fprintf(ficresvij,"\n");
               }      free_matrix(gp,0,nhstepm,1,nlstate);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      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);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    } /* End age */
       }    free_vector(gpp,nlstate+1,nlstate+ndeath);
    }    free_vector(gmp,nlstate+1,nlstate+ndeath);
   }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
      free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   if (popforecast==1) {    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     free_ivector(popage,0,AGESUP);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     free_vector(popeffectif,0,AGESUP);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     free_vector(popcount,0,AGESUP);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   fclose(ficrespop);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
 }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),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);
 /***********************************************/  */
 /**************** Main Program *****************/  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
 /***********************************************/    fprintf(ficgp,"\nset out \"%s%s.png\";replot;",digitp,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
 int main(int argc, char *argv[])    free_vector(xp,1,npar);
 {    free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double agedeb, agefin,hf;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   double fret;    fclose(ficresprobmorprev);
   double **xi,tmp,delta;    fflush(ficgp);
     fflush(fichtm); 
   double dum; /* Dummy variable */  }  /* end varevsij */
   double ***p3mat;  
   int *indx;  /************ Variance of prevlim ******************/
   char line[MAXLINE], linepar[MAXLINE];  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)
   char title[MAXLINE];  {
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    /* Variance of prevalence limit */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
      double **newm;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   char filerest[FILENAMELENGTH];    int k, cptcode;
   char fileregp[FILENAMELENGTH];    double *xp;
   char popfile[FILENAMELENGTH];    double *gp, *gm;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    double **gradg, **trgradg;
   int firstobs=1, lastobs=10;    double age,agelim;
   int sdeb, sfin; /* Status at beginning and end */    int theta;
   int c,  h , cpt,l;     
   int ju,jl, mi;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    fprintf(ficresvpl,"# Age");
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    for(i=1; i<=nlstate;i++)
   int mobilav=0,popforecast=0;        fprintf(ficresvpl," %1d-%1d",i,i);
   int hstepm, nhstepm;    fprintf(ficresvpl,"\n");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  
     xp=vector(1,npar);
   double bage, fage, age, agelim, agebase;    dnewm=matrix(1,nlstate,1,npar);
   double ftolpl=FTOL;    doldm=matrix(1,nlstate,1,nlstate);
   double **prlim;    
   double *severity;    hstepm=1*YEARM; /* Every year of age */
   double ***param; /* Matrix of parameters */    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   double  *p;    agelim = AGESUP;
   double **matcov; /* Matrix of covariance */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double ***delti3; /* Scale */      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   double *delti; /* Scale */      if (stepm >= YEARM) hstepm=1;
   double ***eij, ***vareij;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   double **varpl; /* Variances of prevalence limits by age */      gradg=matrix(1,npar,1,nlstate);
   double *epj, vepp;      gp=vector(1,nlstate);
   double kk1, kk2;      gm=vector(1,nlstate);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
        for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
   char version[80]="Imach version 0.8a1, June 2003, INED-EUROREVES ";          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   char *alph[]={"a","a","b","c","d","e"}, str[4];        }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
   char z[1]="c", occ;          gp[i] = prlim[i][i];
 #include <sys/time.h>      
 #include <time.h>        for(i=1; i<=npar; i++) /* Computes gradient */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /* long total_usecs;        for(i=1;i<=nlstate;i++)
   struct timeval start_time, end_time;          gm[i] = prlim[i][i];
    
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        for(i=1;i<=nlstate;i++)
   getcwd(pathcd, size);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   printf("\n%s",version);  
   if(argc <=1){      trgradg =matrix(1,nlstate,1,npar);
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);      for(j=1; j<=nlstate;j++)
   }        for(theta=1; theta <=npar; theta++)
   else{          trgradg[j][theta]=gradg[theta][j];
     strcpy(pathtot,argv[1]);  
   }      for(i=1;i<=nlstate;i++)
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        varpl[i][(int)age] =0.;
   /*cygwin_split_path(pathtot,path,optionfile);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   /* cutv(path,optionfile,pathtot,'\\');*/      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      fprintf(ficresvpl,"%.0f ",age );
   chdir(path);      for(i=1; i<=nlstate;i++)
   replace(pathc,path);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
 /*-------- arguments in the command line --------*/      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
   strcpy(fileres,"r");      free_matrix(gradg,1,npar,1,nlstate);
   strcat(fileres, optionfilefiname);      free_matrix(trgradg,1,nlstate,1,npar);
   strcat(fileres,".txt");    /* Other files have txt extension */    } /* End age */
   
   /*---------arguments file --------*/    free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    free_matrix(dnewm,1,nlstate,1,nlstate);
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;  }
   }  
   /************ Variance of one-step probabilities  ******************/
   strcpy(filereso,"o");  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   strcat(filereso,fileres);  {
   if((ficparo=fopen(filereso,"w"))==NULL) {    int i, j=0,  i1, k1, l1, t, tj;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    int k2, l2, j1,  z1;
   }    int k=0,l, cptcode;
     int first=1, first1;
   /* Reads comments: lines beginning with '#' */    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   while((c=getc(ficpar))=='#' && c!= EOF){    double **dnewm,**doldm;
     ungetc(c,ficpar);    double *xp;
     fgets(line, MAXLINE, ficpar);    double *gp, *gm;
     puts(line);    double **gradg, **trgradg;
     fputs(line,ficparo);    double **mu;
   }    double age,agelim, cov[NCOVMAX];
   ungetc(c,ficpar);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    char fileresprob[FILENAMELENGTH];
   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);    char fileresprobcov[FILENAMELENGTH];
   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);    char fileresprobcor[FILENAMELENGTH];
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    double ***varpij;
     fgets(line, MAXLINE, ficpar);  
     puts(line);    strcpy(fileresprob,"prob"); 
     fputs(line,ficparo);    strcat(fileresprob,fileres);
   }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   ungetc(c,ficpar);      printf("Problem with resultfile: %s\n", fileresprob);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
        }
   covar=matrix(0,NCOVMAX,1,n);    strcpy(fileresprobcov,"probcov"); 
   cptcovn=0;    strcat(fileresprobcov,fileres);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
   ncovmodel=2+cptcovn;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    }
      strcpy(fileresprobcor,"probcor"); 
   /* Read guess parameters */    strcat(fileresprobcor,fileres);
   /* Reads comments: lines beginning with '#' */    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with resultfile: %s\n", fileresprobcor);
     ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fputs(line,ficparo);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   ungetc(c,ficpar);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     for(i=1; i <=nlstate; i++)    
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(ficresprob,"# Age");
       fprintf(ficparo,"%1d%1d",i1,j1);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       printf("%1d%1d",i,j);    fprintf(ficresprobcov,"# Age");
       for(k=1; k<=ncovmodel;k++){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
         fscanf(ficpar," %lf",&param[i][j][k]);    fprintf(ficresprobcov,"# Age");
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);  
       }    for(i=1; i<=nlstate;i++)
       fscanf(ficpar,"\n");      for(j=1; j<=(nlstate+ndeath);j++){
       printf("\n");        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       fprintf(ficparo,"\n");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;   /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
   p=param[1][1];    fprintf(ficresprobcor,"\n");
     */
   /* Reads comments: lines beginning with '#' */   xp=vector(1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     ungetc(c,ficpar);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     fgets(line, MAXLINE, ficpar);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     puts(line);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     fputs(line,ficparo);    first=1;
   }    fprintf(ficgp,"\n# Routine varprob");
   ungetc(c,ficpar);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   for(i=1; i <=nlstate; i++){    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");
     for(j=1; j <=nlstate+ndeath-1; j++){    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");
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    cov[1]=1;
       fprintf(ficparo,"%1d%1d",i1,j1);    tj=cptcoveff;
       for(k=1; k<=ncovmodel;k++){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         fscanf(ficpar,"%le",&delti3[i][j][k]);    j1=0;
         printf(" %le",delti3[i][j][k]);    for(t=1; t<=tj;t++){
         fprintf(ficparo," %le",delti3[i][j][k]);      for(i1=1; i1<=ncodemax[t];i1++){ 
       }        j1++;
       fscanf(ficpar,"\n");        if  (cptcovn>0) {
       printf("\n");          fprintf(ficresprob, "\n#********** Variable "); 
       fprintf(ficparo,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresprob, "**********\n#\n");
   }          fprintf(ficresprobcov, "\n#********** Variable "); 
   delti=delti3[1][1];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprobcov, "**********\n#\n");
   /* Reads comments: lines beginning with '#' */          
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp, "\n#********** Variable "); 
     ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp, "**********\n#\n");
     puts(line);          
     fputs(line,ficparo);          
   }          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   ungetc(c,ficpar);          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\">");
   matcov=matrix(1,npar,1,npar);          
   for(i=1; i <=npar; i++){          fprintf(ficresprobcor, "\n#********** Variable ");    
     fscanf(ficpar,"%s",&str);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("%s",str);          fprintf(ficresprobcor, "**********\n#");    
     fprintf(ficparo,"%s",str);        }
     for(j=1; j <=i; j++){        
       fscanf(ficpar," %le",&matcov[i][j]);        for (age=bage; age<=fage; age ++){ 
       printf(" %.5le",matcov[i][j]);          cov[2]=age;
       fprintf(ficparo," %.5le",matcov[i][j]);          for (k=1; k<=cptcovn;k++) {
     }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     fscanf(ficpar,"\n");          }
     printf("\n");          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     fprintf(ficparo,"\n");          for (k=1; k<=cptcovprod;k++)
   }            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for(i=1; i <=npar; i++)          
     for(j=i+1;j<=npar;j++)          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       matcov[i][j]=matcov[j][i];          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
              gp=vector(1,(nlstate)*(nlstate+ndeath));
   printf("\n");          gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
     /*-------- Rewriting paramater file ----------*/            for(i=1; i<=npar; i++)
      strcpy(rfileres,"r");    /* "Rparameterfile */              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            
      strcat(rfileres,".");    /* */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */            
     if((ficres =fopen(rfileres,"w"))==NULL) {            k=0;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;            for(i=1; i<= (nlstate); i++){
     }              for(j=1; j<=(nlstate+ndeath);j++){
     fprintf(ficres,"#%s\n",version);                k=k+1;
                    gp[k]=pmmij[i][j];
     /*-------- data file ----------*/              }
     if((fic=fopen(datafile,"r"))==NULL)    {            }
       printf("Problem with datafile: %s\n", datafile);goto end;            
     }            for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     n= lastobs;      
     severity = vector(1,maxwav);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     outcome=imatrix(1,maxwav+1,1,n);            k=0;
     num=ivector(1,n);            for(i=1; i<=(nlstate); i++){
     moisnais=vector(1,n);              for(j=1; j<=(nlstate+ndeath);j++){
     annais=vector(1,n);                k=k+1;
     moisdc=vector(1,n);                gm[k]=pmmij[i][j];
     andc=vector(1,n);              }
     agedc=vector(1,n);            }
     cod=ivector(1,n);       
     weight=vector(1,n);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     mint=matrix(1,maxwav,1,n);          }
     anint=matrix(1,maxwav,1,n);  
     s=imatrix(1,maxwav+1,1,n);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     adl=imatrix(1,maxwav+1,1,n);                for(theta=1; theta <=npar; theta++)
     tab=ivector(1,NCOVMAX);              trgradg[j][theta]=gradg[theta][j];
     ncodemax=ivector(1,8);          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     i=1;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     while (fgets(line, MAXLINE, fic) != NULL)    {          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
       if ((i >= firstobs) && (i <=lastobs)) {          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
                  free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         for (j=maxwav;j>=1;j--){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  
           strcpy(line,stra);          pmij(pmmij,cov,ncovmodel,x,nlstate);
           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);          k=0;
         }          for(i=1; i<=(nlstate); i++){
                    for(j=1; j<=(nlstate+ndeath);j++){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              k=k+1;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              mu[k][(int) age]=pmmij[i][j];
             }
         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)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              varpij[i][j][(int)age] = doldm[i][j];
         for (j=ncovcol;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          /*printf("\n%d ",(int)age);
         }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         num[i]=atol(stra);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                    fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            }*/
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  
           fprintf(ficresprob,"\n%d ",(int)age);
         i=i+1;          fprintf(ficresprobcov,"\n%d ",(int)age);
       }          fprintf(ficresprobcor,"\n%d ",(int)age);
     }  
     /* printf("ii=%d", ij);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
        scanf("%d",i);*/            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   imx=i-1; /* Number of individuals */          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   /* for (i=1; i<=imx; i++){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     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;          i=0;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          for (k=1; k<=(nlstate);k++){
     }*/            for (l=1; l<=(nlstate+ndeath);l++){ 
    /*  for (i=1; i<=imx; i++){              i=i++;
      if (s[4][i]==9)  s[4][i]=-1;              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
      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]));}*/              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                for (j=1; j<=i;j++){
                  fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   /* Calculation of the number of parameter from char model*/                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   Tvar=ivector(1,15);              }
   Tprod=ivector(1,15);            }
   Tvaraff=ivector(1,15);          }/* end of loop for state */
   Tvard=imatrix(1,15,1,2);        } /* end of loop for age */
   Tage=ivector(1,15);        
            /* Confidence intervalle of pij  */
   if (strlen(model) >1){        /*
     j=0, j1=0, k1=1, k2=1;          fprintf(ficgp,"\nset noparametric;unset label");
     j=nbocc(model,'+');          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     j1=nbocc(model,'*');          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     cptcovn=j+1;          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);
     cptcovprod=j1;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
              fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     strcpy(modelsav,model);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        */
       printf("Error. Non available option model=%s ",model);  
       goto end;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     }        first1=1;
            for (k2=1; k2<=(nlstate);k2++){
     for(i=(j+1); i>=1;i--){          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       cutv(stra,strb,modelsav,'+');            if(l2==k2) continue;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);            j=(k2-1)*(nlstate+ndeath)+l2;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/            for (k1=1; k1<=(nlstate);k1++){
       /*scanf("%d",i);*/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       if (strchr(strb,'*')) {                if(l1==k1) continue;
         cutv(strd,strc,strb,'*');                i=(k1-1)*(nlstate+ndeath)+l1;
         if (strcmp(strc,"age")==0) {                if(i<=j) continue;
           cptcovprod--;                for (age=bage; age<=fage; age ++){ 
           cutv(strb,stre,strd,'V');                  if ((int)age %5==0){
           Tvar[i]=atoi(stre);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
           cptcovage++;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
             Tage[cptcovage]=i;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
             /*printf("stre=%s ", stre);*/                    mu1=mu[i][(int) age]/stepm*YEARM ;
         }                    mu2=mu[j][(int) age]/stepm*YEARM;
         else if (strcmp(strd,"age")==0) {                    c12=cv12/sqrt(v1*v2);
           cptcovprod--;                    /* Computing eigen value of matrix of covariance */
           cutv(strb,stre,strc,'V');                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           Tvar[i]=atoi(stre);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           cptcovage++;                    /* Eigen vectors */
           Tage[cptcovage]=i;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
         }                    /*v21=sqrt(1.-v11*v11); *//* error */
         else {                    v21=(lc1-v1)/cv12*v11;
           cutv(strb,stre,strc,'V');                    v12=-v21;
           Tvar[i]=ncovcol+k1;                    v22=v11;
           cutv(strb,strc,strd,'V');                    tnalp=v21/v11;
           Tprod[k1]=i;                    if(first1==1){
           Tvard[k1][1]=atoi(strc);                      first1=0;
           Tvard[k1][2]=atoi(stre);                      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);
           Tvar[cptcovn+k2]=Tvard[k1][1];                    }
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                    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);
           for (k=1; k<=lastobs;k++)                    /*printf(fignu*/
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           k1++;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           k2=k2+2;                    if(first==1){
         }                      first=0;
       }                      fprintf(ficgp,"\nset parametric;unset label");
       else {                      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);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
        /*  scanf("%d",i);*/                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
       cutv(strd,strc,strb,'V');   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
       Tvar[i]=atoi(strc);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
       }                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
       strcpy(modelsav,stra);                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                      fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         scanf("%d",i);*/                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     }                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), 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);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                      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",\
   printf("cptcovprod=%d ", cptcovprod);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   scanf("%d ",i);*/                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     fclose(fic);                    }else{
                       first=0;
     /*  if(mle==1){*/                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
     if (weightopt != 1) { /* Maximisation without weights*/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       for(i=1;i<=n;i++) weight[i]=1.0;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     }                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     /*-calculation of age at interview from date of interview and age at death -*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     agev=matrix(1,maxwav,1,imx);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
     for (i=1; i<=imx; i++) {                  } /* age mod 5 */
       for(m=2; (m<= maxwav); m++) {                } /* end loop age */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
          anint[m][i]=9999;                first=1;
          s[m][i]=-1;              } /*l12 */
        }            } /* k12 */
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;          } /*l1 */
       }        }/* k1 */
     }      } /* loop covariates */
     }
     for (i=1; i<=imx; i++)  {    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       for(m=1; (m<= maxwav); m++){    free_vector(xp,1,npar);
         if(s[m][i] >0){    fclose(ficresprob);
           if (s[m][i] >= nlstate+1) {    fclose(ficresprobcov);
             if(agedc[i]>0)    fclose(ficresprobcor);
               if(moisdc[i]!=99 && andc[i]!=9999)    /*  fclose(ficgp);*/
                 agev[m][i]=agedc[i];  }
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  
            else {  
               if (andc[i]!=9999){  /******************* Printing html file ***********/
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
               agev[m][i]=-1;                    int lastpass, int stepm, int weightopt, char model[],\
               }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
             }                    int popforecast, int estepm ,\
           }                    double jprev1, double mprev1,double anprev1, \
           else if(s[m][i] !=9){ /* Should no more exist */                    double jprev2, double mprev2,double anprev2){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    int jj1, k1, i1, cpt;
             if(mint[m][i]==99 || anint[m][i]==9999)    /*char optionfilehtm[FILENAMELENGTH];*/
               agev[m][i]=1;  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
             else if(agev[m][i] <agemin){  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
               agemin=agev[m][i];  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
               /*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){     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
               agemax=agev[m][i];   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
             }   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
             /*agev[m][i]=anint[m][i]-annais[i];*/   - Life expectancies by age and initial health status (estepm=%2d months): \
             /*   agev[m][i] = age[i]+2*m;*/     <a href=\"%s\">%s</a> <br>\n</li>", \
           }             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
           else { /* =9 */             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
             agev[m][i]=1;             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
             s[m][i]=-1;             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
           }  
         }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
         else /*= 0 Unknown */  
           agev[m][i]=1;   m=cptcoveff;
       }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
      
     }   jj1=0;
     for (i=1; i<=imx; i++)  {   for(k1=1; k1<=m;k1++){
       for(m=1; (m<= maxwav); m++){     for(i1=1; i1<=ncodemax[k1];i1++){
         if (s[m][i] > (nlstate+ndeath)) {       jj1++;
           printf("Error: Wrong value in nlstate or ndeath\n");         if (cptcovn > 0) {
           goto end;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         }         for (cpt=1; cpt<=cptcoveff;cpt++) 
       }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
     free_vector(severity,1,maxwav);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
     free_imatrix(outcome,1,maxwav+1,1,n);       /* Quasi-incidences */
     free_vector(moisnais,1,n);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
     free_vector(annais,1,n);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
     /* free_matrix(mint,1,maxwav,1,n);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        free_matrix(anint,1,maxwav,1,n);*/         /* Stable prevalence in each health state */
     free_vector(moisdc,1,n);         for(cpt=1; cpt<nlstate;cpt++){
     free_vector(andc,1,n);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
             }
     wav=ivector(1,imx);       for(cpt=1; cpt<=nlstate;cpt++) {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exo"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
           }
     /* Concatenates waves */       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
       Tcode=ivector(1,100);   }/* End k1 */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);   fprintf(fichtm,"</ul>");
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
         fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
    codtab=imatrix(1,100,1,10);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
    h=0;   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    m=pow(2,cptcoveff);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
     - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    for(k=1;k<=cptcoveff; k++){   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
      for(i=1; i <=(m/pow(2,k));i++){   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
        for(j=1; j <= ncodemax[k]; j++){   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){           rfileres,rfileres,\
            h++;           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
          }           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
        }           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
      }           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
    }  
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);  /*  if(popforecast==1) fprintf(fichtm,"\n */
       codtab[1][2]=1;codtab[2][2]=2; */  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
    /* for(i=1; i <=m ;i++){  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
       for(k=1; k <=cptcovn; k++){  /*      <br>",fileres,fileres,fileres,fileres); */
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);  /*  else  */
       }  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
       printf("\n");  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       }  
       scanf("%d",i);*/   m=cptcoveff;
       if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */   jj1=0;
    for(k1=1; k1<=m;k1++){
         for(i1=1; i1<=ncodemax[k1];i1++){
           jj1++;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       if (cptcovn > 0) {
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         for (cpt=1; cpt<=cptcoveff;cpt++) 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
             }
     /* For Powell, parameters are in a vector p[] starting at p[1]       for(cpt=1; cpt<=nlstate;cpt++) {
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"pe"),cpt,jj1,subdirf2(optionfilefiname,"pe"),cpt,jj1);  
     if(mle==1){       }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);     } /* end i1 */
     }   }/* End k1 */
       fprintf(fichtm,"</ul>");
     /*--------- results files --------------*/   fflush(fichtm);
     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);  }
    
   /******************* Gnuplot file **************/
    jk=1;  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char path[], double p[]){
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    char dirfileres[132],optfileres[132];
    for(i=1,jk=1; i <=nlstate; i++){    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
      for(k=1; k <=(nlstate+ndeath); k++){    int ng;
        if (k != i)  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
          {  /*     printf("Problem with file %s",optionfilegnuplot); */
            printf("%d%d ",i,k);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
            fprintf(ficres,"%1d%1d ",i,k);  /*   } */
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);    /*#ifdef windows */
              fprintf(ficres,"%f ",p[jk]);    fprintf(ficgp,"cd \"%s\" \n",path);
              jk++;      /*#endif */
            }    m=pow(2,cptcoveff);
            printf("\n");  
            fprintf(ficres,"\n");    strcpy(dirfileres,optionfilefiname);
          }    strcpy(optfileres,"vpl");
      }   /* 1eme*/
    }    for (cpt=1; cpt<= nlstate ; cpt ++) {
  if(mle==1){     for (k1=1; k1<= m ; k1 ++) {
     /* Computing hessian and covariance matrix */       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
     ftolhess=ftol; /* Usually correct */       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
     hesscov(matcov, p, npar, delti, ftolhess, func);       fprintf(ficgp,"set xlabel \"Age\" \n\
  }  set ylabel \"Probability\" \n\
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  set ter png small\n\
     printf("# Scales (for hessian or gradient estimation)\n");  set size 0.65,0.65\n\
      for(i=1,jk=1; i <=nlstate; i++){  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {       for (i=1; i<= nlstate ; i ++) {
           fprintf(ficres,"%1d%1d",i,j);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           printf("%1d%1d",i,j);         else fprintf(ficgp," \%%*lf (\%%*lf)");
           for(k=1; k<=ncovmodel;k++){       }
             printf(" %.5e",delti[jk]);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
             fprintf(ficres," %.5e",delti[jk]);       for (i=1; i<= nlstate ; i ++) {
             jk++;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           }         else fprintf(ficgp," \%%*lf (\%%*lf)");
           printf("\n");       } 
           fprintf(ficres,"\n");       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
         }       for (i=1; i<= nlstate ; i ++) {
       }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
      }         else fprintf(ficgp," \%%*lf (\%%*lf)");
           }  
     k=1;       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");     }
     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");    }
     for(i=1;i<=npar;i++){    /*2 eme*/
       /*  if (k>nlstate) k=1;    
       i1=(i-1)/(ncovmodel*nlstate)+1;    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       printf("%s%d%d",alph[k],i1,tab[i]);*/      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       fprintf(ficres,"%3d",i);      
       printf("%3d",i);      for (i=1; i<= nlstate+1 ; i ++) {
       for(j=1; j<=i;j++){        k=2*i;
         fprintf(ficres," %.5e",matcov[i][j]);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         printf(" %.5e",matcov[i][j]);        for (j=1; j<= nlstate+1 ; j ++) {
       }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficres,"\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf("\n");        }   
       k++;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     }        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     while((c=getc(ficpar))=='#' && c!= EOF){        for (j=1; j<= nlstate+1 ; j ++) {
       ungetc(c,ficpar);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       fgets(line, MAXLINE, ficpar);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       puts(line);        }   
       fputs(line,ficparo);        fprintf(ficgp,"\" t\"\" w l 0,");
     }        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     ungetc(c,ficpar);        for (j=1; j<= nlstate+1 ; j ++) {
     estepm=0;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     if (estepm==0 || estepm < stepm) estepm=stepm;        }   
     if (fage <= 2) {        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       bage = ageminpar;        else fprintf(ficgp,"\" t\"\" w l 0,");
       fage = agemaxpar;      }
     }    }
        
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    /*3eme*/
     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);    for (k1=1; k1<= m ; k1 ++) { 
        for (cpt=1; cpt<= nlstate ; cpt ++) {
     while((c=getc(ficpar))=='#' && c!= EOF){        k=2+nlstate*(2*cpt-2);
     ungetc(c,ficpar);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
     fgets(line, MAXLINE, ficpar);        fprintf(ficgp,"set ter png small\n\
     puts(line);  set size 0.65,0.65\n\
     fputs(line,ficparo);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),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);
   ungetc(c,ficpar);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
            fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                
   while((c=getc(ficpar))=='#' && c!= EOF){        */
     ungetc(c,ficpar);        for (i=1; i< nlstate ; i ++) {
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
     puts(line);          
     fputs(line,ficparo);        } 
   }      }
   ungetc(c,ficpar);    }
      
     /* CV preval stable (period) */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    for (k1=1; k1<= m ; k1 ++) { 
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
   fscanf(ficpar,"pop_based=%d\n",&popbased);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   fprintf(ficparo,"pop_based=%d\n",popbased);          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   fprintf(ficres,"pop_based=%d\n",popbased);    set ter png small\nset size 0.65,0.65\n\
    plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   while((c=getc(ficpar))=='#' && c!= EOF){        
     ungetc(c,ficpar);        for (i=1; i< nlstate ; i ++)
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp,"+$%d",k+i+1);
     puts(line);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     fputs(line,ficparo);        
   }        l=3+(nlstate+ndeath)*cpt;
   ungetc(c,ficpar);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          l=3+(nlstate+ndeath)*cpt;
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          fprintf(ficgp,"+$%d",l+i+1);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
 while((c=getc(ficpar))=='#' && c!= EOF){    }  
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    /* proba elementaires */
     puts(line);    for(i=1,jk=1; i <=nlstate; i++){
     fputs(line,ficparo);      for(k=1; k <=(nlstate+ndeath); k++){
   }        if (k != i) {
   ungetc(c,ficpar);          for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            jk++; 
   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(ficgp,"\n");
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          }
         }
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      }
      }
 /*------------ gnuplot -------------*/  
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
         for(jk=1; jk <=m; jk++) {
 /*------------ free_vector  -------------*/         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
  chdir(path);         if (ng==2)
             fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
  free_ivector(wav,1,imx);         else
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);           fprintf(ficgp,"\nset title \"Probability\"\n");
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
  free_ivector(num,1,n);         i=1;
  free_vector(agedc,1,n);         for(k2=1; k2<=nlstate; k2++) {
  /*free_matrix(covar,1,NCOVMAX,1,n);*/           k3=i;
  fclose(ficparo);           for(k=1; k<=(nlstate+ndeath); k++) {
  fclose(ficres);             if (k != k2){
                if(ng==2)
 /*--------- index.htm --------*/                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                 for(j=3; j <=ncovmodel; j++) {
   /*--------------- Prevalence limit --------------*/                 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]]]);
   strcpy(filerespl,"pl");                   ij++;
   strcat(filerespl,fileres);                 }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                 else
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   }               }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);               fprintf(ficgp,")/(1");
   fprintf(ficrespl,"#Prevalence limit\n");               
   fprintf(ficrespl,"#Age ");               for(k1=1; k1 <=nlstate; k1++){   
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   fprintf(ficrespl,"\n");                 ij=1;
                   for(j=3; j <=ncovmodel; j++){
   prlim=matrix(1,nlstate,1,nlstate);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                     ij++;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                   }
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                   else
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   k=0;                 }
   agebase=ageminpar;                 fprintf(ficgp,")");
   agelim=agemaxpar;               }
   ftolpl=1.e-10;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   i1=cptcoveff;               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   if (cptcovn < 1){i1=1;}               i=i+ncovmodel;
              }
   for(cptcov=1;cptcov<=i1;cptcov++){           } /* end k */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         } /* end k2 */
         k=k+1;       } /* end jk */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/     } /* end ng */
         fprintf(ficrespl,"\n#******");     fflush(ficgp); 
         for(j=1;j<=cptcoveff;j++)  }  /* end gnuplot */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");  
          /*************** Moving average **************/
         for (age=agebase; age<=agelim; age++){  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );    int i, cpt, cptcod;
           for(i=1; i<=nlstate;i++)    int modcovmax =1;
           fprintf(ficrespl," %.5f", prlim[i][i]);    int mobilavrange, mob;
           fprintf(ficrespl,"\n");    double age;
         }  
       }    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
     }                             a covariate has 2 modalities */
   fclose(ficrespl);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   /*------------- h Pij x at various ages ------------*/    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
        if(mobilav==1) mobilavrange=5; /* default */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      else mobilavrange=mobilav;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      for (age=bage; age<=fage; age++)
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        for (i=1; i<=nlstate;i++)
   }          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   printf("Computing pij: result on file '%s' \n", filerespij);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        /* We keep the original values on the extreme ages bage, fage and for 
   stepsize=(int) (stepm+YEARM-1)/YEARM;         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   /*if (stepm<=24) stepsize=2;*/         we use a 5 terms etc. until the borders are no more concerned. 
       */ 
   agelim=AGESUP;      for (mob=3;mob <=mobilavrange;mob=mob+2){
   hstepm=stepsize*YEARM; /* Every year of age */        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          for (i=1; i<=nlstate;i++){
              for (cptcod=1;cptcod<=modcovmax;cptcod++){
   k=0;              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   for(cptcov=1;cptcov<=i1;cptcov++){                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       k=k+1;                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
         fprintf(ficrespij,"\n#****** ");                }
         for(j=1;j<=cptcoveff;j++)              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            }
         fprintf(ficrespij,"******\n");          }
                }/* end age */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      }/* end mob */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    }else return -1;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    return 0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }/* End movingaverage */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");  /************** Forecasting ******************/
           for(i=1; i<=nlstate;i++)  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){
             for(j=1; j<=nlstate+ndeath;j++)    /* proj1, year, month, day of starting projection 
               fprintf(ficrespij," %1d-%1d",i,j);       agemin, agemax range of age
           fprintf(ficrespij,"\n");       dateprev1 dateprev2 range of dates during which prevalence is computed
            for (h=0; h<=nhstepm; h++){       anproj2 year of en of projection (same day and month as proj1).
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    */
             for(i=1; i<=nlstate;i++)    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
               for(j=1; j<=nlstate+ndeath;j++)    int *popage;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    double agec; /* generic age */
             fprintf(ficrespij,"\n");    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
              }    double *popeffectif,*popcount;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double ***p3mat;
           fprintf(ficrespij,"\n");    double ***mobaverage;
         }    char fileresf[FILENAMELENGTH];
     }  
   }    agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);   
     strcpy(fileresf,"f"); 
   fclose(ficrespij);    strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
   /*---------- Forecasting ------------------*/      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   if((stepm == 1) && (strcmp(model,".")==0)){    }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    printf("Computing forecasting: result on file '%s' \n", fileresf);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   }  
   else{    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     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);    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);
   /*---------- Health expectancies and variances ------------*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
   strcpy(filerest,"t");    }
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {    stepsize=(int) (stepm+YEARM-1)/YEARM;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    if (stepm<=12) stepsize=1;
   }    if(estepm < stepm){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   strcpy(filerese,"e");  
   strcat(filerese,fileres);    hstepm=hstepm/stepm; 
   if((ficreseij=fopen(filerese,"w"))==NULL) {    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                                 fractional in yp1 */
   }    anprojmean=yp;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    yp2=modf((yp1*12),&yp);
     mprojmean=yp;
  strcpy(fileresv,"v");    yp1=modf((yp2*30.5),&yp);
   strcat(fileresv,fileres);    jprojmean=yp;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    if(jprojmean==0) jprojmean=1;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    if(mprojmean==0) jprojmean=1;
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    i1=cptcoveff;
   calagedate=-1;    if (cptcovn < 1){i1=1;}
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresf,"#****** Routine prevforecast **\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;  /*            if (h==(int)(YEARM*yearp)){ */
       fprintf(ficrest,"\n#****** ");    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(j=1;j<=cptcoveff;j++)      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        k=k+1;
       fprintf(ficrest,"******\n");        fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
       fprintf(ficreseij,"\n#****** ");          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]]);
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficresf,"******\n");
       fprintf(ficreseij,"******\n");        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
       fprintf(ficresvij,"\n#****** ");          for(i=1; i<=nlstate;i++)              
       for(j=1;j<=cptcoveff;j++)            fprintf(ficresf," p%d%d",i,j);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficresf," p.%d",j);
       fprintf(ficresvij,"******\n");        }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          fprintf(ficresf,"\n");
       oldm=oldms;savm=savms;          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    
            for (agec=fage; agec>=(ageminpar-1); agec--){ 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
       oldm=oldms;savm=savms;            nhstepm = nhstepm/hstepm; 
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);            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);  
            
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");            for (h=0; h<=nhstepm; h++){
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);              if (h*hstepm/YEARM*stepm ==yearp) {
       fprintf(ficrest,"\n");                fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
       epj=vector(1,nlstate+1);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       for(age=bage; age <=fage ;age++){                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              } 
         if (popbased==1) {              for(j=1; j<=nlstate+ndeath;j++) {
           for(i=1; i<=nlstate;i++)                ppij=0.;
             prlim[i][i]=probs[(int)age][i][k];                for(i=1; i<=nlstate;i++) {
         }                  if (mobilav==1) 
                            ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
         fprintf(ficrest," %4.0f",age);                  else {
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                  }
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                  if (h*hstepm/YEARM*stepm== yearp) {
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
           }                  }
           epj[nlstate+1] +=epj[j];                } /* end i */
         }                if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
         for(i=1, vepp=0.;i <=nlstate;i++)                }
           for(j=1;j <=nlstate;j++)              }/* end j */
             vepp += vareij[i][j][(int)age];            } /* end h */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(j=1;j <=nlstate;j++){          } /* end agec */
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));        } /* end yearp */
         }      } /* end cptcod */
         fprintf(ficrest,"\n");    } /* end  cptcov */
       }         
     }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }  
 free_matrix(mint,1,maxwav,1,n);    fclose(ficresf);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  }
     free_vector(weight,1,n);  
   fclose(ficreseij);  /************** Forecasting *****not tested NB*************/
   fclose(ficresvij);  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){
   fclose(ficrest);    
   fclose(ficpar);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   free_vector(epj,1,nlstate+1);    int *popage;
      double calagedatem, agelim, kk1, kk2;
   /*------- Variance limit prevalence------*/      double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
   strcpy(fileresvpl,"vpl");    double ***mobaverage;
   strcat(fileresvpl,fileres);    char filerespop[FILENAMELENGTH];
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     exit(0);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }    agelim=AGESUP;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
   k=0;    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    strcpy(filerespop,"pop"); 
       fprintf(ficresvpl,"\n#****** ");    strcat(filerespop,fileres);
       for(j=1;j<=cptcoveff;j++)    if((ficrespop=fopen(filerespop,"w"))==NULL) {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficresvpl,"******\n");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
          }
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    printf("Computing forecasting: result on file '%s' \n", filerespop);
       oldm=oldms;savm=savms;    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
     }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
  }  
     if (mobilav!=0) {
   fclose(ficresvpl);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   /*---------- End : free ----------------*/        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
      stepsize=(int) (stepm+YEARM-1)/YEARM;
      if (stepm<=12) stepsize=1;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    agelim=AGESUP;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    hstepm=1;
      hstepm=hstepm/stepm; 
   free_matrix(matcov,1,npar,1,npar);    
   free_vector(delti,1,npar);    if (popforecast==1) {
   free_matrix(agev,1,maxwav,1,imx);      if((ficpop=fopen(popfile,"r"))==NULL) {
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
   if(erreur >0)      } 
     printf("End of Imach with error or warning %d\n",erreur);      popage=ivector(0,AGESUP);
   else   printf("End of Imach\n");      popeffectif=vector(0,AGESUP);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      popcount=vector(0,AGESUP);
        
   /* 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);*/      i=1;   
   /*printf("Total time was %d uSec.\n", total_usecs);*/      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   /*------ End -----------*/     
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
  end:    }
   /* chdir(pathcd);*/  
  /*system("wgnuplot graph.plt");*/    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
  /*system("../gp37mgw/wgnuplot graph.plt");*/     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
  /*system("cd ../gp37mgw");*/        k=k+1;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        fprintf(ficrespop,"\n#******");
  strcpy(plotcmd,GNUPLOTPROGRAM);        for(j=1;j<=cptcoveff;j++) {
  strcat(plotcmd," ");          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
  strcat(plotcmd,optionfilegnuplot);        }
  system(plotcmd);        fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
  /*#ifdef windows*/        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   while (z[0] != 'q') {        if (popforecast==1)  fprintf(ficrespop," [Population]");
     /* chdir(path); */        
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        for (cpt=0; cpt<=0;cpt++) { 
     scanf("%s",z);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     if (z[0] == 'c') system("./imach");          
     else if (z[0] == 'e') system(optionfilehtm);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     else if (z[0] == 'g') system(plotcmd);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     else if (z[0] == 'q') exit(0);            nhstepm = nhstepm/hstepm; 
   }            
   /*#endif */            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);
   }
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# 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(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     }
   
   } /* end of prwizard */
   
   /***********************************************/
   /**************** 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, imk;
     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[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     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 strstart[80], *strt, strtend[80];
     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);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  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",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     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, MAXLINE)!= 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);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- 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\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Localtime (at start):%s",strstart);
     fprintf(ficlog,"Localtime (at start): %s",strstart);
     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) { /* opened on subdirectory */
       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 */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* 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,strstart);
     /*fclose(fichtm);*/
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     strcpy(lfileres,fileres);
     strcat(lfileres,"/");
     strcat(lfileres,optionfilefiname);
     
     /*  replace(pathc,path);*/
   
     /* 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);
   
     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);
     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, optionfilefiname,ageminpar,agemaxpar,fage, path,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);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Localtime at start %s\nLocal time at end   %s",strstart, 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>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(ficgp);
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
     chdir(path);
    /*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.1.41.2.2  
changed lines
  Added in v.1.88


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