Diff for /imach/src/imach.c between versions 1.35 and 1.90

version 1.35, 2002/03/26 17:08:39 version 1.90, 2003/06/24 12:34:15
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.90  2003/06/24 12:34:15  brouard
      (Module): Some bugs corrected for windows. Also, when
   This program computes Healthy Life Expectancies from    mle=-1 a template is output in file "or"mypar.txt with the design
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    of the covariance matrix to be input.
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.89  2003/06/24 12:30:52  brouard
   case of a health survey which is our main interest) -2- at least a    (Module): Some bugs corrected for windows. Also, when
   second wave of interviews ("longitudinal") which measure each change    mle=-1 a template is output in file "or"mypar.txt with the design
   (if any) in individual health status.  Health expectancies are    of the covariance matrix to be input.
   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 1.88  2003/06/23 17:54:56  brouard
   Maximum Likelihood of the parameters involved in the model.  The    * 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.
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.87  2003/06/18 12:26:01  brouard
   conditional to be observed in state i at the first wave. Therefore    Version 0.96
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.86  2003/06/17 20:04:08  brouard
   complex model than "constant and age", you should modify the program    (Module): Change position of html and gnuplot routines and added
   where the markup *Covariates have to be included here again* invites    routine fileappend.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
   The advantage of this computer programme, compared to a simple    current date of interview. It may happen when the death was just
   multinomial logistic model, is clear when the delay between waves is not    prior to the death. In this case, dh was negative and likelihood
   identical for each individual. Also, if a individual missed an    was wrong (infinity). We still send an "Error" but patch by
   intermediate interview, the information is lost, but taken into    assuming that the date of death was just one stepm after the
   account using an interpolation or extrapolation.      interview.
     (Repository): Because some people have very long ID (first column)
   hPijx is the probability to be observed in state i at age x+h    we changed int to long in num[] and we added a new lvector for
   conditional to the observed state i at age x. The delay 'h' can be    memory allocation. But we also truncated to 8 characters (left
   split into an exact number (nh*stepm) of unobserved intermediate    truncation)
   states. This elementary transition (by month or quarter trimester,    (Repository): No more line truncation errors.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.84  2003/06/13 21:44:43  brouard
   and the contribution of each individual to the likelihood is simply    * imach.c (Repository): Replace "freqsummary" at a correct
   hPijx.    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
   Also this programme outputs the covariance matrix of the parameters but also    parcimony.
   of the life expectancies. It also computes the prevalence limits.    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.83  2003/06/10 13:39:11  lievre
            Institut national d'études démographiques, Paris.    *** empty log message ***
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.82  2003/06/05 15:57:20  brouard
   It is copyrighted identically to a GNU software product, ie programme and    Add log in  imach.c and  fullversion number is now printed.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .  */
   **********************************************************************/  /*
       Interpolated Markov Chain
 #include <math.h>  
 #include <stdio.h>    Short summary of the programme:
 #include <stdlib.h>    
 #include <unistd.h>    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define MAXLINE 256    first survey ("cross") where individuals from different ages are
 #define GNUPLOTPROGRAM "wgnuplot"    interviewed on their health status or degree of disability (in the
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    case of a health survey which is our main interest) -2- at least a
 #define FILENAMELENGTH 80    second wave of interviews ("longitudinal") which measure each change
 /*#define DEBUG*/    (if any) in individual health status.  Health expectancies are
 #define windows    computed from the time spent in each health state according to a
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    model. More health states you consider, more time is necessary to reach the
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    probability to be observed in state j at the second wave
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define NINTERVMAX 8    'age' is age and 'sex' is a covariate. If you want to have a more
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    complex model than "constant and age", you should modify the program
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    where the markup *Covariates have to be included here again* invites
 #define NCOVMAX 8 /* Maximum number of covariates */    you to do it.  More covariates you add, slower the
 #define MAXN 20000    convergence.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    The advantage of this computer programme, compared to a simple
 #define AGEBASE 40    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 int erreur; /* Error number */    account using an interpolation or extrapolation.  
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    hPijx is the probability to be observed in state i at age x+h
 int npar=NPARMAX;    conditional to the observed state i at age x. The delay 'h' can be
 int nlstate=2; /* Number of live states */    split into an exact number (nh*stepm) of unobserved intermediate
 int ndeath=1; /* Number of dead states */    states. This elementary transition (by month, quarter,
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    semester or year) is modelled as a multinomial logistic.  The hPx
 int popbased=0;    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 int *wav; /* Number of waves for this individuual 0 is possible */    hPijx.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Also this programme outputs the covariance matrix of the parameters but also
 int mle, weightopt;    of the life expectancies. It also computes the stable prevalence. 
 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 */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 double jmean; /* Mean space between 2 waves */             Institut national d'études démographiques, Paris.
 double **oldm, **newm, **savm; /* Working pointers to matrices */    This software have been partly granted by Euro-REVES, a concerted action
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    from the European Union.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    It is copyrighted identically to a GNU software product, ie programme and
 FILE *ficgp,*ficresprob,*ficpop;    software can be distributed freely for non commercial use. Latest version
 FILE *ficreseij;    can be accessed at http://euroreves.ined.fr/imach .
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   char fileresv[FILENAMELENGTH];    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
  FILE  *ficresvpl;    
   char fileresvpl[FILENAMELENGTH];    **********************************************************************/
   /*
 #define NR_END 1    main
 #define FREE_ARG char*    read parameterfile
 #define FTOL 1.0e-10    read datafile
     concatwav
 #define NRANSI    freqsummary
 #define ITMAX 200    if (mle >= 1)
       mlikeli
 #define TOL 2.0e-4    print results files
     if mle==1 
 #define CGOLD 0.3819660       computes hessian
 #define ZEPS 1.0e-10    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);        begin-prev-date,...
     open gnuplot file
 #define GOLD 1.618034    open html file
 #define GLIMIT 100.0    stable prevalence
 #define TINY 1.0e-20     for age prevalim()
     h Pij x
 static double maxarg1,maxarg2;    variance of p varprob
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    forecasting if prevfcast==1 prevforecast call prevalence()
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    health expectancies
      Variance-covariance of DFLE
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    prevalence()
 #define rint(a) floor(a+0.5)     movingaverage()
     varevsij() 
 static double sqrarg;    if popbased==1 varevsij(,popbased)
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    total life expectancies
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Variance of stable prevalence
    end
 int imx;  */
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  
   
 int m,nb;   
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #include <math.h>
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #include <stdio.h>
 double **pmmij, ***probs, ***mobaverage;  #include <stdlib.h>
 double dateintmean=0;  #include <unistd.h>
   
 double *weight;  #include <sys/time.h>
 int **s; /* Status */  #include <time.h>
 double *agedc, **covar, idx;  #include "timeval.h"
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   #define MAXLINE 256
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define GNUPLOTPROGRAM "gnuplot"
 double ftolhess; /* Tolerance for computing hessian */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 /**************** split *************************/  /*#define DEBUG*/
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  /*#define windows*/
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
    char *s;                             /* pointer */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    int  l1, l2;                         /* length counters */  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    l1 = strlen( path );                 /* length of path */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows  #define NINTERVMAX 8
    s = strrchr( path, '\\' );           /* find last / */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #else  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    s = strrchr( path, '/' );            /* find last / */  #define NCOVMAX 8 /* Maximum number of covariates */
 #endif  #define MAXN 20000
    if ( s == NULL ) {                   /* no directory, so use current */  #define YEARM 12. /* Number of months per year */
 #if     defined(__bsd__)                /* get current working directory */  #define AGESUP 130
       extern char       *getwd( );  #define AGEBASE 40
   #ifdef unix
       if ( getwd( dirc ) == NULL ) {  #define DIRSEPARATOR '/'
 #else  #define ODIRSEPARATOR '\\'
       extern char       *getcwd( );  #else
   #define DIRSEPARATOR '\\'
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define ODIRSEPARATOR '/'
 #endif  #endif
          return( GLOCK_ERROR_GETCWD );  
       }  /* $Id$ */
       strcpy( name, path );             /* we've got it */  /* $State$ */
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
       l2 = strlen( s );                 /* length of filename */  char fullversion[]="$Revision$ $Date$"; 
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int erreur; /* Error number */
       strcpy( name, s );                /* save file name */  int nvar;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
       dirc[l1-l2] = 0;                  /* add zero */  int npar=NPARMAX;
    }  int nlstate=2; /* Number of live states */
    l1 = strlen( dirc );                 /* length of directory */  int ndeath=1; /* Number of dead states */
 #ifdef windows  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int popbased=0;
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int *wav; /* Number of waves for this individuual 0 is possible */
 #endif  int maxwav; /* Maxim number of waves */
    s = strrchr( name, '.' );            /* find last / */  int jmin, jmax; /* min, max spacing between 2 waves */
    s++;  int gipmx, gsw; /* Global variables on the number of contributions 
    strcpy(ext,s);                       /* save extension */                     to the likelihood and the sum of weights (done by funcone)*/
    l1= strlen( name);  int mle, weightopt;
    l2= strlen( s)+1;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
    strncpy( finame, name, l1-l2);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    finame[l1-l2]= 0;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
    return( 0 );                         /* we're done */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 }  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 /******************************************/  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 void replace(char *s, char*t)  int globpr; /* Global variable for printing or not */
 {  double fretone; /* Only one call to likelihood */
   int i;  long ipmx; /* Number of contributions */
   int lg=20;  double sw; /* Sum of weights */
   i=0;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   lg=strlen(t);  FILE *ficresilk;
   for(i=0; i<= lg; i++) {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     (s[i] = t[i]);  FILE *ficresprobmorprev;
     if (t[i]== '\\') s[i]='/';  FILE *fichtm; /* Html File */
   }  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 int nbocc(char *s, char occ)  char fileresv[FILENAMELENGTH];
 {  FILE  *ficresvpl;
   int i,j=0;  char fileresvpl[FILENAMELENGTH];
   int lg=20;  char title[MAXLINE];
   i=0;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   lg=strlen(s);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   for(i=0; i<= lg; i++) {  char tmpout[FILENAMELENGTH]; 
   if  (s[i] == occ ) j++;  char command[FILENAMELENGTH];
   }  int  outcmd=0;
   return j;  
 }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char lfileres[FILENAMELENGTH];
 void cutv(char *u,char *v, char*t, char occ)  char filelog[FILENAMELENGTH]; /* Log file */
 {  char filerest[FILENAMELENGTH];
   int i,lg,j,p=0;  char fileregp[FILENAMELENGTH];
   i=0;  char popfile[FILENAMELENGTH];
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   }  
   #define NR_END 1
   lg=strlen(t);  #define FREE_ARG char*
   for(j=0; j<p; j++) {  #define FTOL 1.0e-10
     (u[j] = t[j]);  
   }  #define NRANSI 
      u[p]='\0';  #define ITMAX 200 
   
    for(j=0; j<= lg; j++) {  #define TOL 2.0e-4 
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }  #define CGOLD 0.3819660 
 }  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 /********************** nrerror ********************/  
   #define GOLD 1.618034 
 void nrerror(char error_text[])  #define GLIMIT 100.0 
 {  #define TINY 1.0e-20 
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  static double maxarg1,maxarg2;
   exit(1);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 /*********************** vector *******************/    
 double *vector(int nl, int nh)  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 {  #define rint(a) floor(a+0.5)
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  static double sqrarg;
   if (!v) nrerror("allocation failure in vector");  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   return v-nl+NR_END;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 }  
   int imx; 
 /************************ free vector ******************/  int stepm;
 void free_vector(double*v, int nl, int nh)  /* Stepm, step in month: minimum step interpolation*/
 {  
   free((FREE_ARG)(v+nl-NR_END));  int estepm;
 }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 /************************ivector *******************************/  int m,nb;
 int *ivector(long nl,long nh)  long *num;
 {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   int *v;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  double **pmmij, ***probs;
   if (!v) nrerror("allocation failure in ivector");  double dateintmean=0;
   return v-nl+NR_END;  
 }  double *weight;
   int **s; /* Status */
 /******************free ivector **************************/  double *agedc, **covar, idx;
 void free_ivector(int *v, long nl, long nh)  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 */
   
 /******************* imatrix *******************************/  /**************** split *************************/
 int **imatrix(long nrl, long nrh, long ncl, long nch)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  {
 {    char  *ss;                            /* pointer */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    int   l1, l2;                         /* length counters */
   int **m;  
      l1 = strlen(path );                   /* length of path */
   /* allocate pointers to rows */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   if (!m) nrerror("allocation failure 1 in matrix()");    if ( ss == NULL ) {                   /* no directory, so use current */
   m += NR_END;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   m -= nrl;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
        /* get current working directory */
        /*    extern  char* getcwd ( char *buf , int len);*/
   /* allocate rows and set pointers to them */      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));        return( GLOCK_ERROR_GETCWD );
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      }
   m[nrl] += NR_END;      strcpy( name, path );               /* we've got it */
   m[nrl] -= ncl;    } else {                              /* strip direcotry from path */
        ss++;                               /* after this, the filename */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;      l2 = strlen( ss );                  /* length of filename */
        if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   /* return pointer to array of pointers to rows */      strcpy( name, ss );         /* save file name */
   return m;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 }      dirc[l1-l2] = 0;                    /* add zero */
     }
 /****************** free_imatrix *************************/    l1 = strlen( dirc );                  /* length of directory */
 void free_imatrix(m,nrl,nrh,ncl,nch)    /*#ifdef windows
       int **m;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
       long nch,ncl,nrh,nrl;  #else
      /* free an int matrix allocated by imatrix() */    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 {  #endif
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    */
   free((FREE_ARG) (m+nrl-NR_END));    ss = strrchr( name, '.' );            /* find last / */
 }    ss++;
     strcpy(ext,ss);                       /* save extension */
 /******************* matrix *******************************/    l1= strlen( name);
 double **matrix(long nrl, long nrh, long ncl, long nch)    l2= strlen(ss)+1;
 {    strncpy( finame, name, l1-l2);
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    finame[l1-l2]= 0;
   double **m;    return( 0 );                          /* we're done */
   }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /******************************************/
   m -= nrl;  
   void replace_back_to_slash(char *s, char*t)
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    int i;
   m[nrl] += NR_END;    int lg=0;
   m[nrl] -= ncl;    i=0;
     lg=strlen(t);
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    for(i=0; i<= lg; i++) {
   return m;      (s[i] = t[i]);
 }      if (t[i]== '\\') s[i]='/';
     }
 /*************************free matrix ************************/  }
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  int nbocc(char *s, char occ)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  {
   free((FREE_ARG)(m+nrl-NR_END));    int i,j=0;
 }    int lg=20;
     i=0;
 /******************* ma3x *******************************/    lg=strlen(s);
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    for(i=0; i<= lg; i++) {
 {    if  (s[i] == occ ) j++;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    }
   double ***m;    return j;
   }
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  void cutv(char *u,char *v, char*t, char occ)
   m += NR_END;  {
   m -= nrl;    /* cuts string t into u and v where u is ended by char occ excluding it
        and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));       gives u="abcedf" and v="ghi2j" */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    int i,lg,j,p=0;
   m[nrl] += NR_END;    i=0;
   m[nrl] -= ncl;    for(j=0; j<=strlen(t)-1; j++) {
       if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    }
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    lg=strlen(t);
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    for(j=0; j<p; j++) {
   m[nrl][ncl] += NR_END;      (u[j] = t[j]);
   m[nrl][ncl] -= nll;    }
   for (j=ncl+1; j<=nch; j++)       u[p]='\0';
     m[nrl][j]=m[nrl][j-1]+nlay;  
       for(j=0; j<= lg; j++) {
   for (i=nrl+1; i<=nrh; i++) {      if (j>=(p+1))(v[j-p-1] = t[j]);
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    }
     for (j=ncl+1; j<=nch; j++)  }
       m[i][j]=m[i][j-1]+nlay;  
   }  /********************** nrerror ********************/
   return m;  
 }  void nrerror(char error_text[])
   {
 /*************************free ma3x ************************/    fprintf(stderr,"ERREUR ...\n");
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    fprintf(stderr,"%s\n",error_text);
 {    exit(EXIT_FAILURE);
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /*********************** vector *******************/
   free((FREE_ARG)(m+nrl-NR_END));  double *vector(int nl, int nh)
 }  {
     double *v;
 /***************** f1dim *************************/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 extern int ncom;    if (!v) nrerror("allocation failure in vector");
 extern double *pcom,*xicom;    return v-nl+NR_END;
 extern double (*nrfunc)(double []);  }
    
 double f1dim(double x)  /************************ free vector ******************/
 {  void free_vector(double*v, int nl, int nh)
   int j;  {
   double f;    free((FREE_ARG)(v+nl-NR_END));
   double *xt;  }
    
   xt=vector(1,ncom);  /************************ivector *******************************/
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int *ivector(long nl,long nh)
   f=(*nrfunc)(xt);  {
   free_vector(xt,1,ncom);    int *v;
   return f;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 }    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
 /*****************brent *************************/  }
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  /******************free ivector **************************/
   int iter;  void free_ivector(int *v, long nl, long nh)
   double a,b,d,etemp;  {
   double fu,fv,fw,fx;    free((FREE_ARG)(v+nl-NR_END));
   double ftemp;  }
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  /************************lvector *******************************/
    long *lvector(long nl,long nh)
   a=(ax < cx ? ax : cx);  {
   b=(ax > cx ? ax : cx);    long *v;
   x=w=v=bx;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   fw=fv=fx=(*f)(x);    if (!v) nrerror("allocation failure in ivector");
   for (iter=1;iter<=ITMAX;iter++) {    return v-nl+NR_END;
     xm=0.5*(a+b);  }
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  /******************free lvector **************************/
     printf(".");fflush(stdout);  void free_lvector(long *v, long nl, long nh)
 #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);    free((FREE_ARG)(v+nl-NR_END));
     /*          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))){  /******************* imatrix *******************************/
       *xmin=x;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       return fx;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     }  { 
     ftemp=fu;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     if (fabs(e) > tol1) {    int **m; 
       r=(x-w)*(fx-fv);    
       q=(x-v)*(fx-fw);    /* allocate pointers to rows */ 
       p=(x-v)*q-(x-w)*r;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       q=2.0*(q-r);    if (!m) nrerror("allocation failure 1 in matrix()"); 
       if (q > 0.0) p = -p;    m += NR_END; 
       q=fabs(q);    m -= nrl; 
       etemp=e;    
       e=d;    
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    /* allocate rows and set pointers to them */ 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       else {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         d=p/q;    m[nrl] += NR_END; 
         u=x+d;    m[nrl] -= ncl; 
         if (u-a < tol2 || b-u < tol2)    
           d=SIGN(tol1,xm-x);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       }    
     } else {    /* return pointer to array of pointers to rows */ 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    return m; 
     }  } 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  /****************** free_imatrix *************************/
     if (fu <= fx) {  void free_imatrix(m,nrl,nrh,ncl,nch)
       if (u >= x) a=x; else b=x;        int **m;
       SHFT(v,w,x,u)        long nch,ncl,nrh,nrl; 
         SHFT(fv,fw,fx,fu)       /* free an int matrix allocated by imatrix() */ 
         } else {  { 
           if (u < x) a=u; else b=u;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
           if (fu <= fw || w == x) {    free((FREE_ARG) (m+nrl-NR_END)); 
             v=w;  } 
             w=u;  
             fv=fw;  /******************* matrix *******************************/
             fw=fu;  double **matrix(long nrl, long nrh, long ncl, long nch)
           } else if (fu <= fv || v == x || v == w) {  {
             v=u;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
             fv=fu;    double **m;
           }  
         }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   }    if (!m) nrerror("allocation failure 1 in matrix()");
   nrerror("Too many iterations in brent");    m += NR_END;
   *xmin=x;    m -= nrl;
   return fx;  
 }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 /****************** mnbrak ***********************/    m[nrl] += NR_END;
     m[nrl] -= ncl;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 {    return m;
   double ulim,u,r,q, dum;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   double fu;     */
    }
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  /*************************free matrix ************************/
   if (*fb > *fa) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     SHFT(dum,*ax,*bx,dum)  {
       SHFT(dum,*fb,*fa,dum)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       }    free((FREE_ARG)(m+nrl-NR_END));
   *cx=(*bx)+GOLD*(*bx-*ax);  }
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  /******************* ma3x *******************************/
     r=(*bx-*ax)*(*fb-*fc);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     q=(*bx-*cx)*(*fb-*fa);  {
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    double ***m;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       fu=(*func)(u);    if (!m) nrerror("allocation failure 1 in matrix()");
     } else if ((*cx-u)*(u-ulim) > 0.0) {    m += NR_END;
       fu=(*func)(u);    m -= nrl;
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
           SHFT(*fb,*fc,fu,(*func)(u))    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
           }    m[nrl] += NR_END;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    m[nrl] -= ncl;
       u=ulim;  
       fu=(*func)(u);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       fu=(*func)(u);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     }    m[nrl][ncl] += NR_END;
     SHFT(*ax,*bx,*cx,u)    m[nrl][ncl] -= nll;
       SHFT(*fa,*fb,*fc,fu)    for (j=ncl+1; j<=nch; j++) 
       }      m[nrl][j]=m[nrl][j-1]+nlay;
 }    
     for (i=nrl+1; i<=nrh; i++) {
 /*************** linmin ************************/      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
 int ncom;        m[i][j]=m[i][j-1]+nlay;
 double *pcom,*xicom;    }
 double (*nrfunc)(double []);    return m; 
      /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 {    */
   double brent(double ax, double bx, double cx,  }
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  /*************************free ma3x ************************/
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
               double *fc, double (*func)(double));  {
   int j;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double xx,xmin,bx,ax;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double fx,fb,fa;    free((FREE_ARG)(m+nrl-NR_END));
    }
   ncom=n;  
   pcom=vector(1,n);  /***************** f1dim *************************/
   xicom=vector(1,n);  extern int ncom; 
   nrfunc=func;  extern double *pcom,*xicom;
   for (j=1;j<=n;j++) {  extern double (*nrfunc)(double []); 
     pcom[j]=p[j];   
     xicom[j]=xi[j];  double f1dim(double x) 
   }  { 
   ax=0.0;    int j; 
   xx=1.0;    double f;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double *xt; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);   
 #ifdef DEBUG    xt=vector(1,ncom); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 #endif    f=(*nrfunc)(xt); 
   for (j=1;j<=n;j++) {    free_vector(xt,1,ncom); 
     xi[j] *= xmin;    return f; 
     p[j] += xi[j];  } 
   }  
   free_vector(xicom,1,n);  /*****************brent *************************/
   free_vector(pcom,1,n);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 }  { 
     int iter; 
 /*************** powell ************************/    double a,b,d,etemp;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    double fu,fv,fw,fx;
             double (*func)(double []))    double ftemp;
 {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   void linmin(double p[], double xi[], int n, double *fret,    double e=0.0; 
               double (*func)(double []));   
   int i,ibig,j;    a=(ax < cx ? ax : cx); 
   double del,t,*pt,*ptt,*xit;    b=(ax > cx ? ax : cx); 
   double fp,fptt;    x=w=v=bx; 
   double *xits;    fw=fv=fx=(*f)(x); 
   pt=vector(1,n);    for (iter=1;iter<=ITMAX;iter++) { 
   ptt=vector(1,n);      xm=0.5*(a+b); 
   xit=vector(1,n);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   xits=vector(1,n);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   *fret=(*func)(p);      printf(".");fflush(stdout);
   for (j=1;j<=n;j++) pt[j]=p[j];      fprintf(ficlog,".");fflush(ficlog);
   for (*iter=1;;++(*iter)) {  #ifdef DEBUG
     fp=(*fret);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     ibig=0;      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);
     del=0.0;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #endif
     for (i=1;i<=n;i++)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       printf(" %d %.12f",i, p[i]);        *xmin=x; 
     printf("\n");        return fx; 
     for (i=1;i<=n;i++) {      } 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      ftemp=fu;
       fptt=(*fret);      if (fabs(e) > tol1) { 
 #ifdef DEBUG        r=(x-w)*(fx-fv); 
       printf("fret=%lf \n",*fret);        q=(x-v)*(fx-fw); 
 #endif        p=(x-v)*q-(x-w)*r; 
       printf("%d",i);fflush(stdout);        q=2.0*(q-r); 
       linmin(p,xit,n,fret,func);        if (q > 0.0) p = -p; 
       if (fabs(fptt-(*fret)) > del) {        q=fabs(q); 
         del=fabs(fptt-(*fret));        etemp=e; 
         ibig=i;        e=d; 
       }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 #ifdef DEBUG          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       printf("%d %.12e",i,(*fret));        else { 
       for (j=1;j<=n;j++) {          d=p/q; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);          u=x+d; 
         printf(" x(%d)=%.12e",j,xit[j]);          if (u-a < tol2 || b-u < tol2) 
       }            d=SIGN(tol1,xm-x); 
       for(j=1;j<=n;j++)        } 
         printf(" p=%.12e",p[j]);      } else { 
       printf("\n");        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 #endif      } 
     }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      fu=(*f)(u); 
 #ifdef DEBUG      if (fu <= fx) { 
       int k[2],l;        if (u >= x) a=x; else b=x; 
       k[0]=1;        SHFT(v,w,x,u) 
       k[1]=-1;          SHFT(fv,fw,fx,fu) 
       printf("Max: %.12e",(*func)(p));          } else { 
       for (j=1;j<=n;j++)            if (u < x) a=u; else b=u; 
         printf(" %.12e",p[j]);            if (fu <= fw || w == x) { 
       printf("\n");              v=w; 
       for(l=0;l<=1;l++) {              w=u; 
         for (j=1;j<=n;j++) {              fv=fw; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];              fw=fu; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);            } else if (fu <= fv || v == x || v == w) { 
         }              v=u; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));              fv=fu; 
       }            } 
 #endif          } 
     } 
     nrerror("Too many iterations in brent"); 
       free_vector(xit,1,n);    *xmin=x; 
       free_vector(xits,1,n);    return fx; 
       free_vector(ptt,1,n);  } 
       free_vector(pt,1,n);  
       return;  /****************** mnbrak ***********************/
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     for (j=1;j<=n;j++) {              double (*func)(double)) 
       ptt[j]=2.0*p[j]-pt[j];  { 
       xit[j]=p[j]-pt[j];    double ulim,u,r,q, dum;
       pt[j]=p[j];    double fu; 
     }   
     fptt=(*func)(ptt);    *fa=(*func)(*ax); 
     if (fptt < fp) {    *fb=(*func)(*bx); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    if (*fb > *fa) { 
       if (t < 0.0) {      SHFT(dum,*ax,*bx,dum) 
         linmin(p,xit,n,fret,func);        SHFT(dum,*fb,*fa,dum) 
         for (j=1;j<=n;j++) {        } 
           xi[j][ibig]=xi[j][n];    *cx=(*bx)+GOLD*(*bx-*ax); 
           xi[j][n]=xit[j];    *fc=(*func)(*cx); 
         }    while (*fb > *fc) { 
 #ifdef DEBUG      r=(*bx-*ax)*(*fb-*fc); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      q=(*bx-*cx)*(*fb-*fa); 
         for(j=1;j<=n;j++)      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
           printf(" %.12e",xit[j]);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
         printf("\n");      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 #endif      if ((*bx-u)*(u-*cx) > 0.0) { 
       }        fu=(*func)(u); 
     }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   }        fu=(*func)(u); 
 }        if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 /**** Prevalence limit ****************/            SHFT(*fb,*fc,fu,(*func)(u)) 
             } 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 {        u=ulim; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        fu=(*func)(u); 
      matrix by transitions matrix until convergence is reached */      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
   int i, ii,j,k;        fu=(*func)(u); 
   double min, max, maxmin, maxmax,sumnew=0.;      } 
   double **matprod2();      SHFT(*ax,*bx,*cx,u) 
   double **out, cov[NCOVMAX], **pmij();        SHFT(*fa,*fb,*fc,fu) 
   double **newm;        } 
   double agefin, delaymax=50 ; /* Max number of years to converge */  } 
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  /*************** linmin ************************/
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int ncom; 
     }  double *pcom,*xicom;
   double (*nrfunc)(double []); 
    cov[1]=1.;   
    void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    double brent(double ax, double bx, double cx, 
     newm=savm;                 double (*f)(double), double tol, double *xmin); 
     /* Covariates have to be included here again */    double f1dim(double x); 
      cov[2]=agefin;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                  double *fc, double (*func)(double)); 
       for (k=1; k<=cptcovn;k++) {    int j; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    double xx,xmin,bx,ax; 
         /*      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]]);*/    double fx,fb,fa;
       }   
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    ncom=n; 
       for (k=1; k<=cptcovprod;k++)    pcom=vector(1,n); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    xicom=vector(1,n); 
     nrfunc=func; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    for (j=1;j<=n;j++) { 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      pcom[j]=p[j]; 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      xicom[j]=xi[j]; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    } 
     ax=0.0; 
     savm=oldm;    xx=1.0; 
     oldm=newm;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     maxmax=0.;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     for(j=1;j<=nlstate;j++){  #ifdef DEBUG
       min=1.;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       max=0.;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for(i=1; i<=nlstate; i++) {  #endif
         sumnew=0;    for (j=1;j<=n;j++) { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      xi[j] *= xmin; 
         prlim[i][j]= newm[i][j]/(1-sumnew);      p[j] += xi[j]; 
         max=FMAX(max,prlim[i][j]);    } 
         min=FMIN(min,prlim[i][j]);    free_vector(xicom,1,n); 
       }    free_vector(pcom,1,n); 
       maxmin=max-min;  } 
       maxmax=FMAX(maxmax,maxmin);  
     }  /*************** powell ************************/
     if(maxmax < ftolpl){  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       return prlim;              double (*func)(double [])) 
     }  { 
   }    void linmin(double p[], double xi[], int n, double *fret, 
 }                double (*func)(double [])); 
     int i,ibig,j; 
 /*************** transition probabilities ***************/    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    double *xits;
 {    pt=vector(1,n); 
   double s1, s2;    ptt=vector(1,n); 
   /*double t34;*/    xit=vector(1,n); 
   int i,j,j1, nc, ii, jj;    xits=vector(1,n); 
     *fret=(*func)(p); 
     for(i=1; i<= nlstate; i++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for(j=1; j<i;j++){    for (*iter=1;;++(*iter)) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      fp=(*fret); 
         /*s2 += param[i][j][nc]*cov[nc];*/      ibig=0; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      del=0.0; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       ps[i][j]=s2;      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
     for(j=i+1; j<=nlstate+ndeath;j++){        fprintf(ficlog," %d %.12lf",i, p[i]);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        fprintf(ficrespow," %.12lf", p[i]);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      }
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      printf("\n");
       }      fprintf(ficlog,"\n");
       ps[i][j]=s2;      fprintf(ficrespow,"\n");
     }      for (i=1;i<=n;i++) { 
   }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     /*ps[3][2]=1;*/        fptt=(*fret); 
   #ifdef DEBUG
   for(i=1; i<= nlstate; i++){        printf("fret=%lf \n",*fret);
      s1=0;        fprintf(ficlog,"fret=%lf \n",*fret);
     for(j=1; j<i; j++)  #endif
       s1+=exp(ps[i][j]);        printf("%d",i);fflush(stdout);
     for(j=i+1; j<=nlstate+ndeath; j++)        fprintf(ficlog,"%d",i);fflush(ficlog);
       s1+=exp(ps[i][j]);        linmin(p,xit,n,fret,func); 
     ps[i][i]=1./(s1+1.);        if (fabs(fptt-(*fret)) > del) { 
     for(j=1; j<i; j++)          del=fabs(fptt-(*fret)); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];          ibig=i; 
     for(j=i+1; j<=nlstate+ndeath; j++)        } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #ifdef DEBUG
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        printf("%d %.12e",i,(*fret));
   } /* end i */        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for(jj=1; jj<= nlstate+ndeath; jj++){          printf(" x(%d)=%.12e",j,xit[j]);
       ps[ii][jj]=0;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       ps[ii][ii]=1;        }
     }        for(j=1;j<=n;j++) {
   }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
         }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        printf("\n");
     for(jj=1; jj<= nlstate+ndeath; jj++){        fprintf(ficlog,"\n");
      printf("%lf ",ps[ii][jj]);  #endif
    }      } 
     printf("\n ");      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
     printf("\n ");printf("%lf ",cov[2]);*/        int k[2],l;
 /*        k[0]=1;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        k[1]=-1;
   goto end;*/        printf("Max: %.12e",(*func)(p));
     return ps;        fprintf(ficlog,"Max: %.12e",(*func)(p));
 }        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
 /**************** Product of 2 matrices ******************/          fprintf(ficlog," %.12e",p[j]);
         }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        printf("\n");
 {        fprintf(ficlog,"\n");
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        for(l=0;l<=1;l++) {
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          for (j=1;j<=n;j++) {
   /* in, b, out are matrice of pointers which should have been initialized            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
      before: only the contents of out is modified. The function returns            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
      a pointer to pointers identical to out */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   long i, j, k;          }
   for(i=nrl; i<= nrh; i++)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(k=ncolol; k<=ncoloh; k++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        }
         out[i][k] +=in[i][j]*b[j][k];  #endif
   
   return out;  
 }        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
 /************* Higher Matrix Product ***************/        free_vector(pt,1,n); 
         return; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      } 
 {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      for (j=1;j<=n;j++) { 
      duration (i.e. until        ptt[j]=2.0*p[j]-pt[j]; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        xit[j]=p[j]-pt[j]; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        pt[j]=p[j]; 
      (typically every 2 years instead of every month which is too big).      } 
      Model is determined by parameters x and covariates have to be      fptt=(*func)(ptt); 
      included manually here.      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); 
   int i, j, d, h, k;          for (j=1;j<=n;j++) { 
   double **out, cov[NCOVMAX];            xi[j][ibig]=xi[j][n]; 
   double **newm;            xi[j][n]=xit[j]; 
           }
   /* Hstepm could be zero and should return the unit matrix */  #ifdef DEBUG
   for (i=1;i<=nlstate+ndeath;i++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for (j=1;j<=nlstate+ndeath;j++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       oldm[i][j]=(i==j ? 1.0 : 0.0);          for(j=1;j<=n;j++){
       po[i][j][0]=(i==j ? 1.0 : 0.0);            printf(" %.12e",xit[j]);
     }            fprintf(ficlog," %.12e",xit[j]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          }
   for(h=1; h <=nhstepm; h++){          printf("\n");
     for(d=1; d <=hstepm; d++){          fprintf(ficlog,"\n");
       newm=savm;  #endif
       /* Covariates have to be included here again */        }
       cov[1]=1.;      } 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    } 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  } 
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /**** Prevalence limit (stable prevalence)  ****************/
       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]]];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/       matrix by transitions matrix until convergence is reached */
       /*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,    int i, ii,j,k;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    double min, max, maxmin, maxmax,sumnew=0.;
       savm=oldm;    double **matprod2();
       oldm=newm;    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
     for(i=1; i<=nlstate+ndeath; i++)    double agefin, delaymax=50 ; /* Max number of years to converge */
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];    for (ii=1;ii<=nlstate+ndeath;ii++)
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      for (j=1;j<=nlstate+ndeath;j++){
          */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }      }
   } /* end h */  
   return po;     cov[1]=1.;
 }   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 /*************** log-likelihood *************/      newm=savm;
 double func( double *x)      /* Covariates have to be included here again */
 {       cov[2]=agefin;
   int i, ii, j, k, mi, d, kk;    
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        for (k=1; k<=cptcovn;k++) {
   double **out;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double sw; /* Sum of weights */          /*      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]]);*/
   double lli; /* Individual log likelihood */        }
   long ipmx;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /*extern weight */        for (k=1; k<=cptcovprod;k++)
   /* We are differentiating ll according to initial status */          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++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     printf(" %d\n",s[4][i]);        /*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]);*/
   cov[1]=1.;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;      savm=oldm;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      oldm=newm;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      maxmax=0.;
     for(mi=1; mi<= wav[i]-1; mi++){      for(j=1;j<=nlstate;j++){
       for (ii=1;ii<=nlstate+ndeath;ii++)        min=1.;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        max=0.;
       for(d=0; d<dh[mi][i]; d++){        for(i=1; i<=nlstate; i++) {
         newm=savm;          sumnew=0;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         for (kk=1; kk<=cptcovage;kk++) {          prlim[i][j]= newm[i][j]/(1-sumnew);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          max=FMAX(max,prlim[i][j]);
         }          min=FMIN(min,prlim[i][j]);
                }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        maxmin=max-min;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        maxmax=FMAX(maxmax,maxmin);
         savm=oldm;      }
         oldm=newm;      if(maxmax < ftolpl){
                return prlim;
              }
       } /* end mult */    }
        }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  /*************** transition probabilities ***************/ 
       ipmx +=1;  
       sw += weight[i];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  {
     } /* end of wave */    double s1, s2;
   } /* end of individual */    /*double t34;*/
     int i,j,j1, nc, ii, jj;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      for(i=1; i<= nlstate; i++){
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      for(j=1; j<i;j++){
   return -l;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 }          /*s2 += param[i][j][nc]*cov[nc];*/
           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 /*********** Maximum Likelihood Estimation ***************/        }
         ps[i][j]=s2;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 {      }
   int i,j, iter;      for(j=i+1; j<=nlstate+ndeath;j++){
   double **xi,*delti;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double fret;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   xi=matrix(1,npar,1,npar);          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   for (i=1;i<=npar;i++)        }
     for (j=1;j<=npar;j++)        ps[i][j]=s2;
       xi[i][j]=(i==j ? 1.0 : 0.0);      }
   printf("Powell\n");    }
   powell(p,xi,npar,ftol,&iter,&fret,func);      /*ps[3][2]=1;*/
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    for(i=1; i<= nlstate; i++){
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));       s1=0;
       for(j=1; j<i; j++)
 }        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
 /**** Computes Hessian and covariance matrix ***/        s1+=exp(ps[i][j]);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      ps[i][i]=1./(s1+1.);
 {      for(j=1; j<i; j++)
   double  **a,**y,*x,pd;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   double **hess;      for(j=i+1; j<=nlstate+ndeath; j++)
   int i, j,jk;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   int *indx;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     } /* end i */
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   void lubksb(double **a, int npar, int *indx, double b[]) ;      for(jj=1; jj<= nlstate+ndeath; jj++){
   void ludcmp(double **a, int npar, int *indx, double *d) ;        ps[ii][jj]=0;
         ps[ii][ii]=1;
   hess=matrix(1,npar,1,npar);      }
     }
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     hess[i][i]=hessii(p,ftolhess,i,delti);      for(jj=1; jj<= nlstate+ndeath; jj++){
     /*printf(" %f ",p[i]);*/       printf("%lf ",ps[ii][jj]);
     /*printf(" %lf ",hess[i][i]);*/     }
   }      printf("\n ");
        }
   for (i=1;i<=npar;i++) {      printf("\n ");printf("%lf ",cov[2]);*/
     for (j=1;j<=npar;j++)  {  /*
       if (j>i) {    for(i=1; i<= npar; i++) printf("%f ",x[i]);
         printf(".%d%d",i,j);fflush(stdout);    goto end;*/
         hess[i][j]=hessij(p,delti,i,j);      return ps;
         hess[j][i]=hess[i][j];      }
         /*printf(" %lf ",hess[i][j]);*/  
       }  /**************** Product of 2 matrices ******************/
     }  
   }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   printf("\n");  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      /* in, b, out are matrice of pointers which should have been initialized 
   a=matrix(1,npar,1,npar);       before: only the contents of out is modified. The function returns
   y=matrix(1,npar,1,npar);       a pointer to pointers identical to out */
   x=vector(1,npar);    long i, j, k;
   indx=ivector(1,npar);    for(i=nrl; i<= nrh; i++)
   for (i=1;i<=npar;i++)      for(k=ncolol; k<=ncoloh; k++)
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   ludcmp(a,npar,indx,&pd);          out[i][k] +=in[i][j]*b[j][k];
   
   for (j=1;j<=npar;j++) {    return out;
     for (i=1;i<=npar;i++) x[i]=0;  }
     x[j]=1;  
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  /************* Higher Matrix Product ***************/
       matcov[i][j]=x[i];  
     }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   }  {
     /* Computes the transition matrix starting at age 'age' over 
   printf("\n#Hessian matrix#\n");       'nhstepm*hstepm*stepm' months (i.e. until
   for (i=1;i<=npar;i++) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     for (j=1;j<=npar;j++) {       nhstepm*hstepm matrices. 
       printf("%.3e ",hess[i][j]);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     }       (typically every 2 years instead of every month which is too big 
     printf("\n");       for the memory).
   }       Model is determined by parameters x and covariates have to be 
        included manually here. 
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)       */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
   /*  printf("\n#Hessian matrix recomputed#\n");    double **newm;
   
   for (j=1;j<=npar;j++) {    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=npar;i++) x[i]=0;    for (i=1;i<=nlstate+ndeath;i++)
     x[j]=1;      for (j=1;j<=nlstate+ndeath;j++){
     lubksb(a,npar,indx,x);        oldm[i][j]=(i==j ? 1.0 : 0.0);
     for (i=1;i<=npar;i++){        po[i][j][0]=(i==j ? 1.0 : 0.0);
       y[i][j]=x[i];      }
       printf("%.3e ",y[i][j]);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    for(h=1; h <=nhstepm; h++){
     printf("\n");      for(d=1; d <=hstepm; d++){
   }        newm=savm;
   */        /* Covariates have to be included here again */
         cov[1]=1.;
   free_matrix(a,1,npar,1,npar);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   free_matrix(y,1,npar,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   free_vector(x,1,npar);        for (k=1; k<=cptcovage;k++)
   free_ivector(indx,1,npar);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   free_matrix(hess,1,npar,1,npar);        for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
 }  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 /*************** hessian matrix ****************/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 double hessii( double x[], double delta, int theta, double delti[])        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i;        savm=oldm;
   int l=1, lmax=20;        oldm=newm;
   double k1,k2;      }
   double p2[NPARMAX+1];      for(i=1; i<=nlstate+ndeath; i++)
   double res;        for(j=1;j<=nlstate+ndeath;j++) {
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          po[i][j][h]=newm[i][j];
   double fx;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   int k=0,kmax=10;           */
   double l1;        }
     } /* end h */
   fx=func(x);    return po;
   for (i=1;i<=npar;i++) p2[i]=x[i];  }
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);  
     delts=delt;  /*************** log-likelihood *************/
     for(k=1 ; k <kmax; k=k+1){  double func( double *x)
       delt = delta*(l1*k);  {
       p2[theta]=x[theta] +delt;    int i, ii, j, k, mi, d, kk;
       k1=func(p2)-fx;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       p2[theta]=x[theta]-delt;    double **out;
       k2=func(p2)-fx;    double sw; /* Sum of weights */
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double lli; /* Individual log likelihood */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    int s1, s2;
          double bbh, survp;
 #ifdef DEBUG    long ipmx;
       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);    /*extern weight */
 #endif    /* We are differentiating ll according to initial status */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    /*for(i=1;i<imx;i++) 
         k=kmax;      printf(" %d\n",s[4][i]);
       }    */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    cov[1]=1.;
         k=kmax; l=lmax*10.;  
       }    for(k=1; k<=nlstate; k++) ll[k]=0.;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;    if(mle==1){
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   delti[theta]=delts;          for (ii=1;ii<=nlstate+ndeath;ii++)
   return res;            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);
             }
 double hessij( double x[], double delti[], int thetai,int thetaj)          for(d=0; d<dh[mi][i]; d++){
 {            newm=savm;
   int i;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int l=1, l1, lmax=20;            for (kk=1; kk<=cptcovage;kk++) {
   double k1,k2,k3,k4,res,fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double p2[NPARMAX+1];            }
   int k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fx=func(x);            savm=oldm;
   for (k=1; k<=2; k++) {            oldm=newm;
     for (i=1;i<=npar;i++) p2[i]=x[i];          } /* end mult */
     p2[thetai]=x[thetai]+delti[thetai]/k;        
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     k1=func(p2)-fx;          /* But now since version 0.9 we anticipate for bias and large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
     p2[thetai]=x[thetai]+delti[thetai]/k;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * the nearest (and in case of equal distance, to the lowest) interval but now
     k2=func(p2)-fx;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
             * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     p2[thetai]=x[thetai]-delti[thetai]/k;           * probability in order to take into account the bias as a fraction of the way
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     k3=func(p2)-fx;           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
     p2[thetai]=x[thetai]-delti[thetai]/k;           * For stepm > 1 the results are less biased than in previous versions. 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           */
     k4=func(p2)-fx;          s1=s[mw[mi][i]][i];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          s2=s[mw[mi+1][i]][i];
 #ifdef DEBUG          bbh=(double)bh[mi][i]/(double)stepm; 
     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);          /* bias is positive if real duration
 #endif           * is higher than the multiple of stepm and negative otherwise.
   }           */
   return res;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 }          if( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known then the contribution
 /************** Inverse of matrix **************/               to the likelihood is the probability to die between last step unit time and current 
 void ludcmp(double **a, int n, int *indx, double *d)               step unit time, which is also the differences between probability to die before dh 
 {               and probability to die before dh-stepm . 
   int i,imax,j,k;               In version up to 0.92 likelihood was computed
   double big,dum,sum,temp;          as if date of death was unknown. Death was treated as any other
   double *vv;          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
   vv=vector(1,n);          to consider that at each interview the state was recorded
   *d=1.0;          (healthy, disable or death) and IMaCh was corrected; but when we
   for (i=1;i<=n;i++) {          introduced the exact date of death then we should have modified
     big=0.0;          the contribution of an exact death to the likelihood. This new
     for (j=1;j<=n;j++)          contribution is smaller and very dependent of the step unit
       if ((temp=fabs(a[i][j])) > big) big=temp;          stepm. It is no more the probability to die between last interview
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          and month of death but the probability to survive from last
     vv[i]=1.0/big;          interview up to one month before death multiplied by the
   }          probability to die within a month. Thanks to Chris
   for (j=1;j<=n;j++) {          Jackson for correcting this bug.  Former versions increased
     for (i=1;i<j;i++) {          mortality artificially. The bad side is that we add another loop
       sum=a[i][j];          which slows down the processing. The difference can be up to 10%
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          lower mortality.
       a[i][j]=sum;            */
     }            lli=log(out[s1][s2] - savm[s1][s2]);
     big=0.0;          }else{
     for (i=j;i<=n;i++) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       sum=a[i][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 */
       for (k=1;k<j;k++)          } 
         sum -= a[i][k]*a[k][j];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       a[i][j]=sum;          /*if(lli ==000.0)*/
       if ( (dum=vv[i]*fabs(sum)) >= big) {          /*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); */
         big=dum;          ipmx +=1;
         imax=i;          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     if (j != imax) {      } /* end of individual */
       for (k=1;k<=n;k++) {    }  else if(mle==2){
         dum=a[imax][k];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         a[imax][k]=a[j][k];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         a[j][k]=dum;        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
       *d = -(*d);            for (j=1;j<=nlstate+ndeath;j++){
       vv[imax]=vv[j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     indx[j]=imax;            }
     if (a[j][j] == 0.0) a[j][j]=TINY;          for(d=0; d<=dh[mi][i]; d++){
     if (j != n) {            newm=savm;
       dum=1.0/(a[j][j]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   free_vector(vv,1,n);  /* Doesn't work */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 void lubksb(double **a, int n, int *indx, double b[])          } /* end mult */
 {        
   int i,ii=0,ip,j;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double sum;          /* But now since version 0.9 we anticipate for bias and large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
   for (i=1;i<=n;i++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
     ip=indx[i];           * the nearest (and in case of equal distance, to the lowest) interval but now
     sum=b[ip];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     b[ip]=b[i];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     if (ii)           * probability in order to take into account the bias as a fraction of the way
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     else if (sum) ii=i;           * -stepm/2 to stepm/2 .
     b[i]=sum;           * For stepm=1 the results are the same as for previous versions of Imach.
   }           * For stepm > 1 the results are less biased than in previous versions. 
   for (i=n;i>=1;i--) {           */
     sum=b[i];          s1=s[mw[mi][i]][i];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          s2=s[mw[mi+1][i]][i];
     b[i]=sum/a[i][i];          bbh=(double)bh[mi][i]/(double)stepm; 
   }          /* bias is positive if real duration
 }           * is higher than the multiple of stepm and negative otherwise.
            */
 /************ 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 */
 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)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 {  /* Some frequencies */          /*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 */
            /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          /*if(lli ==000.0)*/
   double ***freq; /* Frequencies */          /*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); */
   double *pp;          ipmx +=1;
   double pos, k2, dateintsum=0,k2cpt=0;          sw += weight[i];
   FILE *ficresp;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char fileresp[FILENAMELENGTH];        } /* end of wave */
        } /* end of individual */
   pp=vector(1,nlstate);    }  else if(mle==3){  /* exponential inter-extrapolation */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcpy(fileresp,"p");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   strcat(fileresp,fileres);        for(mi=1; mi<= wav[i]-1; mi++){
   if((ficresp=fopen(fileresp,"w"))==NULL) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("Problem with prevalence resultfile: %s\n", fileresp);            for (j=1;j<=nlstate+ndeath;j++){
     exit(0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            }
   j1=0;          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   j=cptcoveff;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(k1=1; k1<=j;k1++){            }
     for(i1=1; i1<=ncodemax[k1];i1++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       j1++;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            savm=oldm;
         scanf("%d", i);*/            oldm=newm;
       for (i=-1; i<=nlstate+ndeath; i++)            } /* end mult */
         for (jk=-1; jk<=nlstate+ndeath; jk++)          
           for(m=agemin; m <= agemax+3; m++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
             freq[i][jk][m]=0;          /* But now since version 0.9 we anticipate for bias and large stepm.
                 * If stepm is larger than one month (smallest stepm) and if the exact delay 
       dateintsum=0;           * (in months) between two waves is not a multiple of stepm, we rounded to 
       k2cpt=0;           * the nearest (and in case of equal distance, to the lowest) interval but now
       for (i=1; i<=imx; i++) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         bool=1;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         if  (cptcovn>0) {           * probability in order to take into account the bias as a fraction of the way
           for (z1=1; z1<=cptcoveff; z1++)           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           * -stepm/2 to stepm/2 .
               bool=0;           * For stepm=1 the results are the same as for previous versions of Imach.
         }           * For stepm > 1 the results are less biased than in previous versions. 
         if (bool==1) {           */
           for(m=firstpass; m<=lastpass; m++){          s1=s[mw[mi][i]][i];
             k2=anint[m][i]+(mint[m][i]/12.);          s2=s[mw[mi+1][i]][i];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          bbh=(double)bh[mi][i]/(double)stepm; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;          /* bias is positive if real duration
               if(agev[m][i]==1) agev[m][i]=agemax+2;           * is higher than the multiple of stepm and negative otherwise.
               if (m<lastpass) {           */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[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 */
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
               }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                        /*if(lli ==000.0)*/
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          /*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); */
                 dateintsum=dateintsum+k2;          ipmx +=1;
                 k2cpt++;          sw += weight[i];
               }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             }        } /* end of wave */
           }      } /* end of individual */
         }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
       if  (cptcovn>0) {            for (j=1;j<=nlstate+ndeath;j++){
         fprintf(ficresp, "\n#********** Variable ");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficresp, "**********\n#");            }
       }          for(d=0; d<dh[mi][i]; d++){
       for(i=1; i<=nlstate;i++)            newm=savm;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       fprintf(ficresp, "\n");            for (kk=1; kk<=cptcovage;kk++) {
                    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(i=(int)agemin; i <= (int)agemax+3; i++){            }
         if(i==(int)agemax+3)          
           printf("Total");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           printf("Age %d", i);            savm=oldm;
         for(jk=1; jk <=nlstate ; jk++){            oldm=newm;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          } /* end mult */
             pp[jk] += freq[jk][m][i];        
         }          s1=s[mw[mi][i]][i];
         for(jk=1; jk <=nlstate ; jk++){          s2=s[mw[mi+1][i]][i];
           for(m=-1, pos=0; m <=0 ; m++)          if( s2 > nlstate){ 
             pos += freq[jk][m][i];            lli=log(out[s1][s2] - savm[s1][s2]);
           if(pp[jk]>=1.e-10)          }else{
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           else          }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          ipmx +=1;
         }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(jk=1; jk <=nlstate ; jk++){  /*      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]); */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        } /* end of wave */
             pp[jk] += freq[jk][m][i];      } /* end of individual */
         }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(jk=1,pos=0; jk <=nlstate ; jk++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           pos += pp[jk];        for(mi=1; mi<= wav[i]-1; mi++){
         for(jk=1; jk <=nlstate ; jk++){          for (ii=1;ii<=nlstate+ndeath;ii++)
           if(pos>=1.e-5)            for (j=1;j<=nlstate+ndeath;j++){
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            }
           if( i <= (int) agemax){          for(d=0; d<dh[mi][i]; d++){
             if(pos>=1.e-5){            newm=savm;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               probs[i][jk][j1]= pp[jk]/pos;            for (kk=1; kk<=cptcovage;kk++) {
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }            }
             else          
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
                    oldm=newm;
         for(jk=-1; jk <=nlstate+ndeath; jk++)          } /* end mult */
           for(m=-1; m <=nlstate+ndeath; m++)        
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          s1=s[mw[mi][i]][i];
         if(i <= (int) agemax)          s2=s[mw[mi+1][i]][i];
           fprintf(ficresp,"\n");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         printf("\n");          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 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]);*/
   dateintmean=dateintsum/k2cpt;        } /* end of wave */
        } /* end of individual */
   fclose(ficresp);    } /* End of if */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   free_vector(pp,1,nlstate);    /* 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 */
   /* End of Freq */    return -l;
 }  }
   
 /************ Prevalence ********************/  /*************** log-likelihood *************/
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  double funcone( double *x)
 {  /* Some frequencies */  {
      /* Same as likeli but slower because of a lot of printf and if */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int i, ii, j, k, mi, d, kk;
   double ***freq; /* Frequencies */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double *pp;    double **out;
   double pos, k2;    double lli; /* Individual log likelihood */
     double llt;
   pp=vector(1,nlstate);    int s1, s2;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    double bbh, survp;
      /*extern weight */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    /* We are differentiating ll according to initial status */
   j1=0;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      /*for(i=1;i<imx;i++) 
   j=cptcoveff;      printf(" %d\n",s[4][i]);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    */
      cov[1]=1.;
  for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
       j1++;  
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (i=-1; i<=nlstate+ndeath; i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for (jk=-1; jk<=nlstate+ndeath; jk++)        for(mi=1; mi<= wav[i]-1; mi++){
           for(m=agemin; m <= agemax+3; m++)        for (ii=1;ii<=nlstate+ndeath;ii++)
             freq[i][jk][m]=0;          for (j=1;j<=nlstate+ndeath;j++){
                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (i=1; i<=imx; i++) {            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         bool=1;          }
         if  (cptcovn>0) {        for(d=0; d<dh[mi][i]; d++){
           for (z1=1; z1<=cptcoveff; z1++)          newm=savm;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               bool=0;          for (kk=1; kk<=cptcovage;kk++) {
         }            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         if (bool==1) {          }
           for(m=firstpass; m<=lastpass; m++){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             k2=anint[m][i]+(mint[m][i]/12.);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          savm=oldm;
               if(agev[m][i]==0) agev[m][i]=agemax+1;          oldm=newm;
               if(agev[m][i]==1) agev[m][i]=agemax+2;        } /* end mult */
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */        s1=s[mw[mi][i]][i];
             }        s2=s[mw[mi+1][i]][i];
           }        bbh=(double)bh[mi][i]/(double)stepm; 
         }        /* bias is positive if real duration
       }         * is higher than the multiple of stepm and negative otherwise.
         for(i=(int)agemin; i <= (int)agemax+3; i++){         */
           for(jk=1; jk <=nlstate ; jk++){        if( s2 > nlstate && (mle <5) ){  /* Jackson */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          lli=log(out[s1][s2] - savm[s1][s2]);
               pp[jk] += freq[jk][m][i];        } else if (mle==1){
           }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           for(jk=1; jk <=nlstate ; jk++){        } else if(mle==2){
             for(m=-1, pos=0; m <=0 ; m++)          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 */
             pos += freq[jk][m][i];        } else if(mle==3){  /* exponential inter-extrapolation */
         }          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 */
                } else if (mle==4){  /* mle=4 no inter-extrapolation */
          for(jk=1; jk <=nlstate ; jk++){          lli=log(out[s1][s2]); /* Original formula */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
              pp[jk] += freq[jk][m][i];          lli=log(out[s1][s2]); /* Original formula */
          }        } /* End of if */
                  ipmx +=1;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          for(jk=1; jk <=nlstate ; jk++){            /*       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( i <= (int) agemax){        if(globpr){
              if(pos>=1.e-5){          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
                probs[i][jk][j1]= pp[jk]/pos;   %10.6f %10.6f %10.6f ", \
              }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
            }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
          }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                      llt +=ll[k]*gipmx/gsw;
         }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     }          }
   }          fprintf(ficresilk," %10.6f\n", -llt);
          }
        } /* end of wave */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    } /* end of individual */
   free_vector(pp,1,nlstate);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 }  /* End of Freq */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
 /************* Waves Concatenation ***************/      gipmx=ipmx;
       gsw=sw;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    }
 {    return -l;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  }
      Death is a valid wave (if date is known).  
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  char *subdirf(char fileres[])
      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.    
      */    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
   int i, mi, m;    strcat(tmpout,fileres);
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    return tmpout;
      double sum=0., jmean=0.;*/  }
   
   int j, k=0,jk, ju, jl;  char *subdirf2(char fileres[], char *preop)
   double sum=0.;  {
   jmin=1e+5;    
   jmax=-1;    strcpy(tmpout,optionfilefiname);
   jmean=0.;    strcat(tmpout,"/");
   for(i=1; i<=imx; i++){    strcat(tmpout,preop);
     mi=0;    strcat(tmpout,fileres);
     m=firstpass;    return tmpout;
     while(s[m][i] <= nlstate){  }
       if(s[m][i]>=1)  char *subdirf3(char fileres[], char *preop, char *preop2)
         mw[++mi][i]=m;  {
       if(m >=lastpass)    
         break;    strcpy(tmpout,optionfilefiname);
       else    strcat(tmpout,"/");
         m++;    strcat(tmpout,preop);
     }/* end while */    strcat(tmpout,preop2);
     if (s[m][i] > nlstate){    strcat(tmpout,fileres);
       mi++;     /* Death is another wave */    return tmpout;
       /* if(mi==0)  never been interviewed correctly before death */  }
          /* Only death is a correct wave */  
       mw[mi][i]=m;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     }  {
     /* This routine should help understanding what is done with 
     wav[i]=mi;       the selection of individuals/waves and
     if(mi==0)       to check the exact contribution to the likelihood.
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);       Plotting could be done.
   }     */
     int k;
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){    if(*globpri !=0){ /* Just counts and sums, no printings */
       if (stepm <=0)      strcpy(fileresilk,"ilk"); 
         dh[mi][i]=1;      strcat(fileresilk,fileres);
       else{      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         if (s[mw[mi+1][i]][i] > nlstate) {        printf("Problem with resultfile: %s\n", fileresilk);
           if (agedc[i] < 2*AGESUP) {        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      }
           if(j==0) j=1;  /* Survives at least one month after exam */      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");
           k=k+1;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
           if (j >= jmax) jmax=j;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
           if (j <= jmin) jmin=j;      for(k=1; k<=nlstate; k++) 
           sum=sum+j;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           }    }
         }  
         else{    *fretone=(*funcone)(p);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    if(*globpri !=0){
           k=k+1;      fclose(ficresilk);
           if (j >= jmax) jmax=j;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           else if (j <= jmin)jmin=j;      fflush(fichtm); 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    } 
           sum=sum+j;    return;
         }  }
         jk= j/stepm;  
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;  /*********** Maximum Likelihood Estimation ***************/
         if(jl <= -ju)  
           dh[mi][i]=jk;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         else  {
           dh[mi][i]=jk+1;    int i,j, iter;
         if(dh[mi][i]==0)    double **xi;
           dh[mi][i]=1; /* At least one step */    double fret;
       }    double fretone; /* Only one call to likelihood */
     }    char filerespow[FILENAMELENGTH];
   }    xi=matrix(1,npar,1,npar);
   jmean=sum/k;    for (i=1;i<=npar;i++)
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      for (j=1;j<=npar;j++)
  }        xi[i][j]=(i==j ? 1.0 : 0.0);
 /*********** Tricode ****************************/    printf("Powell\n");  fprintf(ficlog,"Powell\n");
 void tricode(int *Tvar, int **nbcode, int imx)    strcpy(filerespow,"pow"); 
 {    strcat(filerespow,fileres);
   int Ndum[20],ij=1, k, j, i;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   int cptcode=0;      printf("Problem with resultfile: %s\n", filerespow);
   cptcoveff=0;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      }
   for (k=0; k<19; k++) Ndum[k]=0;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   for (k=1; k<=7; k++) ncodemax[k]=0;    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     for (i=1; i<=imx; i++) {    fprintf(ficrespow,"\n");
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;    powell(p,xi,npar,ftol,&iter,&fret,func);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;    fclose(ficrespow);
     }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for (i=0; i<=cptcode; i++) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       if(Ndum[i]!=0) ncodemax[j]++;  
     }  }
     ij=1;  
   /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for (i=1; i<=ncodemax[j]; i++) {  {
       for (k=0; k<=19; k++) {    double  **a,**y,*x,pd;
         if (Ndum[k] != 0) {    double **hess;
           nbcode[Tvar[j]][ij]=k;    int i, j,jk;
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/    int *indx;
           ij++;  
         }    double hessii(double p[], double delta, int theta, double delti[]);
         if (ij > ncodemax[j]) break;    double hessij(double p[], double delti[], int i, int j);
       }      void lubksb(double **a, int npar, int *indx, double b[]) ;
     }    void ludcmp(double **a, int npar, int *indx, double *d) ;
   }    
     hess=matrix(1,npar,1,npar);
  for (k=0; k<19; k++) Ndum[k]=0;  
     printf("\nCalculation of the hessian matrix. Wait...\n");
  for (i=1; i<=ncovmodel-2; i++) {    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       ij=Tvar[i];    for (i=1;i<=npar;i++){
       Ndum[ij]++;      printf("%d",i);fflush(stdout);
     }      fprintf(ficlog,"%d",i);fflush(ficlog);
       hess[i][i]=hessii(p,ftolhess,i,delti);
  ij=1;      /*printf(" %f ",p[i]);*/
  for (i=1; i<=10; i++) {      /*printf(" %lf ",hess[i][i]);*/
    if((Ndum[i]!=0) && (i<=ncovcol)){    }
      Tvaraff[ij]=i;    
      ij++;    for (i=1;i<=npar;i++) {
    }      for (j=1;j<=npar;j++)  {
  }        if (j>i) { 
            printf(".%d%d",i,j);fflush(stdout);
     cptcoveff=ij-1;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 }          hess[i][j]=hessij(p,delti,i,j);
           hess[j][i]=hess[i][j];    
 /*********** Health Expectancies ****************/          /*printf(" %lf ",hess[i][j]);*/
         }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      }
 {    }
   /* Health expectancies */    printf("\n");
   int i, j, nhstepm, hstepm, h, nstepm, k;    fprintf(ficlog,"\n");
   double age, agelim, hf;  
   double ***p3mat;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
      fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   fprintf(ficreseij,"# Health expectancies\n");    
   fprintf(ficreseij,"# Age");    a=matrix(1,npar,1,npar);
   for(i=1; i<=nlstate;i++)    y=matrix(1,npar,1,npar);
     for(j=1; j<=nlstate;j++)    x=vector(1,npar);
       fprintf(ficreseij," %1d-%1d",i,j);    indx=ivector(1,npar);
   fprintf(ficreseij,"\n");    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   k=1;             /* For example stepm=6 months */    ludcmp(a,npar,indx,&pd);
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */  
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */    for (j=1;j<=npar;j++) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (i=1;i<=npar;i++) x[i]=0;
      nhstepm is the number of hstepm from age to agelim      x[j]=1;
      nstepm is the number of stepm from age to agelin.      lubksb(a,npar,indx,x);
      Look at hpijx to understand the reason of that which relies in memory size      for (i=1;i<=npar;i++){ 
      and note for a fixed period like k years */        matcov[i][j]=x[i];
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      }
      survival function given by stepm (the optimization length). Unfortunately it    }
      means that if the survival funtion is printed only each two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    printf("\n#Hessian matrix#\n");
      results. So we changed our mind and took the option of the best precision.    fprintf(ficlog,"\n#Hessian matrix#\n");
   */    for (i=1;i<=npar;i++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
   agelim=AGESUP;        fprintf(ficlog,"%.3e ",hess[i][j]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     /* nhstepm age range expressed in number of stepm */      printf("\n");
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      fprintf(ficlog,"\n");
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    }
     /* if (stepm >= YEARM) hstepm=1;*/  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    /* Recompute Inverse */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=1;i<=npar;i++)
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    ludcmp(a,npar,indx,&pd);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    /*  printf("\n#Hessian matrix recomputed#\n");
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++)    for (j=1;j<=npar;j++) {
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      for (i=1;i<=npar;i++) x[i]=0;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      x[j]=1;
           /* 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]);*/      lubksb(a,npar,indx,x);
         }      for (i=1;i<=npar;i++){ 
     fprintf(ficreseij,"%3.0f",age );        y[i][j]=x[i];
     for(i=1; i<=nlstate;i++)        printf("%.3e ",y[i][j]);
       for(j=1; j<=nlstate;j++){        fprintf(ficlog,"%.3e ",y[i][j]);
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);      }
       }      printf("\n");
     fprintf(ficreseij,"\n");      fprintf(ficlog,"\n");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
   }    */
 }  
     free_matrix(a,1,npar,1,npar);
 /************ Variance ******************/    free_matrix(y,1,npar,1,npar);
 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)    free_vector(x,1,npar);
 {    free_ivector(indx,1,npar);
   /* Variance of health expectancies */    free_matrix(hess,1,npar,1,npar);
   /*  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, h, nstepm, kk;  
   int k, cptcode;  /*************** hessian matrix ****************/
   double *xp;  double hessii( double x[], double delta, int theta, double delti[])
   double **gp, **gm;  {
   double ***gradg, ***trgradg;    int i;
   double ***p3mat;    int l=1, lmax=20;
   double age,agelim, hf;    double k1,k2;
   int theta;    double p2[NPARMAX+1];
     double res;
    fprintf(ficresvij,"# Covariances of life expectancies\n");    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   fprintf(ficresvij,"# Age");    double fx;
   for(i=1; i<=nlstate;i++)    int k=0,kmax=10;
     for(j=1; j<=nlstate;j++)    double l1;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  
   fprintf(ficresvij,"\n");    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
   xp=vector(1,npar);    for(l=0 ; l <=lmax; l++){
   dnewm=matrix(1,nlstate,1,npar);      l1=pow(10,l);
   doldm=matrix(1,nlstate,1,nlstate);      delts=delt;
        for(k=1 ; k <kmax; k=k+1){
   kk=1;             /* For example stepm=6 months */        delt = delta*(l1*k);
   hstepm=kk*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */        p2[theta]=x[theta] +delt;
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */        k1=func(p2)-fx;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        p2[theta]=x[theta]-delt;
      nhstepm is the number of hstepm from age to agelim        k2=func(p2)-fx;
      nstepm is the number of stepm from age to agelin.        /*res= (k1-2.0*fx+k2)/delt/delt; */
      Look at hpijx to understand the reason of that which relies in memory size        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
      and note for a fixed period like k years */        
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  #ifdef DEBUG
      survival function given by stepm (the optimization length). Unfortunately it        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);
      means that if the survival funtion is printed only each two years of age and if        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);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  #endif
      results. So we changed our mind and took the option of the best precision.        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */          k=kmax;
   agelim = AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          k=kmax; l=lmax*10.;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          delts=delt;
     gp=matrix(0,nhstepm,1,nlstate);        }
     gm=matrix(0,nhstepm,1,nlstate);      }
     }
     for(theta=1; theta <=npar; theta++){    delti[theta]=delts;
       for(i=1; i<=npar; i++){ /* Computes gradient */    return res; 
         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);  double hessij( double x[], double delti[], int thetai,int thetaj)
   {
       if (popbased==1) {    int i;
         for(i=1; i<=nlstate;i++)    int l=1, l1, lmax=20;
           prlim[i][i]=probs[(int)age][i][ij];    double k1,k2,k3,k4,res,fx;
       }    double p2[NPARMAX+1];
      int k;
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    fx=func(x);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    for (k=1; k<=2; k++) {
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      for (i=1;i<=npar;i++) p2[i]=x[i];
         }      p2[thetai]=x[thetai]+delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          k1=func(p2)-fx;
       for(i=1; i<=npar; i++) /* Computes gradient */    
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      p2[thetai]=x[thetai]+delti[thetai]/k;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      k2=func(p2)-fx;
      
       if (popbased==1) {      p2[thetai]=x[thetai]-delti[thetai]/k;
         for(i=1; i<=nlstate;i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           prlim[i][i]=probs[(int)age][i][ij];      k3=func(p2)-fx;
       }    
       p2[thetai]=x[thetai]-delti[thetai]/k;
       for(j=1; j<= nlstate; j++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         for(h=0; h<=nhstepm; h++){      k4=func(p2)-fx;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  #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);
       }      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);
   #endif
       for(j=1; j<= nlstate; j++)    }
         for(h=0; h<=nhstepm; h++){    return res;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  }
         }  
     } /* End theta */  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  { 
     int i,imax,j,k; 
     for(h=0; h<=nhstepm; h++)    double big,dum,sum,temp; 
       for(j=1; j<=nlstate;j++)    double *vv; 
         for(theta=1; theta <=npar; theta++)   
           trgradg[h][j][theta]=gradg[h][theta][j];    vv=vector(1,n); 
     *d=1.0; 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    for (i=1;i<=n;i++) { 
     for(i=1;i<=nlstate;i++)      big=0.0; 
       for(j=1;j<=nlstate;j++)      for (j=1;j<=n;j++) 
         vareij[i][j][(int)age] =0.;        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     for(h=0;h<=nhstepm;h++){      vv[i]=1.0/big; 
       for(k=0;k<=nhstepm;k++){    } 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    for (j=1;j<=n;j++) { 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      for (i=1;i<j;i++) { 
         for(i=1;i<=nlstate;i++)        sum=a[i][j]; 
           for(j=1;j<=nlstate;j++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        a[i][j]=sum; 
       }      } 
     }      big=0.0; 
       for (i=j;i<=n;i++) { 
     fprintf(ficresvij,"%.0f ",age );        sum=a[i][j]; 
     for(i=1; i<=nlstate;i++)        for (k=1;k<j;k++) 
       for(j=1; j<=nlstate;j++){          sum -= a[i][k]*a[k][j]; 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);        a[i][j]=sum; 
       }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     fprintf(ficresvij,"\n");          big=dum; 
     free_matrix(gp,0,nhstepm,1,nlstate);          imax=i; 
     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);      if (j != imax) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1;k<=n;k++) { 
   } /* End age */          dum=a[imax][k]; 
            a[imax][k]=a[j][k]; 
   free_vector(xp,1,npar);          a[j][k]=dum; 
   free_matrix(doldm,1,nlstate,1,npar);        } 
   free_matrix(dnewm,1,nlstate,1,nlstate);        *d = -(*d); 
         vv[imax]=vv[j]; 
 }      } 
       indx[j]=imax; 
 /************ Variance of prevlim ******************/      if (a[j][j] == 0.0) a[j][j]=TINY; 
 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)      if (j != n) { 
 {        dum=1.0/(a[j][j]); 
   /* Variance of prevalence limit */        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      } 
   double **newm;    } 
   double **dnewm,**doldm;    free_vector(vv,1,n);  /* Doesn't work */
   int i, j, nhstepm, hstepm;  ;
   int k, cptcode;  } 
   double *xp;  
   double *gp, *gm;  void lubksb(double **a, int n, int *indx, double b[]) 
   double **gradg, **trgradg;  { 
   double age,agelim;    int i,ii=0,ip,j; 
   int theta;    double sum; 
       
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    for (i=1;i<=n;i++) { 
   fprintf(ficresvpl,"# Age");      ip=indx[i]; 
   for(i=1; i<=nlstate;i++)      sum=b[ip]; 
       fprintf(ficresvpl," %1d-%1d",i,i);      b[ip]=b[i]; 
   fprintf(ficresvpl,"\n");      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   xp=vector(1,npar);      else if (sum) ii=i; 
   dnewm=matrix(1,nlstate,1,npar);      b[i]=sum; 
   doldm=matrix(1,nlstate,1,nlstate);    } 
      for (i=n;i>=1;i--) { 
   hstepm=1*YEARM; /* Every year of age */      sum=b[i]; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   agelim = AGESUP;      b[i]=sum/a[i][i]; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    } 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  } 
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  /************ Frequencies ********************/
     gradg=matrix(1,npar,1,nlstate);  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)
     gp=vector(1,nlstate);  {  /* Some frequencies */
     gm=vector(1,nlstate);    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     for(theta=1; theta <=npar; theta++){    int first;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double ***freq; /* Frequencies */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double *pp, **prop;
       }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    FILE *ficresp;
       for(i=1;i<=nlstate;i++)    char fileresp[FILENAMELENGTH];
         gp[i] = prlim[i][i];    
        pp=vector(1,nlstate);
       for(i=1; i<=npar; i++) /* Computes gradient */    prop=matrix(1,nlstate,iagemin,iagemax+3);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    strcpy(fileresp,"p");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    strcat(fileresp,fileres);
       for(i=1;i<=nlstate;i++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
         gm[i] = prlim[i][i];      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       for(i=1;i<=nlstate;i++)      exit(0);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    }
     } /* End theta */    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
     trgradg =matrix(1,nlstate,1,npar);    
     j=cptcoveff;
     for(j=1; j<=nlstate;j++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];    first=1;
   
     for(i=1;i<=nlstate;i++)    for(k1=1; k1<=j;k1++){
       varpl[i][(int)age] =0.;      for(i1=1; i1<=ncodemax[k1];i1++){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        j1++;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     for(i=1;i<=nlstate;i++)          scanf("%d", i);*/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
     fprintf(ficresvpl,"%.0f ",age );            for(m=iagemin; m <= iagemax+3; m++)
     for(i=1; i<=nlstate;i++)              freq[i][jk][m]=0;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");      for (i=1; i<=nlstate; i++)  
     free_vector(gp,1,nlstate);        for(m=iagemin; m <= iagemax+3; m++)
     free_vector(gm,1,nlstate);          prop[i][m]=0;
     free_matrix(gradg,1,npar,1,nlstate);        
     free_matrix(trgradg,1,nlstate,1,npar);        dateintsum=0;
   } /* End age */        k2cpt=0;
         for (i=1; i<=imx; i++) {
   free_vector(xp,1,npar);          bool=1;
   free_matrix(doldm,1,nlstate,1,npar);          if  (cptcovn>0) {
   free_matrix(dnewm,1,nlstate,1,nlstate);            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 }                bool=0;
           }
 /************ Variance of one-step probabilities  ******************/          if (bool==1){
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)            for(m=firstpass; m<=lastpass; m++){
 {              k2=anint[m][i]+(mint[m][i]/12.);
   int i, j;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   int k=0, cptcode;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   double **dnewm,**doldm;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   double *xp;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   double *gp, *gm;                if (m<lastpass) {
   double **gradg, **trgradg;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   double age,agelim, cov[NCOVMAX];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   int theta;                }
   char fileresprob[FILENAMELENGTH];                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   strcpy(fileresprob,"prob");                  dateintsum=dateintsum+k2;
   strcat(fileresprob,fileres);                  k2cpt++;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {                }
     printf("Problem with resultfile: %s\n", fileresprob);                /*}*/
   }            }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          }
          }
          
   xp=vector(1,npar);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        if  (cptcovn>0) {
            fprintf(ficresp, "\n#********** Variable "); 
   cov[1]=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for (age=bage; age<=fage; age ++){          fprintf(ficresp, "**********\n#");
     cov[2]=age;        }
     gradg=matrix(1,npar,1,9);        for(i=1; i<=nlstate;i++) 
     trgradg=matrix(1,9,1,npar);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        fprintf(ficresp, "\n");
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        
            for(i=iagemin; i <= iagemax+3; i++){
     for(theta=1; theta <=npar; theta++){          if(i==iagemax+3){
       for(i=1; i<=npar; i++)            fprintf(ficlog,"Total");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }else{
                  if(first==1){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              first=0;
                  printf("See log file for details...\n");
       k=0;            }
       for(i=1; i<= (nlstate+ndeath); i++){            fprintf(ficlog,"Age %d", i);
         for(j=1; j<=(nlstate+ndeath);j++){          }
            k=k+1;          for(jk=1; jk <=nlstate ; jk++){
           gp[k]=pmmij[i][j];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         }              pp[jk] += freq[jk][m][i]; 
       }          }
           for(jk=1; jk <=nlstate ; jk++){
       for(i=1; i<=npar; i++)            for(m=-1, pos=0; m <=0 ; m++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              pos += freq[jk][m][i];
                if(pp[jk]>=1.e-10){
               if(first==1){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       k=0;              }
       for(i=1; i<=(nlstate+ndeath); i++){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for(j=1; j<=(nlstate+ndeath);j++){            }else{
           k=k+1;              if(first==1)
           gm[k]=pmmij[i][j];                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       }            }
                }
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            for(jk=1; jk <=nlstate ; jk++){
     }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          }       
       for(theta=1; theta <=npar; theta++)          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       trgradg[j][theta]=gradg[theta][j];            pos += pp[jk];
              posprop += prop[jk][i];
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
      pmij(pmmij,cov,ncovmodel,x,nlstate);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      k=0;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      for(i=1; i<=(nlstate+ndeath); i++){            }else{
        for(j=1; j<=(nlstate+ndeath);j++){              if(first==1)
          k=k+1;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
          gm[k]=pmmij[i][j];              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         }            }
      }            if( i <= iagemax){
                    if(pos>=1.e-5){
      /*printf("\n%d ",(int)age);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){                /*probs[i][jk][j1]= pp[jk]/pos;*/
                        /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              else
      }*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
   fprintf(ficresprob,"\n%d ",(int)age);          }
           
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            for(m=-1; m <=nlstate+ndeath; m++)
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);              if(freq[jk][m][i] !=0 ) {
   }              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));              }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          if(i <= iagemax)
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            fprintf(ficresp,"\n");
 }          if(first==1)
  free_vector(xp,1,npar);            printf("Others in log...\n");
 fclose(ficresprob);          fprintf(ficlog,"\n");
         }
 }      }
     }
 /******************* Printing html file ***********/    dateintmean=dateintsum/k2cpt; 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \   
  int lastpass, int stepm, int weightopt, char model[],\    fclose(ficresp);
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    free_vector(pp,1,nlstate);
  char version[], int popforecast ){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   int jj1, k1, i1, cpt;    /* End of Freq */
   FILE *fichtm;  }
   /*char optionfilehtm[FILENAMELENGTH];*/  
   /************ Prevalence ********************/
   strcpy(optionfilehtm,optionfile);  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)
   strcat(optionfilehtm,".htm");  {  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     printf("Problem with %s \n",optionfilehtm), exit(0);       in each health status at the date of interview (if between dateprev1 and dateprev2).
   }       We still use firstpass and lastpass as another selection.
     */
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %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    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
 \n    double ***freq; /* Frequencies */
 Total number of observations=%d <br>\n    double *pp, **prop;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    double pos,posprop; 
 <hr  size=\"2\" color=\"#EC5E5E\">    double  y2; /* in fractional years */
  <ul><li>Outputs files<br>\n    int iagemin, iagemax;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n  
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    iagemin= (int) agemin;
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    iagemax= (int) agemax;
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    /*pp=vector(1,nlstate);*/
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    prop=matrix(1,nlstate,iagemin,iagemax+3); 
  - Life expectancies by age and initial health status: <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,fileres,fileres);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
  fprintf(fichtm,"\n    
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    j=cptcoveff;
  - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>\n    if (cptcovn<1) {j=1;ncodemax[1]=1;}
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n    
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres);    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
  if(popforecast==1) fprintf(fichtm,"\n        j1++;
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n        
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n        for (i=1; i<=nlstate; i++)  
         <br>",fileres,fileres,fileres,fileres);          for(m=iagemin; m <= iagemax+3; m++)
  else            prop[i][m]=0.0;
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);       
 fprintf(fichtm," <li>Graphs</li><p>");        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
  m=cptcoveff;          if  (cptcovn>0) {
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
  jj1=0;                bool=0;
  for(k1=1; k1<=m;k1++){          } 
    for(i1=1; i1<=ncodemax[k1];i1++){          if (bool==1) { 
        jj1++;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
        if (cptcovn > 0) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
          for (cpt=1; cpt<=cptcoveff;cpt++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                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); 
        }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                      prop[s[m][i]][(int)agev[m][i]] += weight[i];
        for(cpt=1; cpt<nlstate;cpt++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>                } 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              }
        }            } /* end selection of waves */
     for(cpt=1; cpt<=nlstate;cpt++) {          }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        }
 interval) in state (%d): v%s%d%d.gif <br>        for(i=iagemin; i <= iagemax+3; i++){  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            
      }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
      for(cpt=1; cpt<=nlstate;cpt++) {            posprop += prop[jk][i]; 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          } 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
      }          for(jk=1; jk <=nlstate ; jk++){     
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            if( i <=  iagemax){ 
 health expectancies in states (1) and (2): e%s%d.gif<br>              if(posprop>=1.e-5){ 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                probs[i][jk][j1]= prop[jk][i]/posprop;
 fprintf(fichtm,"\n</body>");              } 
    }            } 
    }          }/* end jk */ 
 fclose(fichtm);        }/* end i */ 
 }      } /* end i1 */
     } /* end k1 */
 /******************* Gnuplot file **************/    
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".gp.txt");  /************* Waves Concatenation ***************/
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);  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)
   }  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 #ifdef windows       Death is a valid wave (if date is known).
     fprintf(ficgp,"cd \"%s\" \n",pathc);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 #endif       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 m=pow(2,cptcoveff);       and mw[mi+1][i]. dh depends on stepm.
         */
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {    int i, mi, m;
    for (k1=1; k1<= m ; k1 ++) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
 #ifdef windows    int first;
     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);    int j, k=0,jk, ju, jl;
 #endif    double sum=0.;
 #ifdef unix    first=0;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    jmin=1e+5;
 #endif    jmax=-1;
     jmean=0.;
 for (i=1; i<= nlstate ; i ++) {    for(i=1; i<=imx; i++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      mi=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      m=firstpass;
 }      while(s[m][i] <= nlstate){
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        if(s[m][i]>=1)
     for (i=1; i<= nlstate ; i ++) {          mw[++mi][i]=m;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if(m >=lastpass)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          break;
 }        else
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          m++;
      for (i=1; i<= nlstate ; i ++) {      }/* end while */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      if (s[m][i] > nlstate){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        mi++;     /* Death is another wave */
 }          /* if(mi==0)  never been interviewed correctly before death */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));           /* Only death is a correct wave */
 #ifdef unix        mw[mi][i]=m;
 fprintf(ficgp,"\nset ter gif small size 400,300");      }
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      wav[i]=mi;
    }      if(mi==0){
   }        if(first==0){
   /*2 eme*/          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
   for (k1=1; k1<= m ; k1 ++) {        }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);        if(first==1){
              fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
     for (i=1; i<= nlstate+1 ; i ++) {        }
       k=2*i;      } /* end mi==0 */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    } /* End individuals */
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for(i=1; i<=imx; i++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(mi=1; mi<wav[i];mi++){
 }          if (stepm <=0)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          dh[mi][i]=1;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        else{
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       for (j=1; j<= nlstate+1 ; j ++) {            if (agedc[i] < 2*AGESUP) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         else fprintf(ficgp," \%%*lf (\%%*lf)");              if(j==0) j=1;  /* Survives at least one month after exam */
 }                else if(j<0){
       fprintf(ficgp,"\" t\"\" w l 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]);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);                j=1; /* Careful Patch */
       for (j=1; j<= nlstate+1 ; j ++) {                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);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");                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);
 }                }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              k=k+1;
       else fprintf(ficgp,"\" t\"\" w l 0,");              if (j >= jmax) jmax=j;
     }              if (j <= jmin) jmin=j;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);              sum=sum+j;
   }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   /*3eme*/            }
           }
   for (k1=1; k1<= m ; k1 ++) {          else{
     for (cpt=1; cpt<= nlstate ; cpt ++) {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       k=2+nlstate*(cpt-1);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       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);            k=k+1;
       for (i=1; i< nlstate ; i ++) {            if (j >= jmax) jmax=j;
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);            else if (j <= jmin)jmin=j;
       }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            /*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("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   /* CV preval stat */            }
     for (k1=1; k1<= m ; k1 ++) {            sum=sum+j;
     for (cpt=1; cpt<nlstate ; cpt ++) {          }
       k=3;          jk= j/stepm;
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
       for (i=1; i< nlstate ; i ++)          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         fprintf(ficgp,"+$%d",k+i+1);            if(jl==0){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              dh[mi][i]=jk;
                    bh[mi][i]=0;
       l=3+(nlstate+ndeath)*cpt;            }else{ /* We want a negative bias in order to only have interpolation ie
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                    * at the price of an extra matrix product in likelihood */
       for (i=1; i< nlstate ; i ++) {              dh[mi][i]=jk+1;
         l=3+(nlstate+ndeath)*cpt;              bh[mi][i]=ju;
         fprintf(ficgp,"+$%d",l+i+1);            }
       }          }else{
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              if(jl <= -ju){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              dh[mi][i]=jk;
     }              bh[mi][i]=jl;       /* bias is positive if real duration
   }                                     * is higher than the multiple of stepm and negative otherwise.
                                     */
   /* proba elementaires */            }
    for(i=1,jk=1; i <=nlstate; i++){            else{
     for(k=1; k <=(nlstate+ndeath); k++){              dh[mi][i]=jk+1;
       if (k != i) {              bh[mi][i]=ju;
         for(j=1; j <=ncovmodel; j++){            }
                    if(dh[mi][i]==0){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              dh[mi][i]=1; /* At least one step */
           jk++;              bh[mi][i]=ju; /* At least one step */
           fprintf(ficgp,"\n");              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
         }            }
       }          } /* end if mle */
     }        }
     }      } /* end wave */
     }
     for(jk=1; jk <=m; jk++) {    jmean=sum/k;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    i=1;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    for(k2=1; k2<=nlstate; k2++) {   }
      k3=i;  
      for(k=1; k<=(nlstate+ndeath); k++) {  /*********** Tricode ****************************/
        if (k != k2){  void tricode(int *Tvar, int **nbcode, int imx)
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  {
 ij=1;    
         for(j=3; j <=ncovmodel; j++) {    int Ndum[20],ij=1, k, j, i, maxncov=19;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    int cptcode=0;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    cptcoveff=0; 
             ij++;   
           }    for (k=0; k<maxncov; k++) Ndum[k]=0;
           else    for (k=1; k<=7; k++) ncodemax[k]=0;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
         }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
           fprintf(ficgp,")/(1");      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                         modality*/ 
         for(k1=1; k1 <=nlstate; k1++){          ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        Ndum[ij]++; /*store the modality */
 ij=1;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           for(j=3; j <=ncovmodel; j++){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                                         Tvar[j]. If V=sex and male is 0 and 
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                                         female is 1, then  cptcode=1.*/
             ij++;      }
           }  
           else      for (i=0; i<=cptcode; i++) {
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
           }      }
           fprintf(ficgp,")");  
         }      ij=1; 
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      for (i=1; i<=ncodemax[j]; i++) {
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        for (k=0; k<= maxncov; k++) {
         i=i+ncovmodel;          if (Ndum[k] != 0) {
        }            nbcode[Tvar[j]][ij]=k; 
      }            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
    }            
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            ij++;
    }          }
              if (ij > ncodemax[j]) break; 
   fclose(ficgp);        }  
 }  /* end gnuplot */      } 
     }  
   
 /*************** Moving average **************/   for (k=0; k< maxncov; k++) Ndum[k]=0;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  
    for (i=1; i<=ncovmodel-2; i++) { 
   int i, cpt, cptcod;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)     ij=Tvar[i];
       for (i=1; i<=nlstate;i++)     Ndum[ij]++;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)   }
           mobaverage[(int)agedeb][i][cptcod]=0.;  
       ij=1;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){   for (i=1; i<= maxncov; i++) {
       for (i=1; i<=nlstate;i++){     if((Ndum[i]!=0) && (i<=ncovcol)){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       Tvaraff[ij]=i; /*For printing */
           for (cpt=0;cpt<=4;cpt++){       ij++;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];     }
           }   }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;   
         }   cptcoveff=ij-1; /*Number of simple covariates*/
       }  }
     }  
      /*********** 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 )
   
 /************** Forecasting ******************/  {
 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){    /* Health expectancies */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    double age, agelim, hf;
   int *popage;    double ***p3mat,***varhe;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double **dnewm,**doldm;
   double *popeffectif,*popcount;    double *xp;
   double ***p3mat;    double **gp, **gm;
   char fileresf[FILENAMELENGTH];    double ***gradg, ***trgradg;
     int theta;
  agelim=AGESUP;  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    dnewm=matrix(1,nlstate*nlstate,1,npar);
      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      
   strcpy(fileresf,"f");    fprintf(ficreseij,"# Health expectancies\n");
   strcat(fileresf,fileres);    fprintf(ficreseij,"# Age");
   if((ficresf=fopen(fileresf,"w"))==NULL) {    for(i=1; i<=nlstate;i++)
     printf("Problem with forecast resultfile: %s\n", fileresf);      for(j=1; j<=nlstate;j++)
   }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    fprintf(ficreseij,"\n");
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   if (mobilav==1) {    }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    else  hstepm=estepm;   
     movingaverage(agedeb, fage, ageminpar, mobaverage);    /* We compute the life expectancy from trapezoids spaced every estepm months
   }     * 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
   stepsize=(int) (stepm+YEARM-1)/YEARM;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   if (stepm<=12) stepsize=1;     * progression in between and thus overestimating or underestimating according
       * to the curvature of the survival function. If, for the same date, we 
   agelim=AGESUP;     * 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 
   hstepm=1;     * hypothesis. A more precise result, taking into account a more precise
   hstepm=hstepm/stepm;     * curvature will be obtained if estepm is as small as stepm. */
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;    /* For example we decided to compute the life expectancy with the smallest unit */
   yp2=modf((yp1*12),&yp);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   mprojmean=yp;       nhstepm is the number of hstepm from age to agelim 
   yp1=modf((yp2*30.5),&yp);       nstepm is the number of stepm from age to agelin. 
   jprojmean=yp;       Look at hpijx to understand the reason of that which relies in memory size
   if(jprojmean==0) jprojmean=1;       and note for a fixed period like estepm months */
   if(mprojmean==0) jprojmean=1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         survival function given by stepm (the optimization length). Unfortunately it
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);       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(cptcov=1;cptcov<=i2;cptcov++){       results. So we changed our mind and took the option of the best precision.
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    */
       k=k+1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficresf,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {    agelim=AGESUP;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       }      /* nhstepm age range expressed in number of stepm */
       fprintf(ficresf,"******\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       fprintf(ficresf,"# StartingAge FinalAge");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      /* if (stepm >= YEARM) hstepm=1;*/
            nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         fprintf(ficresf,"\n");      gp=matrix(0,nhstepm,1,nlstate*nlstate);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           nhstepm = nhstepm/hstepm;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
             
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
              /* Computing Variances of health expectancies */
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {       for(theta=1; theta <=npar; theta++){
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        for(i=1; i<=npar; i++){ 
             }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               for(i=1; i<=nlstate;i++) {                  
                 if (mobilav==1)        cptj=0;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        for(j=1; j<= nlstate; j++){
                 else {          for(i=1; i<=nlstate; i++){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            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.;
               }            }
               if (h==(int)(calagedate+12*cpt)){          }
                 fprintf(ficresf," %.3f", kk1);        }
                               
               }       
             }        for(i=1; i<=npar; i++) 
           }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         }        
       }        cptj=0;
     }        for(j=1; j<= nlstate; j++){
   }          for(i=1;i<=nlstate;i++){
                    cptj=cptj+1;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   
   fclose(ficresf);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 }            }
 /************** Forecasting ******************/          }
 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(j=1; j<= nlstate*nlstate; j++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          for(h=0; h<=nhstepm-1; h++){
   int *popage;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          }
   double *popeffectif,*popcount;       } 
   double ***p3mat,***tabpop,***tabpopprev;     
   char filerespop[FILENAMELENGTH];  /* End theta */
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   agelim=AGESUP;       for(h=0; h<=nhstepm-1; h++)
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        for(j=1; j<=nlstate*nlstate;j++)
            for(theta=1; theta <=npar; theta++)
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            trgradg[h][j][theta]=gradg[h][theta][j];
         
    
   strcpy(filerespop,"pop");       for(i=1;i<=nlstate*nlstate;i++)
   strcat(filerespop,fileres);        for(j=1;j<=nlstate*nlstate;j++)
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          varhe[i][j][(int)age] =0.;
     printf("Problem with forecast resultfile: %s\n", filerespop);  
   }       printf("%d|",(int)age);fflush(stdout);
   printf("Computing forecasting: result on file '%s' \n", filerespop);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   if (mobilav==1) {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(i=1;i<=nlstate*nlstate;i++)
     movingaverage(agedeb, fage, ageminpar, mobaverage);            for(j=1;j<=nlstate*nlstate;j++)
   }              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;      }
   if (stepm<=12) stepsize=1;      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
   agelim=AGESUP;        for(j=1; j<=nlstate;j++)
            for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   hstepm=1;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   hstepm=hstepm/stepm;            
    /* 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]);*/
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {          }
       printf("Problem with population file : %s\n",popfile);exit(0);  
     }      fprintf(ficreseij,"%3.0f",age );
     popage=ivector(0,AGESUP);      cptj=0;
     popeffectif=vector(0,AGESUP);      for(i=1; i<=nlstate;i++)
     popcount=vector(0,AGESUP);        for(j=1; j<=nlstate;j++){
              cptj++;
     i=1;            fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        }
          fprintf(ficreseij,"\n");
     imx=i;     
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   for(cptcov=1;cptcov<=i2;cptcov++){      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k=k+1;    }
       fprintf(ficrespop,"\n#******");    printf("\n");
       for(j=1;j<=cptcoveff;j++) {    fprintf(ficlog,"\n");
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }    free_vector(xp,1,npar);
       fprintf(ficrespop,"******\n");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       fprintf(ficrespop,"# Age");    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       if (popforecast==1)  fprintf(ficrespop," [Population]");  }
        
       for (cpt=0; cpt<=0;cpt++) {  /************ Variance ******************/
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    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)
          {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    /* Variance of health expectancies */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           nhstepm = nhstepm/hstepm;    /* double **newm;*/
              double **dnewm,**doldm;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **dnewmp,**doldmp;
           oldm=oldms;savm=savms;    int i, j, nhstepm, hstepm, h, nstepm ;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int k, cptcode;
            double *xp;
           for (h=0; h<=nhstepm; h++){    double **gp, **gm;  /* for var eij */
             if (h==(int) (calagedate+YEARM*cpt)) {    double ***gradg, ***trgradg; /*for var eij */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    double **gradgp, **trgradgp; /* for var p point j */
             }    double *gpp, *gmp; /* for var p point j */
             for(j=1; j<=nlstate+ndeath;j++) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
               kk1=0.;kk2=0;    double ***p3mat;
               for(i=1; i<=nlstate;i++) {                  double age,agelim, hf;
                 if (mobilav==1)    double ***mobaverage;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    int theta;
                 else {    char digit[4];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    char digitp[25];
                 }  
               }    char fileresprobmorprev[FILENAMELENGTH];
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    if(popbased==1){
                   /*fprintf(ficrespop," %.3f", kk1);      if(mobilav!=0)
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        strcpy(digitp,"-populbased-mobilav-");
               }      else strcpy(digitp,"-populbased-nomobil-");
             }    }
             for(i=1; i<=nlstate;i++){    else 
               kk1=0.;      strcpy(digitp,"-stablbased-");
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    if (mobilav!=0) {
                 }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      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);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    }
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcpy(fileresprobmorprev,"prmorprev"); 
         }    sprintf(digit,"%-d",ij);
       }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      strcat(fileresprobmorprev,digit); /* Tvar to be done */
   /******/    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        printf("Problem with resultfile: %s\n", fileresprobmorprev);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    }
           nhstepm = nhstepm/hstepm;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
              fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    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);
           oldm=oldms;savm=savms;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           for (h=0; h<=nhstepm; h++){      fprintf(ficresprobmorprev," p.%-d SE",j);
             if (h==(int) (calagedate+YEARM*cpt)) {      for(i=1; i<=nlstate;i++)
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
             }    }  
             for(j=1; j<=nlstate+ndeath;j++) {    fprintf(ficresprobmorprev,"\n");
               kk1=0.;kk2=0;    fprintf(ficgp,"\n# Routine varevsij");
               for(i=1; i<=nlstate;i++) {                  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");
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
               }  /*   } */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             }  
           }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresvij,"# Age");
         }    for(i=1; i<=nlstate;i++)
       }      for(j=1; j<=nlstate;j++)
    }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   }    fprintf(ficresvij,"\n");
    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   if (popforecast==1) {    doldm=matrix(1,nlstate,1,nlstate);
     free_ivector(popage,0,AGESUP);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     free_vector(popeffectif,0,AGESUP);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_vector(popcount,0,AGESUP);  
   }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    gpp=vector(nlstate+1,nlstate+ndeath);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    gmp=vector(nlstate+1,nlstate+ndeath);
   fclose(ficrespop);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 }    
     if(estepm < stepm){
 /***********************************************/      printf ("Problem %d lower than %d\n",estepm, stepm);
 /**************** Main Program *****************/    }
 /***********************************************/    else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
 int main(int argc, char *argv[])    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 {       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;       Look at hpijx to understand the reason of that which relies in memory size
   double agedeb, agefin,hf;       and note for a fixed period like k years */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
   double fret;       means that if the survival funtion is printed every two years of age and if
   double **xi,tmp,delta;       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.
   double dum; /* Dummy variable */    */
   double ***p3mat;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   int *indx;    agelim = AGESUP;
   char line[MAXLINE], linepar[MAXLINE];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   char title[MAXLINE];      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];      for(theta=1; theta <=npar; theta++){
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   int firstobs=1, lastobs=10;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   int sdeb, sfin; /* Status at beginning and end */        }
   int c,  h , cpt,l;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   int ju,jl, mi;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        if (popbased==1) {
   int mobilav=0,popforecast=0;          if(mobilav ==0){
   int hstepm, nhstepm;            for(i=1; i<=nlstate;i++)
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   double bage, fage, age, agelim, agebase;            for(i=1; i<=nlstate;i++)
   double ftolpl=FTOL;              prlim[i][i]=mobaverage[(int)age][i][ij];
   double **prlim;          }
   double *severity;        }
   double ***param; /* Matrix of parameters */    
   double  *p;        for(j=1; j<= nlstate; j++){
   double **matcov; /* Matrix of covariance */          for(h=0; h<=nhstepm; h++){
   double ***delti3; /* Scale */            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   double *delti; /* Scale */              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   double ***eij, ***vareij;          }
   double **varpl; /* Variances of prevalence limits by age */        }
   double *epj, vepp;        /* This for computing probability of death (h=1 means
   double kk1, kk2;           computed over hstepm matrices product = hstepm*stepm months) 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;           as a weighted average of prlim.
          */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   char *alph[]={"a","a","b","c","d","e"}, str[4];            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   char z[1]="c", occ;  
 #include <sys/time.h>        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
 #include <time.h>          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /* long total_usecs;   
   struct timeval start_time, end_time;        if (popbased==1) {
            if(mobilav ==0){
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */            for(i=1; i<=nlstate;i++)
   getcwd(pathcd, size);              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   printf("\n%s",version);            for(i=1; i<=nlstate;i++)
   if(argc <=1){              prlim[i][i]=mobaverage[(int)age][i][ij];
     printf("\nEnter the parameter file name: ");          }
     scanf("%s",pathtot);        }
   }  
   else{        for(j=1; j<= nlstate; j++){
     strcpy(pathtot,argv[1]);          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   /*cygwin_split_path(pathtot,path,optionfile);          }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        }
   /* cutv(path,optionfile,pathtot,'\\');*/        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);           as a weighted average of prlim.
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        */
   chdir(path);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   replace(pathc,path);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
 /*-------- arguments in the command line --------*/        }    
         /* end probability of death */
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);        for(j=1; j<= nlstate; j++) /* vareij */
   strcat(fileres,".txt");    /* Other files have txt extension */          for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   /*---------arguments file --------*/          }
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     printf("Problem with optionfile %s\n",optionfile);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     goto end;        }
   }  
       } /* End theta */
   strcpy(filereso,"o");  
   strcat(filereso,fileres);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      for(h=0; h<=nhstepm; h++) /* veij */
   }        for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   /* Reads comments: lines beginning with '#' */            trgradg[h][j][theta]=gradg[h][theta][j];
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     fgets(line, MAXLINE, ficpar);        for(theta=1; theta <=npar; theta++)
     puts(line);          trgradgp[j][theta]=gradgp[theta][j];
     fputs(line,ficparo);    
   }  
   ungetc(c,ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
   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);        for(j=1;j<=nlstate;j++)
   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);          vareij[i][j][(int)age] =0.;
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);  
 while((c=getc(ficpar))=='#' && c!= EOF){      for(h=0;h<=nhstepm;h++){
     ungetc(c,ficpar);        for(k=0;k<=nhstepm;k++){
     fgets(line, MAXLINE, ficpar);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     puts(line);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     fputs(line,ficparo);          for(i=1;i<=nlstate;i++)
   }            for(j=1;j<=nlstate;j++)
   ungetc(c,ficpar);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
          }
   covar=matrix(0,NCOVMAX,1,n);    
   cptcovn=0;      /* pptj */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   ncovmodel=2+cptcovn;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        for(i=nlstate+1;i<=nlstate+ndeath;i++)
            varppt[j][i]=doldmp[j][i];
   /* Read guess parameters */      /* end ppptj */
   /* Reads comments: lines beginning with '#' */      /*  x centered again */
   while((c=getc(ficpar))=='#' && c!= EOF){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     ungetc(c,ficpar);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     fgets(line, MAXLINE, ficpar);   
     puts(line);      if (popbased==1) {
     fputs(line,ficparo);        if(mobilav ==0){
   }          for(i=1; i<=nlstate;i++)
   ungetc(c,ficpar);            prlim[i][i]=probs[(int)age][i][ij];
          }else{ /* mobilav */ 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          for(i=1; i<=nlstate;i++)
     for(i=1; i <=nlstate; i++)            prlim[i][i]=mobaverage[(int)age][i][ij];
     for(j=1; j <=nlstate+ndeath-1; j++){        }
       fscanf(ficpar,"%1d%1d",&i1,&j1);      }
       fprintf(ficparo,"%1d%1d",i1,j1);               
       printf("%1d%1d",i,j);      /* This for computing probability of death (h=1 means
       for(k=1; k<=ncovmodel;k++){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         fscanf(ficpar," %lf",&param[i][j][k]);         as a weighted average of prlim.
         printf(" %lf",param[i][j][k]);      */
         fprintf(ficparo," %lf",param[i][j][k]);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       fscanf(ficpar,"\n");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       printf("\n");      }    
       fprintf(ficparo,"\n");      /* end probability of death */
     }  
        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   p=param[1][1];        for(i=1; i<=nlstate;i++){
            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){      } 
     ungetc(c,ficpar);      fprintf(ficresprobmorprev,"\n");
     fgets(line, MAXLINE, ficpar);  
     puts(line);      fprintf(ficresvij,"%.0f ",age );
     fputs(line,ficparo);      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++){
   ungetc(c,ficpar);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      fprintf(ficresvij,"\n");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      free_matrix(gp,0,nhstepm,1,nlstate);
   for(i=1; i <=nlstate; i++){      free_matrix(gm,0,nhstepm,1,nlstate);
     for(j=1; j <=nlstate+ndeath-1; j++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fscanf(ficpar,"%1d%1d",&i1,&j1);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       printf("%1d%1d",i,j);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficparo,"%1d%1d",i1,j1);    } /* End age */
       for(k=1; k<=ncovmodel;k++){    free_vector(gpp,nlstate+1,nlstate+ndeath);
         fscanf(ficpar,"%le",&delti3[i][j][k]);    free_vector(gmp,nlstate+1,nlstate+ndeath);
         printf(" %le",delti3[i][j][k]);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficparo," %le",delti3[i][j][k]);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       fscanf(ficpar,"\n");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       printf("\n");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       fprintf(ficparo,"\n");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   delti=delti3[1][1];    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   /* Reads comments: lines beginning with '#' */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     ungetc(c,ficpar);    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);
     fgets(line, MAXLINE, ficpar);    /*  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);
     puts(line);  */
     fputs(line,ficparo);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   }    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   ungetc(c,ficpar);  
      free_vector(xp,1,npar);
   matcov=matrix(1,npar,1,npar);    free_matrix(doldm,1,nlstate,1,nlstate);
   for(i=1; i <=npar; i++){    free_matrix(dnewm,1,nlstate,1,npar);
     fscanf(ficpar,"%s",&str);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     printf("%s",str);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     fprintf(ficparo,"%s",str);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for(j=1; j <=i; j++){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fscanf(ficpar," %le",&matcov[i][j]);    fclose(ficresprobmorprev);
       printf(" %.5le",matcov[i][j]);    fflush(ficgp);
       fprintf(ficparo," %.5le",matcov[i][j]);    fflush(fichtm); 
     }  }  /* end varevsij */
     fscanf(ficpar,"\n");  
     printf("\n");  /************ Variance of prevlim ******************/
     fprintf(ficparo,"\n");  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
   }  {
   for(i=1; i <=npar; i++)    /* Variance of prevalence limit */
     for(j=i+1;j<=npar;j++)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       matcov[i][j]=matcov[j][i];    double **newm;
        double **dnewm,**doldm;
   printf("\n");    int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     /*-------- Rewriting paramater file ----------*/    double *gp, *gm;
      strcpy(rfileres,"r");    /* "Rparameterfile */    double **gradg, **trgradg;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    double age,agelim;
      strcat(rfileres,".");    /* */    int theta;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */     
     if((ficres =fopen(rfileres,"w"))==NULL) {    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    fprintf(ficresvpl,"# Age");
     }    for(i=1; i<=nlstate;i++)
     fprintf(ficres,"#%s\n",version);        fprintf(ficresvpl," %1d-%1d",i,i);
        fprintf(ficresvpl,"\n");
     /*-------- data file ----------*/  
     if((fic=fopen(datafile,"r"))==NULL)    {    xp=vector(1,npar);
       printf("Problem with datafile: %s\n", datafile);goto end;    dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
     
     n= lastobs;    hstepm=1*YEARM; /* Every year of age */
     severity = vector(1,maxwav);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     outcome=imatrix(1,maxwav+1,1,n);    agelim = AGESUP;
     num=ivector(1,n);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     moisnais=vector(1,n);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     annais=vector(1,n);      if (stepm >= YEARM) hstepm=1;
     moisdc=vector(1,n);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     andc=vector(1,n);      gradg=matrix(1,npar,1,nlstate);
     agedc=vector(1,n);      gp=vector(1,nlstate);
     cod=ivector(1,n);      gm=vector(1,nlstate);
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      for(theta=1; theta <=npar; theta++){
     mint=matrix(1,maxwav,1,n);        for(i=1; i<=npar; i++){ /* Computes gradient */
     anint=matrix(1,maxwav,1,n);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     s=imatrix(1,maxwav+1,1,n);        }
     adl=imatrix(1,maxwav+1,1,n);            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     tab=ivector(1,NCOVMAX);        for(i=1;i<=nlstate;i++)
     ncodemax=ivector(1,8);          gp[i] = prlim[i][i];
       
     i=1;        for(i=1; i<=npar; i++) /* Computes gradient */
     while (fgets(line, MAXLINE, fic) != NULL)    {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       if ((i >= firstobs) && (i <=lastobs)) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                for(i=1;i<=nlstate;i++)
         for (j=maxwav;j>=1;j--){          gm[i] = prlim[i][i];
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  
           strcpy(line,stra);        for(i=1;i<=nlstate;i++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      } /* End theta */
         }  
              trgradg =matrix(1,nlstate,1,npar);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          trgradg[j][theta]=gradg[theta][j];
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
       for(i=1;i<=nlstate;i++)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        varpl[i][(int)age] =0.;
         for (j=ncovcol;j>=1;j--){      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
         }      for(i=1;i<=nlstate;i++)
         num[i]=atol(stra);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      fprintf(ficresvpl,"%.0f ",age );
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         i=i+1;      fprintf(ficresvpl,"\n");
       }      free_vector(gp,1,nlstate);
     }      free_vector(gm,1,nlstate);
     /* printf("ii=%d", ij);      free_matrix(gradg,1,npar,1,nlstate);
        scanf("%d",i);*/      free_matrix(trgradg,1,nlstate,1,npar);
   imx=i-1; /* Number of individuals */    } /* End age */
   
   /* for (i=1; i<=imx; i++){    free_vector(xp,1,npar);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    free_matrix(doldm,1,nlstate,1,npar);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    free_matrix(dnewm,1,nlstate,1,nlstate);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  
     }*/  }
    
   /* for (i=1; i<=imx; i++){  /************ Variance of one-step probabilities  ******************/
      if (s[4][i]==9)  s[4][i]=-1;  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
      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]));}  {
   */    int i, j=0,  i1, k1, l1, t, tj;
      int k2, l2, j1,  z1;
   /* Calculation of the number of parameter from char model*/    int k=0,l, cptcode;
   Tvar=ivector(1,15);    int first=1, first1;
   Tprod=ivector(1,15);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   Tvaraff=ivector(1,15);    double **dnewm,**doldm;
   Tvard=imatrix(1,15,1,2);    double *xp;
   Tage=ivector(1,15);          double *gp, *gm;
        double **gradg, **trgradg;
   if (strlen(model) >1){    double **mu;
     j=0, j1=0, k1=1, k2=1;    double age,agelim, cov[NCOVMAX];
     j=nbocc(model,'+');    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     j1=nbocc(model,'*');    int theta;
     cptcovn=j+1;    char fileresprob[FILENAMELENGTH];
     cptcovprod=j1;    char fileresprobcov[FILENAMELENGTH];
        char fileresprobcor[FILENAMELENGTH];
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    double ***varpij;
       printf("Error. Non available option model=%s ",model);  
       goto end;    strcpy(fileresprob,"prob"); 
     }    strcat(fileresprob,fileres);
        if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     for(i=(j+1); i>=1;i--){      printf("Problem with resultfile: %s\n", fileresprob);
       cutv(stra,strb,modelsav,'+');      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    strcpy(fileresprobcov,"probcov"); 
       /*scanf("%d",i);*/    strcat(fileresprobcov,fileres);
       if (strchr(strb,'*')) {    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
         cutv(strd,strc,strb,'*');      printf("Problem with resultfile: %s\n", fileresprobcov);
         if (strcmp(strc,"age")==0) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
           cptcovprod--;    }
           cutv(strb,stre,strd,'V');    strcpy(fileresprobcor,"probcor"); 
           Tvar[i]=atoi(stre);    strcat(fileresprobcor,fileres);
           cptcovage++;    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
             Tage[cptcovage]=i;      printf("Problem with resultfile: %s\n", fileresprobcor);
             /*printf("stre=%s ", stre);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         }    }
         else if (strcmp(strd,"age")==0) {    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           cptcovprod--;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           cutv(strb,stre,strc,'V');    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           Tvar[i]=atoi(stre);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           cptcovage++;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           Tage[cptcovage]=i;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         }    
         else {    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           cutv(strb,stre,strc,'V');    fprintf(ficresprob,"# Age");
           Tvar[i]=ncovcol+k1;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           cutv(strb,strc,strd,'V');    fprintf(ficresprobcov,"# Age");
           Tprod[k1]=i;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           Tvard[k1][1]=atoi(strc);    fprintf(ficresprobcov,"# Age");
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    for(i=1; i<=nlstate;i++)
           for (k=1; k<=lastobs;k++)      for(j=1; j<=(nlstate+ndeath);j++){
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
           k1++;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
           k2=k2+2;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
         }      }  
       }   /* fprintf(ficresprob,"\n");
       else {    fprintf(ficresprobcov,"\n");
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    fprintf(ficresprobcor,"\n");
        /*  scanf("%d",i);*/   */
       cutv(strd,strc,strb,'V');   xp=vector(1,npar);
       Tvar[i]=atoi(strc);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       strcpy(modelsav,stra);      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
         scanf("%d",i);*/    first=1;
     }    fprintf(ficgp,"\n# Routine varprob");
 }    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
      fprintf(fichtm,"\n");
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  
   printf("cptcovprod=%d ", cptcovprod);    fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   scanf("%d ",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");
     fclose(fic);    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");
   
     /*  if(mle==1){*/    cov[1]=1;
     if (weightopt != 1) { /* Maximisation without weights*/    tj=cptcoveff;
       for(i=1;i<=n;i++) weight[i]=1.0;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     }    j1=0;
     /*-calculation of age at interview from date of interview and age at death -*/    for(t=1; t<=tj;t++){
     agev=matrix(1,maxwav,1,imx);      for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
     for (i=1; i<=imx; i++) {        if  (cptcovn>0) {
       for(m=2; (m<= maxwav); m++) {          fprintf(ficresprob, "\n#********** Variable "); 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          anint[m][i]=9999;          fprintf(ficresprob, "**********\n#\n");
          s[m][i]=-1;          fprintf(ficresprobcov, "\n#********** Variable "); 
        }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;          fprintf(ficresprobcov, "**********\n#\n");
       }          
     }          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for (i=1; i<=imx; i++)  {          fprintf(ficgp, "**********\n#\n");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          
       for(m=1; (m<= maxwav); m++){          
         if(s[m][i] >0){          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           if (s[m][i] >= nlstate+1) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             if(agedc[i]>0)          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
               if(moisdc[i]!=99 && andc[i]!=9999)          
                 agev[m][i]=agedc[i];          fprintf(ficresprobcor, "\n#********** Variable ");    
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            else {          fprintf(ficresprobcor, "**********\n#");    
               if (andc[i]!=9999){        }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        
               agev[m][i]=-1;        for (age=bage; age<=fage; age ++){ 
               }          cov[2]=age;
             }          for (k=1; k<=cptcovn;k++) {
           }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           else if(s[m][i] !=9){ /* Should no more exist */          }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
             if(mint[m][i]==99 || anint[m][i]==9999)          for (k=1; k<=cptcovprod;k++)
               agev[m][i]=1;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             else if(agev[m][i] <agemin){          
               agemin=agev[m][i];          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
             }          gp=vector(1,(nlstate)*(nlstate+ndeath));
             else if(agev[m][i] >agemax){          gm=vector(1,(nlstate)*(nlstate+ndeath));
               agemax=agev[m][i];      
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          for(theta=1; theta <=npar; theta++){
             }            for(i=1; i<=npar; i++)
             /*agev[m][i]=anint[m][i]-annais[i];*/              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             /*   agev[m][i] = age[i]+2*m;*/            
           }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           else { /* =9 */            
             agev[m][i]=1;            k=0;
             s[m][i]=-1;            for(i=1; i<= (nlstate); i++){
           }              for(j=1; j<=(nlstate+ndeath);j++){
         }                k=k+1;
         else /*= 0 Unknown */                gp[k]=pmmij[i][j];
           agev[m][i]=1;              }
       }            }
                
     }            for(i=1; i<=npar; i++)
     for (i=1; i<=imx; i++)  {              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       for(m=1; (m<= maxwav); m++){      
         if (s[m][i] > (nlstate+ndeath)) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           printf("Error: Wrong value in nlstate or ndeath\n");              k=0;
           goto end;            for(i=1; i<=(nlstate); i++){
         }              for(j=1; j<=(nlstate+ndeath);j++){
       }                k=k+1;
     }                gm[k]=pmmij[i][j];
               }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            }
        
     free_vector(severity,1,maxwav);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     free_imatrix(outcome,1,maxwav+1,1,n);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     free_vector(moisnais,1,n);          }
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
        free_matrix(anint,1,maxwav,1,n);*/            for(theta=1; theta <=npar; theta++)
     free_vector(moisdc,1,n);              trgradg[j][theta]=gradg[theta][j];
     free_vector(andc,1,n);          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
              matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     wav=ivector(1,imx);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
              free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
       Tcode=ivector(1,100);          for(i=1; i<=(nlstate); i++){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            for(j=1; j<=(nlstate+ndeath);j++){
       ncodemax[1]=1;              k=k+1;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              mu[k][(int) age]=pmmij[i][j];
                  }
    codtab=imatrix(1,100,1,10);          }
    h=0;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
    m=pow(2,cptcoveff);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                varpij[i][j][(int)age] = doldm[i][j];
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){          /*printf("\n%d ",(int)age);
        for(j=1; j <= ncodemax[k]; j++){            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
            h++;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
            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]);*/  
          }          fprintf(ficresprob,"\n%d ",(int)age);
        }          fprintf(ficresprobcov,"\n%d ",(int)age);
      }          fprintf(ficresprobcor,"\n%d ",(int)age);
    }  
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       codtab[1][2]=1;codtab[2][2]=2; */            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
    /* for(i=1; i <=m ;i++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       for(k=1; k <=cptcovn; k++){            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       }          }
       printf("\n");          i=0;
       }          for (k=1; k<=(nlstate);k++){
       scanf("%d",i);*/            for (l=1; l<=(nlstate+ndeath);l++){ 
                  i=i++;
    /* Calculates basic frequencies. Computes observed prevalence at single age              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
        and prints on file fileres'p'. */              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                    fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                    fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     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 */          }/* end of loop for state */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        } /* end of loop for age */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
              /* Confidence intervalle of pij  */
     /* 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] */          fprintf(ficgp,"\nset noparametric;unset label");
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     if(mle==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);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
              fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     /*--------- 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);  
          /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
    jk=1;        for (k2=1; k2<=(nlstate);k2++){
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            if(l2==k2) continue;
    for(i=1,jk=1; i <=nlstate; i++){            j=(k2-1)*(nlstate+ndeath)+l2;
      for(k=1; k <=(nlstate+ndeath); k++){            for (k1=1; k1<=(nlstate);k1++){
        if (k != i)              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
          {                if(l1==k1) continue;
            printf("%d%d ",i,k);                i=(k1-1)*(nlstate+ndeath)+l1;
            fprintf(ficres,"%1d%1d ",i,k);                if(i<=j) continue;
            for(j=1; j <=ncovmodel; j++){                for (age=bage; age<=fage; age ++){ 
              printf("%f ",p[jk]);                  if ((int)age %5==0){
              fprintf(ficres,"%f ",p[jk]);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
              jk++;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
            }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
            printf("\n");                    mu1=mu[i][(int) age]/stepm*YEARM ;
            fprintf(ficres,"\n");                    mu2=mu[j][(int) age]/stepm*YEARM;
          }                    c12=cv12/sqrt(v1*v2);
      }                    /* Computing eigen value of matrix of covariance */
    }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
  if(mle==1){                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     /* Computing hessian and covariance matrix */                    /* Eigen vectors */
     ftolhess=ftol; /* Usually correct */                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     hesscov(matcov, p, npar, delti, ftolhess, func);                    /*v21=sqrt(1.-v11*v11); *//* error */
  }                    v21=(lc1-v1)/cv12*v11;
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");                    v12=-v21;
     printf("# Scales (for hessian or gradient estimation)\n");                    v22=v11;
      for(i=1,jk=1; i <=nlstate; i++){                    tnalp=v21/v11;
       for(j=1; j <=nlstate+ndeath; j++){                    if(first1==1){
         if (j!=i) {                      first1=0;
           fprintf(ficres,"%1d%1d",i,j);                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
           printf("%1d%1d",i,j);                    }
           for(k=1; k<=ncovmodel;k++){                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
             printf(" %.5e",delti[jk]);                    /*printf(fignu*/
             fprintf(ficres," %.5e",delti[jk]);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
             jk++;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           }                    if(first==1){
           printf("\n");                      first=0;
           fprintf(ficres,"\n");                      fprintf(ficgp,"\nset parametric;unset label");
         }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
       }                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
      }                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
       :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
     k=1;  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
     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");                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     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");                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     for(i=1;i<=npar;i++){                      fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       /*  if (k>nlstate) k=1;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       i1=(i-1)/(ncovmodel*nlstate)+1;                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       printf("%s%d%d",alph[k],i1,tab[i]);*/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       fprintf(ficres,"%3d",i);                      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("%3d",i);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       for(j=1; j<=i;j++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         fprintf(ficres," %.5e",matcov[i][j]);                    }else{
         printf(" %.5e",matcov[i][j]);                      first=0;
       }                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
       fprintf(ficres,"\n");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       printf("\n");                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       k++;                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                  mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     while((c=getc(ficpar))=='#' && c!= EOF){                    }/* if first */
       ungetc(c,ficpar);                  } /* age mod 5 */
       fgets(line, MAXLINE, ficpar);                } /* end loop age */
       puts(line);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       fputs(line,ficparo);                first=1;
     }              } /*l12 */
     ungetc(c,ficpar);            } /* k12 */
            } /*l1 */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&ageminpar,&agemaxpar, &bage, &fage);        }/* k1 */
          } /* loop covariates */
     if (fage <= 2) {    }
       bage = ageminpar;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       fage = agemaxpar;    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     }    free_vector(xp,1,npar);
        fclose(ficresprob);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    fclose(ficresprobcov);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);    fclose(ficresprobcor);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);    /*  fclose(ficgp);*/
    }
     while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  /******************* Printing html file ***********/
     puts(line);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     fputs(line,ficparo);                    int lastpass, int stepm, int weightopt, char model[],\
   }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   ungetc(c,ficpar);                    int popforecast, int estepm ,\
                      double jprev1, double mprev1,double anprev1, \
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                    double jprev2, double mprev2,double anprev2){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int jj1, k1, i1, cpt;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    /*char optionfilehtm[FILENAMELENGTH];*/
        /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   while((c=getc(ficpar))=='#' && c!= EOF){  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
     ungetc(c,ficpar);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
     fgets(line, MAXLINE, ficpar);  /*   } */
     puts(line);  
     fputs(line,ficparo);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
   }   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
   ungetc(c,ficpar);   - 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 \
    - Life expectancies by age and initial health status (estepm=%2d months): \
    dateprev1=anprev1+mprev1/12.+jprev1/365.;     <a href=\"%s\">%s</a> <br>\n</li>", \
    dateprev2=anprev2+mprev2/12.+jprev2/365.;             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
   fscanf(ficpar,"pop_based=%d\n",&popbased);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
   fprintf(ficparo,"pop_based=%d\n",popbased);               estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   fprintf(ficres,"pop_based=%d\n",popbased);    
    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);   m=cptcoveff;
     fgets(line, MAXLINE, ficpar);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     puts(line);  
     fputs(line,ficparo);   jj1=0;
   }   for(k1=1; k1<=m;k1++){
   ungetc(c,ficpar);     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
   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);       if (cptcovn > 0) {
 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(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 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);         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\">");
 while((c=getc(ficpar))=='#' && c!= EOF){       }
     ungetc(c,ficpar);       /* Pij */
     fgets(line, MAXLINE, ficpar);       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> \
     puts(line);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
     fputs(line,ficparo);       /* Quasi-incidences */
   }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   ungetc(c,ficpar);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);         /* Stable prevalence in each health state */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);         for(cpt=1; cpt<nlstate;cpt++){
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);           fprintf(fichtm,"<br>- 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);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         }
        for(cpt=1; cpt<=nlstate;cpt++) {
 /*------------ gnuplot -------------*/          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
         }
 /*------------ free_vector  -------------*/       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
  chdir(path);  health expectancies in states (1) and (2): %s%d.png<br>\
    <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
  free_ivector(wav,1,imx);     } /* end i1 */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);   }/* End k1 */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);     fprintf(fichtm,"</ul>");
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);  
  /*free_matrix(covar,1,NCOVMAX,1,n);*/   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
  fclose(ficparo);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
  fclose(ficres);   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
 /*--------- index.htm --------*/   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
             rfileres,rfileres,\
   /*--------------- Prevalence limit --------------*/           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
             subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
   strcpy(filerespl,"pl");           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
   strcat(filerespl,fileres);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
   if((ficrespl=fopen(filerespl,"w"))==NULL) {           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  /*  if(popforecast==1) fprintf(fichtm,"\n */
   fprintf(ficrespl,"#Prevalence limit\n");  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   fprintf(ficrespl,"#Age ");  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  /*      <br>",fileres,fileres,fileres,fileres); */
   fprintf(ficrespl,"\n");  /*  else  */
    /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   prlim=matrix(1,nlstate,1,nlstate);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   m=cptcoveff;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */   jj1=0;
   k=0;   for(k1=1; k1<=m;k1++){
   agebase=ageminpar;     for(i1=1; i1<=ncodemax[k1];i1++){
   agelim=agemaxpar;       jj1++;
   ftolpl=1.e-10;       if (cptcovn > 0) {
   i1=cptcoveff;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   if (cptcovn < 1){i1=1;}         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   for(cptcov=1;cptcov<=i1;cptcov++){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       }
         k=k+1;       for(cpt=1; cpt<=nlstate;cpt++) {
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
         fprintf(ficrespl,"\n#******");  interval) in state (%d): %s%d%d.png <br>\
         for(j=1;j<=cptcoveff;j++)  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       }
         fprintf(ficrespl,"******\n");     } /* end i1 */
           }/* End k1 */
         for (age=agebase; age<=agelim; age++){   fprintf(fichtm,"</ul>");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   fflush(fichtm);
           fprintf(ficrespl,"%.0f",age );  }
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);  /******************* Gnuplot file **************/
           fprintf(ficrespl,"\n");  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         }  
       }    char dirfileres[132],optfileres[132];
     }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   fclose(ficrespl);    int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*------------- h Pij x at various ages ------------*/  /*     printf("Problem with file %s",optionfilegnuplot); */
    /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  /*   } */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    /*#ifdef windows */
   }    fprintf(ficgp,"cd \"%s\" \n",pathc);
   printf("Computing pij: result on file '%s' \n", filerespij);      /*#endif */
      m=pow(2,cptcoveff);
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/    strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
   agelim=AGESUP;   /* 1eme*/
   hstepm=stepsize*YEARM; /* Every year of age */    for (cpt=1; cpt<= nlstate ; cpt ++) {
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */     for (k1=1; k1<= m ; k1 ++) {
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   k=0;       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   for(cptcov=1;cptcov<=i1;cptcov++){       fprintf(ficgp,"set xlabel \"Age\" \n\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  set ylabel \"Probability\" \n\
       k=k+1;  set ter png small\n\
         fprintf(ficrespij,"\n#****** ");  set size 0.65,0.65\n\
         for(j=1;j<=cptcoveff;j++)  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");       for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */         else fprintf(ficgp," \%%*lf (\%%*lf)");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       }
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       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);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       for (i=1; i<= nlstate ; i ++) {
           oldm=oldms;savm=savms;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           else fprintf(ficgp," \%%*lf (\%%*lf)");
           fprintf(ficrespij,"# Age");       } 
           for(i=1; i<=nlstate;i++)       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
             for(j=1; j<=nlstate+ndeath;j++)       for (i=1; i<= nlstate ; i ++) {
               fprintf(ficrespij," %1d-%1d",i,j);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           fprintf(ficrespij,"\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
           for (h=0; h<=nhstepm; h++){       }  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
             for(i=1; i<=nlstate;i++)     }
               for(j=1; j<=nlstate+ndeath;j++)    }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    /*2 eme*/
             fprintf(ficrespij,"\n");    
           }    for (k1=1; k1<= m ; k1 ++) { 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
           fprintf(ficrespij,"\n");      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
         }      
     }      for (i=1; i<= nlstate+1 ; i ++) {
   }        k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   fclose(ficrespij);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   /*---------- Forecasting ------------------*/        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   if((stepm == 1) && (strcmp(model,".")==0)){        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);        for (j=1; j<= nlstate+1 ; j ++) {
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     free_matrix(mint,1,maxwav,1,n);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        }   
     free_vector(weight,1,n);}        fprintf(ficgp,"\" t\"\" w l 0,");
   else{        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     erreur=108;        for (j=1; j<= nlstate+1 ; j ++) {
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   }          else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   /*---------- Health expectancies and variances ------------*/        else fprintf(ficgp,"\" t\"\" w l 0,");
       }
   strcpy(filerest,"t");    }
   strcat(filerest,fileres);    
   if((ficrest=fopen(filerest,"w"))==NULL) {    /*3eme*/
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    
   }    for (k1=1; k1<= m ; k1 ++) { 
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
   strcpy(filerese,"e");        fprintf(ficgp,"set ter png small\n\
   strcat(filerese,fileres);  set size 0.65,0.65\n\
   if((ficreseij=fopen(filerese,"w"))==NULL) {  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
  strcpy(fileresv,"v");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   strcat(fileresv,fileres);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        */
   }        for (i=1; i< nlstate ; i ++) {
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          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);
           
   k=0;        } 
   for(cptcov=1;cptcov<=i1;cptcov++){      }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;    
       fprintf(ficrest,"\n#****** ");    /* CV preval stable (period) */
       for(j=1;j<=cptcoveff;j++)    for (k1=1; k1<= m ; k1 ++) { 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for (cpt=1; cpt<=nlstate ; cpt ++) {
       fprintf(ficrest,"******\n");        k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
       fprintf(ficreseij,"\n#****** ");        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
       for(j=1;j<=cptcoveff;j++)  set ter png small\nset size 0.65,0.65\n\
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  unset log y\n\
       fprintf(ficreseij,"******\n");  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
       fprintf(ficresvij,"\n#****** ");        for (i=1; i< nlstate ; i ++)
       for(j=1;j<=cptcoveff;j++)          fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
       fprintf(ficresvij,"******\n");        
         l=3+(nlstate+ndeath)*cpt;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
       oldm=oldms;savm=savms;        for (i=1; i< nlstate ; i ++) {
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            l=3+(nlstate+ndeath)*cpt;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          fprintf(ficgp,"+$%d",l+i+1);
       oldm=oldms;savm=savms;        }
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
          } 
     }  
      
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    /* proba elementaires */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficrest,"\n");      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
       epj=vector(1,nlstate+1);          for(j=1; j <=ncovmodel; j++){
       for(age=bage; age <=fage ;age++){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            jk++; 
         if (popbased==1) {            fprintf(ficgp,"\n");
           for(i=1; i<=nlstate;i++)          }
             prlim[i][i]=probs[(int)age][i][k];        }
         }      }
             }
         fprintf(ficrest," %4.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
           for(i=1, epj[j]=0.;i <=nlstate;i++) {       for(jk=1; jk <=m; jk++) {
             epj[j] += prlim[i][i]*eij[i][j][(int)age];         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
           }         if (ng==2)
           epj[nlstate+1] +=epj[j];           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
         }         else
         for(i=1, vepp=0.;i <=nlstate;i++)           fprintf(ficgp,"\nset title \"Probability\"\n");
           for(j=1;j <=nlstate;j++)         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
             vepp += vareij[i][j][(int)age];         i=1;
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));         for(k2=1; k2<=nlstate; k2++) {
         for(j=1;j <=nlstate;j++){           k3=i;
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));           for(k=1; k<=(nlstate+ndeath); k++) {
         }             if (k != k2){
         fprintf(ficrest,"\n");               if(ng==2)
       }                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     }               else
   }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
   fclose(ficreseij);               for(j=3; j <=ncovmodel; j++) {
   fclose(ficresvij);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   fclose(ficrest);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   fclose(ficpar);                   ij++;
   free_vector(epj,1,nlstate+1);                 }
                   else
   /*------- Variance limit prevalence------*/                     fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
   strcpy(fileresvpl,"vpl");               fprintf(ficgp,")/(1");
   strcat(fileresvpl,fileres);               
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {               for(k1=1; k1 <=nlstate; k1++){   
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     exit(0);                 ij=1;
   }                 for(j=3; j <=ncovmodel; j++){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                   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]]]);
   k=0;                     ij++;
   for(cptcov=1;cptcov<=i1;cptcov++){                   }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                   else
       k=k+1;                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       fprintf(ficresvpl,"\n#****** ");                 }
       for(j=1;j<=cptcoveff;j++)                 fprintf(ficgp,")");
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);               }
       fprintf(ficresvpl,"******\n");               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                     if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
       varpl=matrix(1,nlstate,(int) bage, (int) fage);               i=i+ncovmodel;
       oldm=oldms;savm=savms;             }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);           } /* end k */
     }         } /* end k2 */
  }       } /* end jk */
      } /* end ng */
   fclose(ficresvpl);     fflush(ficgp); 
   }  /* end gnuplot */
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
    /*************** Moving average **************/
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
      int i, cpt, cptcod;
      int modcovmax =1;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    int mobilavrange, mob;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    double age;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                               a covariate has 2 modalities */
   free_matrix(matcov,1,npar,1,npar);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   free_vector(delti,1,npar);  
   free_matrix(agev,1,maxwav,1,imx);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
   if(erreur >0)      for (age=bage; age<=fage; age++)
     printf("End of Imach with error or warning %d\n",erreur);        for (i=1; i<=nlstate;i++)
   else   printf("End of Imach\n");          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        /* We keep the original values on the extreme ages bage, fage and for 
   /* 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);*/         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   /*printf("Total time was %d uSec.\n", total_usecs);*/         we use a 5 terms etc. until the borders are no more concerned. 
   /*------ End -----------*/      */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
  end:          for (i=1; i<=nlstate;i++){
 #ifdef windows            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   /* chdir(pathcd);*/              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
 #endif                for (cpt=1;cpt<=(mob-1)/2;cpt++){
  /*system("wgnuplot graph.plt");*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
  /*system("../gp37mgw/wgnuplot graph.plt");*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
  /*system("cd ../gp37mgw");*/                }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
  strcpy(plotcmd,GNUPLOTPROGRAM);            }
  strcat(plotcmd," ");          }
  strcat(plotcmd,optionfilegnuplot);        }/* end age */
  system(plotcmd);      }/* end mob */
     }else return -1;
 #ifdef windows    return 0;
   while (z[0] != 'q') {  }/* End movingaverage */
     /* chdir(path); */  
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  
     scanf("%s",z);  /************** Forecasting ******************/
     if (z[0] == 'c') system("./imach");  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){
     else if (z[0] == 'e') system(optionfilehtm);    /* proj1, year, month, day of starting projection 
     else if (z[0] == 'g') system(plotcmd);       agemin, agemax range of age
     else if (z[0] == 'q') exit(0);       dateprev1 dateprev2 range of dates during which prevalence is computed
   }       anproj2 year of en of projection (same day and month as proj1).
 #endif    */
 }    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   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);
     
     /* 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);*/
   
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     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 */
   }
   
   
   

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  Added in v.1.90


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