Diff for /imach/src/imach.c between versions 1.35 and 1.88

version 1.35, 2002/03/26 17:08:39 version 1.88, 2003/06/23 17:54:56
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.88  2003/06/23 17:54:56  brouard
      * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.87  2003/06/18 12:26:01  brouard
   first survey ("cross") where individuals from different ages are    Version 0.96
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.86  2003/06/17 20:04:08  brouard
   second wave of interviews ("longitudinal") which measure each change    (Module): Change position of html and gnuplot routines and added
   (if any) in individual health status.  Health expectancies are    routine fileappend.
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.85  2003/06/17 13:12:43  brouard
   Maximum Likelihood of the parameters involved in the model.  The    * imach.c (Repository): Check when date of death was earlier that
   simplest model is the multinomial logistic model where pij is the    current date of interview. It may happen when the death was just
   probabibility to be observed in state j at the second wave    prior to the death. In this case, dh was negative and likelihood
   conditional to be observed in state i at the first wave. Therefore    was wrong (infinity). We still send an "Error" but patch by
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    assuming that the date of death was just one stepm after the
   'age' is age and 'sex' is a covariate. If you want to have a more    interview.
   complex model than "constant and age", you should modify the program    (Repository): Because some people have very long ID (first column)
   where the markup *Covariates have to be included here again* invites    we changed int to long in num[] and we added a new lvector for
   you to do it.  More covariates you add, slower the    memory allocation. But we also truncated to 8 characters (left
   convergence.    truncation)
     (Repository): No more line truncation errors.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.84  2003/06/13 21:44:43  brouard
   identical for each individual. Also, if a individual missed an    * imach.c (Repository): Replace "freqsummary" at a correct
   intermediate interview, the information is lost, but taken into    place. It differs from routine "prevalence" which may be called
   account using an interpolation or extrapolation.      many times. Probs is memory consuming and must be used with
     parcimony.
   hPijx is the probability to be observed in state i at age x+h    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.83  2003/06/10 13:39:11  lievre
   states. This elementary transition (by month or quarter trimester,    *** empty log message ***
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.82  2003/06/05 15:57:20  brouard
   and the contribution of each individual to the likelihood is simply    Add log in  imach.c and  fullversion number is now printed.
   hPijx.  
   */
   Also this programme outputs the covariance matrix of the parameters but also  /*
   of the life expectancies. It also computes the prevalence limits.     Interpolated Markov Chain
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Short summary of the programme:
            Institut national d'études démographiques, Paris.    
   This software have been partly granted by Euro-REVES, a concerted action    This program computes Healthy Life Expectancies from
   from the European Union.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   It is copyrighted identically to a GNU software product, ie programme and    first survey ("cross") where individuals from different ages are
   software can be distributed freely for non commercial use. Latest version    interviewed on their health status or degree of disability (in the
   can be accessed at http://euroreves.ined.fr/imach .    case of a health survey which is our main interest) -2- at least a
   **********************************************************************/    second wave of interviews ("longitudinal") which measure each change
      (if any) in individual health status.  Health expectancies are
 #include <math.h>    computed from the time spent in each health state according to a
 #include <stdio.h>    model. More health states you consider, more time is necessary to reach the
 #include <stdlib.h>    Maximum Likelihood of the parameters involved in the model.  The
 #include <unistd.h>    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 #define MAXLINE 256    conditional to be observed in state i at the first wave. Therefore
 #define GNUPLOTPROGRAM "wgnuplot"    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    'age' is age and 'sex' is a covariate. If you want to have a more
 #define FILENAMELENGTH 80    complex model than "constant and age", you should modify the program
 /*#define DEBUG*/    where the markup *Covariates have to be included here again* invites
 #define windows    you to do it.  More covariates you add, slower the
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    convergence.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     The advantage of this computer programme, compared to a simple
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    multinomial logistic model, is clear when the delay between waves is not
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 #define NINTERVMAX 8    account using an interpolation or extrapolation.  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    hPijx is the probability to be observed in state i at age x+h
 #define NCOVMAX 8 /* Maximum number of covariates */    conditional to the observed state i at age x. The delay 'h' can be
 #define MAXN 20000    split into an exact number (nh*stepm) of unobserved intermediate
 #define YEARM 12. /* Number of months per year */    states. This elementary transition (by month, quarter,
 #define AGESUP 130    semester or year) is modelled as a multinomial logistic.  The hPx
 #define AGEBASE 40    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
     hPijx.
 int erreur; /* Error number */  
 int nvar;    Also this programme outputs the covariance matrix of the parameters but also
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    of the life expectancies. It also computes the stable prevalence. 
 int npar=NPARMAX;    
 int nlstate=2; /* Number of live states */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int ndeath=1; /* Number of dead states */             Institut national d'études démographiques, Paris.
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    This software have been partly granted by Euro-REVES, a concerted action
 int popbased=0;    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 int *wav; /* Number of waves for this individuual 0 is possible */    software can be distributed freely for non commercial use. Latest version
 int maxwav; /* Maxim number of waves */    can be accessed at http://euroreves.ined.fr/imach .
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    
 double jmean; /* Mean space between 2 waves */    **********************************************************************/
 double **oldm, **newm, **savm; /* Working pointers to matrices */  /*
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    main
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    read parameterfile
 FILE *ficgp,*ficresprob,*ficpop;    read datafile
 FILE *ficreseij;    concatwav
   char filerese[FILENAMELENGTH];    freqsummary
  FILE  *ficresvij;    if (mle >= 1)
   char fileresv[FILENAMELENGTH];      mlikeli
  FILE  *ficresvpl;    print results files
   char fileresvpl[FILENAMELENGTH];    if mle==1 
        computes hessian
 #define NR_END 1    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define FREE_ARG char*        begin-prev-date,...
 #define FTOL 1.0e-10    open gnuplot file
     open html file
 #define NRANSI    stable prevalence
 #define ITMAX 200     for age prevalim()
     h Pij x
 #define TOL 2.0e-4    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 #define CGOLD 0.3819660    health expectancies
 #define ZEPS 1.0e-10    Variance-covariance of DFLE
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    prevalence()
      movingaverage()
 #define GOLD 1.618034    varevsij() 
 #define GLIMIT 100.0    if popbased==1 varevsij(,popbased)
 #define TINY 1.0e-20    total life expectancies
     Variance of stable prevalence
 static double maxarg1,maxarg2;   end
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  */
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)   
   #include <math.h>
 static double sqrarg;  #include <stdio.h>
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #include <stdlib.h>
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #include <unistd.h>
   
 int imx;  #include <sys/time.h>
 int stepm;  #include <time.h>
 /* Stepm, step in month: minimum step interpolation*/  #include "timeval.h"
   
 int m,nb;  #define MAXLINE 256
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define GNUPLOTPROGRAM "gnuplot"
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double **pmmij, ***probs, ***mobaverage;  #define FILENAMELENGTH 132
 double dateintmean=0;  /*#define DEBUG*/
   /*#define windows*/
 double *weight;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 int **s; /* Status */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 /**************** split *************************/  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define NCOVMAX 8 /* Maximum number of covariates */
 {  #define MAXN 20000
    char *s;                             /* pointer */  #define YEARM 12. /* Number of months per year */
    int  l1, l2;                         /* length counters */  #define AGESUP 130
   #define AGEBASE 40
    l1 = strlen( path );                 /* length of path */  #ifdef unix
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define DIRSEPARATOR '/'
 #ifdef windows  #define ODIRSEPARATOR '\\'
    s = strrchr( path, '\\' );           /* find last / */  #else
 #else  #define DIRSEPARATOR '\\'
    s = strrchr( path, '/' );            /* find last / */  #define ODIRSEPARATOR '/'
 #endif  #endif
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */  /* $Id$ */
       extern char       *getwd( );  /* $State$ */
   
       if ( getwd( dirc ) == NULL ) {  char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
 #else  char fullversion[]="$Revision$ $Date$"; 
       extern char       *getcwd( );  int erreur; /* Error number */
   int nvar;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #endif  int npar=NPARMAX;
          return( GLOCK_ERROR_GETCWD );  int nlstate=2; /* Number of live states */
       }  int ndeath=1; /* Number of dead states */
       strcpy( name, path );             /* we've got it */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    } else {                             /* strip direcotry from path */  int popbased=0;
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  int *wav; /* Number of waves for this individuual 0 is possible */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int maxwav; /* Maxim number of waves */
       strcpy( name, s );                /* save file name */  int jmin, jmax; /* min, max spacing between 2 waves */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  int gipmx, gsw; /* Global variables on the number of contributions 
       dirc[l1-l2] = 0;                  /* add zero */                     to the likelihood and the sum of weights (done by funcone)*/
    }  int mle, weightopt;
    l1 = strlen( dirc );                 /* length of directory */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #ifdef windows  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 #else             * wave mi and wave mi+1 is not an exact multiple of stepm. */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  double jmean; /* Mean space between 2 waves */
 #endif  double **oldm, **newm, **savm; /* Working pointers to matrices */
    s = strrchr( name, '.' );            /* find last / */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    s++;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    strcpy(ext,s);                       /* save extension */  FILE *ficlog, *ficrespow;
    l1= strlen( name);  int globpr; /* Global variable for printing or not */
    l2= strlen( s)+1;  double fretone; /* Only one call to likelihood */
    strncpy( finame, name, l1-l2);  long ipmx; /* Number of contributions */
    finame[l1-l2]= 0;  double sw; /* Sum of weights */
    return( 0 );                         /* we're done */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 }  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /******************************************/  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 void replace(char *s, char*t)  char filerese[FILENAMELENGTH];
 {  FILE  *ficresvij;
   int i;  char fileresv[FILENAMELENGTH];
   int lg=20;  FILE  *ficresvpl;
   i=0;  char fileresvpl[FILENAMELENGTH];
   lg=strlen(t);  char title[MAXLINE];
   for(i=0; i<= lg; i++) {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     (s[i] = t[i]);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
     if (t[i]== '\\') s[i]='/';  char tmpout[FILENAMELENGTH]; 
   }  char command[FILENAMELENGTH];
 }  int  outcmd=0;
   
 int nbocc(char *s, char occ)  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 {  char lfileres[FILENAMELENGTH];
   int i,j=0;  char filelog[FILENAMELENGTH]; /* Log file */
   int lg=20;  char filerest[FILENAMELENGTH];
   i=0;  char fileregp[FILENAMELENGTH];
   lg=strlen(s);  char popfile[FILENAMELENGTH];
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   }  
   return j;  #define NR_END 1
 }  #define FREE_ARG char*
   #define FTOL 1.0e-10
 void cutv(char *u,char *v, char*t, char occ)  
 {  #define NRANSI 
   int i,lg,j,p=0;  #define ITMAX 200 
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {  #define TOL 2.0e-4 
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
   lg=strlen(t);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  #define GOLD 1.618034 
   }  #define GLIMIT 100.0 
      u[p]='\0';  #define TINY 1.0e-20 
   
    for(j=0; j<= lg; j++) {  static double maxarg1,maxarg2;
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 }    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 /********************** nrerror ********************/  #define rint(a) floor(a+0.5)
   
 void nrerror(char error_text[])  static double sqrarg;
 {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   fprintf(stderr,"ERREUR ...\n");  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  int imx; 
 }  int stepm;
 /*********************** vector *******************/  /* Stepm, step in month: minimum step interpolation*/
 double *vector(int nl, int nh)  
 {  int estepm;
   double *v;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  int m,nb;
   return v-nl+NR_END;  long *num;
 }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 /************************ free vector ******************/  double **pmmij, ***probs;
 void free_vector(double*v, int nl, int nh)  double dateintmean=0;
 {  
   free((FREE_ARG)(v+nl-NR_END));  double *weight;
 }  int **s; /* Status */
   double *agedc, **covar, idx;
 /************************ivector *******************************/  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 int *ivector(long nl,long nh)  
 {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   int *v;  double ftolhess; /* Tolerance for computing hessian */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  /**************** split *************************/
   return v-nl+NR_END;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 }  {
     char  *ss;                            /* pointer */
 /******************free ivector **************************/    int   l1, l2;                         /* length counters */
 void free_ivector(int *v, long nl, long nh)  
 {    l1 = strlen(path );                   /* length of path */
   free((FREE_ARG)(v+nl-NR_END));    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
 /******************* imatrix *******************************/      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 int **imatrix(long nrl, long nrh, long ncl, long nch)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */      /* get current working directory */
 {      /*    extern  char* getcwd ( char *buf , int len);*/
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   int **m;        return( GLOCK_ERROR_GETCWD );
        }
   /* allocate pointers to rows */      strcpy( name, path );               /* we've got it */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    } else {                              /* strip direcotry from path */
   if (!m) nrerror("allocation failure 1 in matrix()");      ss++;                               /* after this, the filename */
   m += NR_END;      l2 = strlen( ss );                  /* length of filename */
   m -= nrl;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
        strcpy( name, ss );         /* save file name */
        strncpy( dirc, path, l1 - l2 );     /* now the directory */
   /* allocate rows and set pointers to them */      dirc[l1-l2] = 0;                    /* add zero */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    l1 = strlen( dirc );                  /* length of directory */
   m[nrl] += NR_END;    /*#ifdef windows
   m[nrl] -= ncl;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
    #else
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
    #endif
   /* return pointer to array of pointers to rows */    */
   return m;    ss = strrchr( name, '.' );            /* find last / */
 }    ss++;
     strcpy(ext,ss);                       /* save extension */
 /****************** free_imatrix *************************/    l1= strlen( name);
 void free_imatrix(m,nrl,nrh,ncl,nch)    l2= strlen(ss)+1;
       int **m;    strncpy( finame, name, l1-l2);
       long nch,ncl,nrh,nrl;    finame[l1-l2]= 0;
      /* free an int matrix allocated by imatrix() */    return( 0 );                          /* we're done */
 {  }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  
 }  /******************************************/
   
 /******************* matrix *******************************/  void replace(char *s, char*t)
 double **matrix(long nrl, long nrh, long ncl, long nch)  {
 {    int i;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    int lg=20;
   double **m;    i=0;
     lg=strlen(t);
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    for(i=0; i<= lg; i++) {
   if (!m) nrerror("allocation failure 1 in matrix()");      (s[i] = t[i]);
   m += NR_END;      if (t[i]== '\\') s[i]='/';
   m -= nrl;    }
   }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int nbocc(char *s, char occ)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    int i,j=0;
     int lg=20;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    i=0;
   return m;    lg=strlen(s);
 }    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 /*************************free matrix ************************/    }
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    return j;
 {  }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  void cutv(char *u,char *v, char*t, char occ)
 }  {
     /* cuts string t into u and v where u is ended by char occ excluding it
 /******************* ma3x *******************************/       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)       gives u="abcedf" and v="ghi2j" */
 {    int i,lg,j,p=0;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    i=0;
   double ***m;    for(j=0; j<=strlen(t)-1; j++) {
       if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    lg=strlen(t);
   m -= nrl;    for(j=0; j<p; j++) {
       (u[j] = t[j]);
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");       u[p]='\0';
   m[nrl] += NR_END;  
   m[nrl] -= ncl;     for(j=0; j<= lg; j++) {
       if (j>=(p+1))(v[j-p-1] = t[j]);
   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)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  /********************** nrerror ********************/
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  void nrerror(char error_text[])
   for (j=ncl+1; j<=nch; j++)  {
     m[nrl][j]=m[nrl][j-1]+nlay;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
   for (i=nrl+1; i<=nrh; i++) {    exit(EXIT_FAILURE);
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  }
     for (j=ncl+1; j<=nch; j++)  /*********************** vector *******************/
       m[i][j]=m[i][j-1]+nlay;  double *vector(int nl, int nh)
   }  {
   return m;    double *v;
 }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 /*************************free ma3x ************************/    return v-nl+NR_END;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  }
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  /************************ free vector ******************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  void free_vector(double*v, int nl, int nh)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /***************** f1dim *************************/  
 extern int ncom;  /************************ivector *******************************/
 extern double *pcom,*xicom;  int *ivector(long nl,long nh)
 extern double (*nrfunc)(double []);  {
      int *v;
 double f1dim(double x)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 {    if (!v) nrerror("allocation failure in ivector");
   int j;    return v-nl+NR_END;
   double f;  }
   double *xt;  
    /******************free ivector **************************/
   xt=vector(1,ncom);  void free_ivector(int *v, long nl, long nh)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  {
   f=(*nrfunc)(xt);    free((FREE_ARG)(v+nl-NR_END));
   free_vector(xt,1,ncom);  }
   return f;  
 }  /************************lvector *******************************/
   long *lvector(long nl,long nh)
 /*****************brent *************************/  {
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    long *v;
 {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   int iter;    if (!v) nrerror("allocation failure in ivector");
   double a,b,d,etemp;    return v-nl+NR_END;
   double fu,fv,fw,fx;  }
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  /******************free lvector **************************/
   double e=0.0;  void free_lvector(long *v, long nl, long nh)
    {
   a=(ax < cx ? ax : cx);    free((FREE_ARG)(v+nl-NR_END));
   b=(ax > cx ? ax : cx);  }
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  /******************* imatrix *******************************/
   for (iter=1;iter<=ITMAX;iter++) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     xm=0.5*(a+b);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  { 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     printf(".");fflush(stdout);    int **m; 
 #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);    /* allocate pointers to rows */ 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 #endif    if (!m) nrerror("allocation failure 1 in matrix()"); 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    m += NR_END; 
       *xmin=x;    m -= nrl; 
       return fx;    
     }    
     ftemp=fu;    /* allocate rows and set pointers to them */ 
     if (fabs(e) > tol1) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       r=(x-w)*(fx-fv);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       q=(x-v)*(fx-fw);    m[nrl] += NR_END; 
       p=(x-v)*q-(x-w)*r;    m[nrl] -= ncl; 
       q=2.0*(q-r);    
       if (q > 0.0) p = -p;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       q=fabs(q);    
       etemp=e;    /* return pointer to array of pointers to rows */ 
       e=d;    return m; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  } 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  /****************** free_imatrix *************************/
         d=p/q;  void free_imatrix(m,nrl,nrh,ncl,nch)
         u=x+d;        int **m;
         if (u-a < tol2 || b-u < tol2)        long nch,ncl,nrh,nrl; 
           d=SIGN(tol1,xm-x);       /* free an int matrix allocated by imatrix() */ 
       }  { 
     } else {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    free((FREE_ARG) (m+nrl-NR_END)); 
     }  } 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  /******************* matrix *******************************/
     if (fu <= fx) {  double **matrix(long nrl, long nrh, long ncl, long nch)
       if (u >= x) a=x; else b=x;  {
       SHFT(v,w,x,u)    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         SHFT(fv,fw,fx,fu)    double **m;
         } else {  
           if (u < x) a=u; else b=u;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
           if (fu <= fw || w == x) {    if (!m) nrerror("allocation failure 1 in matrix()");
             v=w;    m += NR_END;
             w=u;    m -= nrl;
             fv=fw;  
             fw=fu;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
           } else if (fu <= fv || v == x || v == w) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
             v=u;    m[nrl] += NR_END;
             fv=fu;    m[nrl] -= ncl;
           }  
         }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   }    return m;
   nrerror("Too many iterations in brent");    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   *xmin=x;     */
   return fx;  }
 }  
   /*************************free matrix ************************/
 /****************** mnbrak ***********************/  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    free((FREE_ARG)(m[nrl]+ncl-NR_END));
             double (*func)(double))    free((FREE_ARG)(m+nrl-NR_END));
 {  }
   double ulim,u,r,q, dum;  
   double fu;  /******************* ma3x *******************************/
    double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   *fa=(*func)(*ax);  {
   *fb=(*func)(*bx);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   if (*fb > *fa) {    double ***m;
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
   *cx=(*bx)+GOLD*(*bx-*ax);    m += NR_END;
   *fc=(*func)(*cx);    m -= nrl;
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     q=(*bx-*cx)*(*fb-*fa);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    m[nrl] += NR_END;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    m[nrl] -= ncl;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {    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()");
       if (fu < *fc) {    m[nrl][ncl] += NR_END;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    m[nrl][ncl] -= nll;
           SHFT(*fb,*fc,fu,(*func)(u))    for (j=ncl+1; j<=nch; j++) 
           }      m[nrl][j]=m[nrl][j-1]+nlay;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    
       u=ulim;    for (i=nrl+1; i<=nrh; i++) {
       fu=(*func)(u);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     } else {      for (j=ncl+1; j<=nch; j++) 
       u=(*cx)+GOLD*(*cx-*bx);        m[i][j]=m[i][j-1]+nlay;
       fu=(*func)(u);    }
     }    return m; 
     SHFT(*ax,*bx,*cx,u)    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       SHFT(*fa,*fb,*fc,fu)             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       }    */
 }  }
   
 /*************** linmin ************************/  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 int ncom;  {
 double *pcom,*xicom;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 double (*nrfunc)(double []);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  }
 {  
   double brent(double ax, double bx, double cx,  /***************** f1dim *************************/
                double (*f)(double), double tol, double *xmin);  extern int ncom; 
   double f1dim(double x);  extern double *pcom,*xicom;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  extern double (*nrfunc)(double []); 
               double *fc, double (*func)(double));   
   int j;  double f1dim(double x) 
   double xx,xmin,bx,ax;  { 
   double fx,fb,fa;    int j; 
      double f;
   ncom=n;    double *xt; 
   pcom=vector(1,n);   
   xicom=vector(1,n);    xt=vector(1,ncom); 
   nrfunc=func;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   for (j=1;j<=n;j++) {    f=(*nrfunc)(xt); 
     pcom[j]=p[j];    free_vector(xt,1,ncom); 
     xicom[j]=xi[j];    return f; 
   }  } 
   ax=0.0;  
   xx=1.0;  /*****************brent *************************/
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  { 
 #ifdef DEBUG    int iter; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    double a,b,d,etemp;
 #endif    double fu,fv,fw,fx;
   for (j=1;j<=n;j++) {    double ftemp;
     xi[j] *= xmin;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     p[j] += xi[j];    double e=0.0; 
   }   
   free_vector(xicom,1,n);    a=(ax < cx ? ax : cx); 
   free_vector(pcom,1,n);    b=(ax > cx ? ax : cx); 
 }    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
 /*************** powell ************************/    for (iter=1;iter<=ITMAX;iter++) { 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      xm=0.5*(a+b); 
             double (*func)(double []))      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   void linmin(double p[], double xi[], int n, double *fret,      printf(".");fflush(stdout);
               double (*func)(double []));      fprintf(ficlog,".");fflush(ficlog);
   int i,ibig,j;  #ifdef DEBUG
   double del,t,*pt,*ptt,*xit;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   double fp,fptt;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   double *xits;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   pt=vector(1,n);  #endif
   ptt=vector(1,n);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   xit=vector(1,n);        *xmin=x; 
   xits=vector(1,n);        return fx; 
   *fret=(*func)(p);      } 
   for (j=1;j<=n;j++) pt[j]=p[j];      ftemp=fu;
   for (*iter=1;;++(*iter)) {      if (fabs(e) > tol1) { 
     fp=(*fret);        r=(x-w)*(fx-fv); 
     ibig=0;        q=(x-v)*(fx-fw); 
     del=0.0;        p=(x-v)*q-(x-w)*r; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);        q=2.0*(q-r); 
     for (i=1;i<=n;i++)        if (q > 0.0) p = -p; 
       printf(" %d %.12f",i, p[i]);        q=fabs(q); 
     printf("\n");        etemp=e; 
     for (i=1;i<=n;i++) {        e=d; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       fptt=(*fret);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 #ifdef DEBUG        else { 
       printf("fret=%lf \n",*fret);          d=p/q; 
 #endif          u=x+d; 
       printf("%d",i);fflush(stdout);          if (u-a < tol2 || b-u < tol2) 
       linmin(p,xit,n,fret,func);            d=SIGN(tol1,xm-x); 
       if (fabs(fptt-(*fret)) > del) {        } 
         del=fabs(fptt-(*fret));      } else { 
         ibig=i;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }      } 
 #ifdef DEBUG      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       printf("%d %.12e",i,(*fret));      fu=(*f)(u); 
       for (j=1;j<=n;j++) {      if (fu <= fx) { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);        if (u >= x) a=x; else b=x; 
         printf(" x(%d)=%.12e",j,xit[j]);        SHFT(v,w,x,u) 
       }          SHFT(fv,fw,fx,fu) 
       for(j=1;j<=n;j++)          } else { 
         printf(" p=%.12e",p[j]);            if (u < x) a=u; else b=u; 
       printf("\n");            if (fu <= fw || w == x) { 
 #endif              v=w; 
     }              w=u; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {              fv=fw; 
 #ifdef DEBUG              fw=fu; 
       int k[2],l;            } else if (fu <= fv || v == x || v == w) { 
       k[0]=1;              v=u; 
       k[1]=-1;              fv=fu; 
       printf("Max: %.12e",(*func)(p));            } 
       for (j=1;j<=n;j++)          } 
         printf(" %.12e",p[j]);    } 
       printf("\n");    nrerror("Too many iterations in brent"); 
       for(l=0;l<=1;l++) {    *xmin=x; 
         for (j=1;j<=n;j++) {    return fx; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  } 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  /****************** mnbrak ***********************/
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 #endif              double (*func)(double)) 
   { 
     double ulim,u,r,q, dum;
       free_vector(xit,1,n);    double fu; 
       free_vector(xits,1,n);   
       free_vector(ptt,1,n);    *fa=(*func)(*ax); 
       free_vector(pt,1,n);    *fb=(*func)(*bx); 
       return;    if (*fb > *fa) { 
     }      SHFT(dum,*ax,*bx,dum) 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        SHFT(dum,*fb,*fa,dum) 
     for (j=1;j<=n;j++) {        } 
       ptt[j]=2.0*p[j]-pt[j];    *cx=(*bx)+GOLD*(*bx-*ax); 
       xit[j]=p[j]-pt[j];    *fc=(*func)(*cx); 
       pt[j]=p[j];    while (*fb > *fc) { 
     }      r=(*bx-*ax)*(*fb-*fc); 
     fptt=(*func)(ptt);      q=(*bx-*cx)*(*fb-*fa); 
     if (fptt < fp) {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       if (t < 0.0) {      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         linmin(p,xit,n,fret,func);      if ((*bx-u)*(u-*cx) > 0.0) { 
         for (j=1;j<=n;j++) {        fu=(*func)(u); 
           xi[j][ibig]=xi[j][n];      } else if ((*cx-u)*(u-ulim) > 0.0) { 
           xi[j][n]=xit[j];        fu=(*func)(u); 
         }        if (fu < *fc) { 
 #ifdef DEBUG          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);            SHFT(*fb,*fc,fu,(*func)(u)) 
         for(j=1;j<=n;j++)            } 
           printf(" %.12e",xit[j]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         printf("\n");        u=ulim; 
 #endif        fu=(*func)(u); 
       }      } else { 
     }        u=(*cx)+GOLD*(*cx-*bx); 
   }        fu=(*func)(u); 
 }      } 
       SHFT(*ax,*bx,*cx,u) 
 /**** Prevalence limit ****************/        SHFT(*fa,*fb,*fc,fu) 
         } 
 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  /*************** linmin ************************/
      matrix by transitions matrix until convergence is reached */  
   int ncom; 
   int i, ii,j,k;  double *pcom,*xicom;
   double min, max, maxmin, maxmax,sumnew=0.;  double (*nrfunc)(double []); 
   double **matprod2();   
   double **out, cov[NCOVMAX], **pmij();  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   double **newm;  { 
   double agefin, delaymax=50 ; /* Max number of years to converge */    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
   for (ii=1;ii<=nlstate+ndeath;ii++)    double f1dim(double x); 
     for (j=1;j<=nlstate+ndeath;j++){    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);                double *fc, double (*func)(double)); 
     }    int j; 
     double xx,xmin,bx,ax; 
    cov[1]=1.;    double fx,fb,fa;
     
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    ncom=n; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    pcom=vector(1,n); 
     newm=savm;    xicom=vector(1,n); 
     /* Covariates have to be included here again */    nrfunc=func; 
      cov[2]=agefin;    for (j=1;j<=n;j++) { 
        pcom[j]=p[j]; 
       for (k=1; k<=cptcovn;k++) {      xicom[j]=xi[j]; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    } 
         /*      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]]);*/    ax=0.0; 
       }    xx=1.0; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       for (k=1; k<=cptcovprod;k++)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  #endif
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    for (j=1;j<=n;j++) { 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      xi[j] *= xmin; 
       p[j] += xi[j]; 
     savm=oldm;    } 
     oldm=newm;    free_vector(xicom,1,n); 
     maxmax=0.;    free_vector(pcom,1,n); 
     for(j=1;j<=nlstate;j++){  } 
       min=1.;  
       max=0.;  /*************** powell ************************/
       for(i=1; i<=nlstate; i++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         sumnew=0;              double (*func)(double [])) 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  { 
         prlim[i][j]= newm[i][j]/(1-sumnew);    void linmin(double p[], double xi[], int n, double *fret, 
         max=FMAX(max,prlim[i][j]);                double (*func)(double [])); 
         min=FMIN(min,prlim[i][j]);    int i,ibig,j; 
       }    double del,t,*pt,*ptt,*xit;
       maxmin=max-min;    double fp,fptt;
       maxmax=FMAX(maxmax,maxmin);    double *xits;
     }    pt=vector(1,n); 
     if(maxmax < ftolpl){    ptt=vector(1,n); 
       return prlim;    xit=vector(1,n); 
     }    xits=vector(1,n); 
   }    *fret=(*func)(p); 
 }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
 /*************** transition probabilities ***************/      fp=(*fret); 
       ibig=0; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      del=0.0; 
 {      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   double s1, s2;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   /*double t34;*/      fprintf(ficrespow,"%d %.12f",*iter,*fret);
   int i,j,j1, nc, ii, jj;      for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
     for(i=1; i<= nlstate; i++){        fprintf(ficlog," %d %.12lf",i, p[i]);
     for(j=1; j<i;j++){        fprintf(ficrespow," %.12lf", p[i]);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      }
         /*s2 += param[i][j][nc]*cov[nc];*/      printf("\n");
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      fprintf(ficlog,"\n");
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      fprintf(ficrespow,"\n");
       }      for (i=1;i<=n;i++) { 
       ps[i][j]=s2;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        fptt=(*fret); 
     }  #ifdef DEBUG
     for(j=i+1; j<=nlstate+ndeath;j++){        printf("fret=%lf \n",*fret);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        fprintf(ficlog,"fret=%lf \n",*fret);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #endif
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        printf("%d",i);fflush(stdout);
       }        fprintf(ficlog,"%d",i);fflush(ficlog);
       ps[i][j]=s2;        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
     /*ps[3][2]=1;*/          ibig=i; 
         } 
   for(i=1; i<= nlstate; i++){  #ifdef DEBUG
      s1=0;        printf("%d %.12e",i,(*fret));
     for(j=1; j<i; j++)        fprintf(ficlog,"%d %.12e",i,(*fret));
       s1+=exp(ps[i][j]);        for (j=1;j<=n;j++) {
     for(j=i+1; j<=nlstate+ndeath; j++)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       s1+=exp(ps[i][j]);          printf(" x(%d)=%.12e",j,xit[j]);
     ps[i][i]=1./(s1+1.);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     for(j=1; j<i; j++)        }
       ps[i][j]= exp(ps[i][j])*ps[i][i];        for(j=1;j<=n;j++) {
     for(j=i+1; j<=nlstate+ndeath; j++)          printf(" p=%.12e",p[j]);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          fprintf(ficlog," p=%.12e",p[j]);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        }
   } /* end i */        printf("\n");
         fprintf(ficlog,"\n");
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #endif
     for(jj=1; jj<= nlstate+ndeath; jj++){      } 
       ps[ii][jj]=0;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       ps[ii][ii]=1;  #ifdef DEBUG
     }        int k[2],l;
   }        k[0]=1;
         k[1]=-1;
         printf("Max: %.12e",(*func)(p));
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for(jj=1; jj<= nlstate+ndeath; jj++){        for (j=1;j<=n;j++) {
      printf("%lf ",ps[ii][jj]);          printf(" %.12e",p[j]);
    }          fprintf(ficlog," %.12e",p[j]);
     printf("\n ");        }
     }        printf("\n");
     printf("\n ");printf("%lf ",cov[2]);*/        fprintf(ficlog,"\n");
 /*        for(l=0;l<=1;l++) {
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          for (j=1;j<=n;j++) {
   goto end;*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     return ps;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
 /**************** Product of 2 matrices ******************/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        }
 {  #endif
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized        free_vector(xit,1,n); 
      before: only the contents of out is modified. The function returns        free_vector(xits,1,n); 
      a pointer to pointers identical to out */        free_vector(ptt,1,n); 
   long i, j, k;        free_vector(pt,1,n); 
   for(i=nrl; i<= nrh; i++)        return; 
     for(k=ncolol; k<=ncoloh; k++)      } 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         out[i][k] +=in[i][j]*b[j][k];      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
   return out;        xit[j]=p[j]-pt[j]; 
 }        pt[j]=p[j]; 
       } 
       fptt=(*func)(ptt); 
 /************* Higher Matrix Product ***************/      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        if (t < 0.0) { 
 {          linmin(p,xit,n,fret,func); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          for (j=1;j<=n;j++) { 
      duration (i.e. until            xi[j][ibig]=xi[j][n]; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.            xi[j][n]=xit[j]; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          }
      (typically every 2 years instead of every month which is too big).  #ifdef DEBUG
      Model is determined by parameters x and covariates have to be          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
      included manually here.          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
      */            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
   int i, j, d, h, k;          }
   double **out, cov[NCOVMAX];          printf("\n");
   double **newm;          fprintf(ficlog,"\n");
   #endif
   /* Hstepm could be zero and should return the unit matrix */        }
   for (i=1;i<=nlstate+ndeath;i++)      } 
     for (j=1;j<=nlstate+ndeath;j++){    } 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  } 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }  /**** Prevalence limit (stable prevalence)  ****************/
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for(d=1; d <=hstepm; d++){  {
       newm=savm;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       /* Covariates have to be included here again */       matrix by transitions matrix until convergence is reached */
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    int i, ii,j,k;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    double min, max, maxmin, maxmax,sumnew=0.;
       for (k=1; k<=cptcovage;k++)    double **matprod2();
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    double **out, cov[NCOVMAX], **pmij();
       for (k=1; k<=cptcovprod;k++)    double **newm;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double agefin, delaymax=50 ; /* Max number of years to converge */
   
     for (ii=1;ii<=nlstate+ndeath;ii++)
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      for (j=1;j<=nlstate+ndeath;j++){
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;     cov[1]=1.;
       oldm=newm;   
     }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(i=1; i<=nlstate+ndeath; i++)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       for(j=1;j<=nlstate+ndeath;j++) {      newm=savm;
         po[i][j][h]=newm[i][j];      /* Covariates have to be included here again */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);       cov[2]=agefin;
          */    
       }        for (k=1; k<=cptcovn;k++) {
   } /* end h */          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   return po;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
 }        }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
 /*************** log-likelihood *************/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 double func( double *x)  
 {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   int i, ii, j, k, mi, d, kk;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   double **out;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */      savm=oldm;
   long ipmx;      oldm=newm;
   /*extern weight */      maxmax=0.;
   /* We are differentiating ll according to initial status */      for(j=1;j<=nlstate;j++){
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        min=1.;
   /*for(i=1;i<imx;i++)        max=0.;
     printf(" %d\n",s[4][i]);        for(i=1; i<=nlstate; i++) {
   */          sumnew=0;
   cov[1]=1.;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
   for(k=1; k<=nlstate; k++) ll[k]=0.;          max=FMAX(max,prlim[i][j]);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          min=FMIN(min,prlim[i][j]);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        }
     for(mi=1; mi<= wav[i]-1; mi++){        maxmin=max-min;
       for (ii=1;ii<=nlstate+ndeath;ii++)        maxmax=FMAX(maxmax,maxmin);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      }
       for(d=0; d<dh[mi][i]; d++){      if(maxmax < ftolpl){
         newm=savm;        return prlim;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      }
         for (kk=1; kk<=cptcovage;kk++) {    }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  }
         }  
          /*************** transition probabilities ***************/ 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         savm=oldm;  {
         oldm=newm;    double s1, s2;
            /*double t34;*/
            int i,j,j1, nc, ii, jj;
       } /* end mult */  
            for(i=1; i<= nlstate; i++){
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      for(j=1; j<i;j++){
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       ipmx +=1;          /*s2 += param[i][j][nc]*cov[nc];*/
       sw += weight[i];          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
     } /* end of wave */        }
   } /* end of individual */        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      for(j=i+1; j<=nlstate+ndeath;j++){
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   return -l;          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);*/
         }
         ps[i][j]=s2;
 /*********** Maximum Likelihood Estimation ***************/      }
     }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      /*ps[3][2]=1;*/
 {  
   int i,j, iter;    for(i=1; i<= nlstate; i++){
   double **xi,*delti;       s1=0;
   double fret;      for(j=1; j<i; j++)
   xi=matrix(1,npar,1,npar);        s1+=exp(ps[i][j]);
   for (i=1;i<=npar;i++)      for(j=i+1; j<=nlstate+ndeath; j++)
     for (j=1;j<=npar;j++)        s1+=exp(ps[i][j]);
       xi[i][j]=(i==j ? 1.0 : 0.0);      ps[i][i]=1./(s1+1.);
   printf("Powell\n");      for(j=1; j<i; j++)
   powell(p,xi,npar,ftol,&iter,&fret,func);        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        ps[i][j]= exp(ps[i][j])*ps[i][i];
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     } /* end i */
 }  
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 /**** Computes Hessian and covariance matrix ***/      for(jj=1; jj<= nlstate+ndeath; jj++){
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        ps[ii][jj]=0;
 {        ps[ii][ii]=1;
   double  **a,**y,*x,pd;      }
   double **hess;    }
   int i, j,jk;  
   int *indx;  
     /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   double hessii(double p[], double delta, int theta, double delti[]);      for(jj=1; jj<= nlstate+ndeath; jj++){
   double hessij(double p[], double delti[], int i, int j);       printf("%lf ",ps[ii][jj]);
   void lubksb(double **a, int npar, int *indx, double b[]) ;     }
   void ludcmp(double **a, int npar, int *indx, double *d) ;      printf("\n ");
       }
   hess=matrix(1,npar,1,npar);      printf("\n ");printf("%lf ",cov[2]);*/
   /*
   printf("\nCalculation of the hessian matrix. Wait...\n");    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for (i=1;i<=npar;i++){    goto end;*/
     printf("%d",i);fflush(stdout);      return ps;
     hess[i][i]=hessii(p,ftolhess,i,delti);  }
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/  /**************** Product of 2 matrices ******************/
   }  
    double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++)  {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       if (j>i) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         printf(".%d%d",i,j);fflush(stdout);    /* in, b, out are matrice of pointers which should have been initialized 
         hess[i][j]=hessij(p,delti,i,j);       before: only the contents of out is modified. The function returns
         hess[j][i]=hess[i][j];           a pointer to pointers identical to out */
         /*printf(" %lf ",hess[i][j]);*/    long i, j, k;
       }    for(i=nrl; i<= nrh; i++)
     }      for(k=ncolol; k<=ncoloh; k++)
   }        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   printf("\n");          out[i][k] +=in[i][j]*b[j][k];
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    return out;
    }
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);  /************* Higher Matrix Product ***************/
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  {
   ludcmp(a,npar,indx,&pd);    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
   for (j=1;j<=npar;j++) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     for (i=1;i<=npar;i++) x[i]=0;       nhstepm*hstepm matrices. 
     x[j]=1;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     lubksb(a,npar,indx,x);       (typically every 2 years instead of every month which is too big 
     for (i=1;i<=npar;i++){       for the memory).
       matcov[i][j]=x[i];       Model is determined by parameters x and covariates have to be 
     }       included manually here. 
   }  
        */
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {    int i, j, d, h, k;
     for (j=1;j<=npar;j++) {    double **out, cov[NCOVMAX];
       printf("%.3e ",hess[i][j]);    double **newm;
     }  
     printf("\n");    /* Hstepm could be zero and should return the unit matrix */
   }    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   /* Recompute Inverse */        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);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      }
   ludcmp(a,npar,indx,&pd);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
   /*  printf("\n#Hessian matrix recomputed#\n");      for(d=1; d <=hstepm; d++){
         newm=savm;
   for (j=1;j<=npar;j++) {        /* Covariates have to be included here again */
     for (i=1;i<=npar;i++) x[i]=0;        cov[1]=1.;
     x[j]=1;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     lubksb(a,npar,indx,x);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for (i=1;i<=npar;i++){        for (k=1; k<=cptcovage;k++)
       y[i][j]=x[i];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       printf("%.3e ",y[i][j]);        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("\n");  
   }  
   */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   free_matrix(a,1,npar,1,npar);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   free_matrix(y,1,npar,1,npar);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_vector(x,1,npar);        savm=oldm;
   free_ivector(indx,1,npar);        oldm=newm;
   free_matrix(hess,1,npar,1,npar);      }
       for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
 }          po[i][j][h]=newm[i][j];
           /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
 /*************** hessian matrix ****************/           */
 double hessii( double x[], double delta, int theta, double delti[])        }
 {    } /* end h */
   int i;    return po;
   int l=1, lmax=20;  }
   double k1,k2;  
   double p2[NPARMAX+1];  
   double res;  /*************** log-likelihood *************/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  double func( double *x)
   double fx;  {
   int k=0,kmax=10;    int i, ii, j, k, mi, d, kk;
   double l1;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
   fx=func(x);    double sw; /* Sum of weights */
   for (i=1;i<=npar;i++) p2[i]=x[i];    double lli; /* Individual log likelihood */
   for(l=0 ; l <=lmax; l++){    int s1, s2;
     l1=pow(10,l);    double bbh, survp;
     delts=delt;    long ipmx;
     for(k=1 ; k <kmax; k=k+1){    /*extern weight */
       delt = delta*(l1*k);    /* We are differentiating ll according to initial status */
       p2[theta]=x[theta] +delt;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       k1=func(p2)-fx;    /*for(i=1;i<imx;i++) 
       p2[theta]=x[theta]-delt;      printf(" %d\n",s[4][i]);
       k2=func(p2)-fx;    */
       /*res= (k1-2.0*fx+k2)/delt/delt; */    cov[1]=1.;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
          for(k=1; k<=nlstate; k++) ll[k]=0.;
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    if(mle==1){
 #endif      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        for(mi=1; mi<= wav[i]-1; mi++){
         k=kmax;          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         k=kmax; l=lmax*10.;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          for(d=0; d<dh[mi][i]; d++){
         delts=delt;            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
   }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   delti[theta]=delts;            }
   return res;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 double hessij( double x[], double delti[], int thetai,int thetaj)          } /* end mult */
 {        
   int i;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   int l=1, l1, lmax=20;          /* But now since version 0.9 we anticipate for bias and large stepm.
   double k1,k2,k3,k4,res,fx;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double p2[NPARMAX+1];           * (in months) between two waves is not a multiple of stepm, we rounded to 
   int k;           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
   fx=func(x);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   for (k=1; k<=2; k++) {           * probability in order to take into account the bias as a fraction of the way
     for (i=1;i<=npar;i++) p2[i]=x[i];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     p2[thetai]=x[thetai]+delti[thetai]/k;           * -stepm/2 to stepm/2 .
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * For stepm=1 the results are the same as for previous versions of Imach.
     k1=func(p2)-fx;           * For stepm > 1 the results are less biased than in previous versions. 
             */
     p2[thetai]=x[thetai]+delti[thetai]/k;          s1=s[mw[mi][i]][i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          s2=s[mw[mi+1][i]][i];
     k2=func(p2)-fx;          bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias is positive if real duration
     p2[thetai]=x[thetai]-delti[thetai]/k;           * is higher than the multiple of stepm and negative otherwise.
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           */
     k3=func(p2)-fx;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
            if( s2 > nlstate){ 
     p2[thetai]=x[thetai]-delti[thetai]/k;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;               to the likelihood is the probability to die between last step unit time and current 
     k4=func(p2)-fx;               step unit time, which is also the differences between probability to die before dh 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */               and probability to die before dh-stepm . 
 #ifdef DEBUG               In version up to 0.92 likelihood was computed
     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);          as if date of death was unknown. Death was treated as any other
 #endif          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
   return res;          to consider that at each interview the state was recorded
 }          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
 /************** Inverse of matrix **************/          the contribution of an exact death to the likelihood. This new
 void ludcmp(double **a, int n, int *indx, double *d)          contribution is smaller and very dependent of the step unit
 {          stepm. It is no more the probability to die between last interview
   int i,imax,j,k;          and month of death but the probability to survive from last
   double big,dum,sum,temp;          interview up to one month before death multiplied by the
   double *vv;          probability to die within a month. Thanks to Chris
            Jackson for correcting this bug.  Former versions increased
   vv=vector(1,n);          mortality artificially. The bad side is that we add another loop
   *d=1.0;          which slows down the processing. The difference can be up to 10%
   for (i=1;i<=n;i++) {          lower mortality.
     big=0.0;            */
     for (j=1;j<=n;j++)            lli=log(out[s1][s2] - savm[s1][s2]);
       if ((temp=fabs(a[i][j])) > big) big=temp;          }else{
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     vv[i]=1.0/big;            /*  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 (j=1;j<=n;j++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     for (i=1;i<j;i++) {          /*if(lli ==000.0)*/
       sum=a[i][j];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          ipmx +=1;
       a[i][j]=sum;          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     big=0.0;        } /* end of wave */
     for (i=j;i<=n;i++) {      } /* end of individual */
       sum=a[i][j];    }  else if(mle==2){
       for (k=1;k<j;k++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         sum -= a[i][k]*a[k][j];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       a[i][j]=sum;        for(mi=1; mi<= wav[i]-1; mi++){
       if ( (dum=vv[i]*fabs(sum)) >= big) {          for (ii=1;ii<=nlstate+ndeath;ii++)
         big=dum;            for (j=1;j<=nlstate+ndeath;j++){
         imax=i;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
     if (j != imax) {          for(d=0; d<=dh[mi][i]; d++){
       for (k=1;k<=n;k++) {            newm=savm;
         dum=a[imax][k];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         a[imax][k]=a[j][k];            for (kk=1; kk<=cptcovage;kk++) {
         a[j][k]=dum;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
       *d = -(*d);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       vv[imax]=vv[j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     indx[j]=imax;            oldm=newm;
     if (a[j][j] == 0.0) a[j][j]=TINY;          } /* end mult */
     if (j != n) {        
       dum=1.0/(a[j][j]);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          /* But now since version 0.9 we anticipate for bias and large stepm.
     }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   }           * (in months) between two waves is not a multiple of stepm, we rounded to 
   free_vector(vv,1,n);  /* Doesn't work */           * the nearest (and in case of equal distance, to the lowest) interval but now
 ;           * 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
            * probability in order to take into account the bias as a fraction of the way
 void lubksb(double **a, int n, int *indx, double b[])           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 {           * -stepm/2 to stepm/2 .
   int i,ii=0,ip,j;           * For stepm=1 the results are the same as for previous versions of Imach.
   double sum;           * For stepm > 1 the results are less biased than in previous versions. 
             */
   for (i=1;i<=n;i++) {          s1=s[mw[mi][i]][i];
     ip=indx[i];          s2=s[mw[mi+1][i]][i];
     sum=b[ip];          bbh=(double)bh[mi][i]/(double)stepm; 
     b[ip]=b[i];          /* bias is positive if real duration
     if (ii)           * is higher than the multiple of stepm and negative otherwise.
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];           */
     else if (sum) ii=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 */
     b[i]=sum;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   }          /*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 */
   for (i=n;i>=1;i--) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     sum=b[i];          /*if(lli ==000.0)*/
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     b[i]=sum/a[i][i];          ipmx +=1;
   }          sw += weight[i];
 }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
 /************ Frequencies ********************/      } /* end of individual */
 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)    }  else if(mle==3){  /* exponential inter-extrapolation */
 {  /* Some frequencies */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        for(mi=1; mi<= wav[i]-1; mi++){
   double ***freq; /* Frequencies */          for (ii=1;ii<=nlstate+ndeath;ii++)
   double *pp;            for (j=1;j<=nlstate+ndeath;j++){
   double pos, k2, dateintsum=0,k2cpt=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   FILE *ficresp;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   char fileresp[FILENAMELENGTH];            }
            for(d=0; d<dh[mi][i]; d++){
   pp=vector(1,nlstate);            newm=savm;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   strcpy(fileresp,"p");            for (kk=1; kk<=cptcovage;kk++) {
   strcat(fileresp,fileres);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   if((ficresp=fopen(fileresp,"w"))==NULL) {            }
     printf("Problem with prevalence resultfile: %s\n", fileresp);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     exit(0);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            oldm=newm;
   j1=0;          } /* end mult */
          
   j=cptcoveff;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          /* 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(k1=1; k1<=j;k1++){           * (in months) between two waves is not a multiple of stepm, we rounded to 
     for(i1=1; i1<=ncodemax[k1];i1++){           * the nearest (and in case of equal distance, to the lowest) interval but now
       j1++;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         scanf("%d", i);*/           * probability in order to take into account the bias as a fraction of the way
       for (i=-1; i<=nlstate+ndeath; i++)             * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         for (jk=-1; jk<=nlstate+ndeath; jk++)             * -stepm/2 to stepm/2 .
           for(m=agemin; m <= agemax+3; m++)           * For stepm=1 the results are the same as for previous versions of Imach.
             freq[i][jk][m]=0;           * For stepm > 1 the results are less biased than in previous versions. 
                 */
       dateintsum=0;          s1=s[mw[mi][i]][i];
       k2cpt=0;          s2=s[mw[mi+1][i]][i];
       for (i=1; i<=imx; i++) {          bbh=(double)bh[mi][i]/(double)stepm; 
         bool=1;          /* bias is positive if real duration
         if  (cptcovn>0) {           * is higher than the multiple of stepm and negative otherwise.
           for (z1=1; z1<=cptcoveff; z1++)           */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          /* 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 */
               bool=0;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         if (bool==1) {          /*if(lli ==000.0)*/
           for(m=firstpass; m<=lastpass; m++){          /*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); */
             k2=anint[m][i]+(mint[m][i]/12.);          ipmx +=1;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          sw += weight[i];
               if(agev[m][i]==0) agev[m][i]=agemax+1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               if(agev[m][i]==1) agev[m][i]=agemax+2;        } /* end of wave */
               if (m<lastpass) {      } /* end of individual */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    }else if (mle==4){  /* ml=4 no inter-extrapolation */
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                      for(mi=1; mi<= wav[i]-1; mi++){
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          for (ii=1;ii<=nlstate+ndeath;ii++)
                 dateintsum=dateintsum+k2;            for (j=1;j<=nlstate+ndeath;j++){
                 k2cpt++;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }            }
           }          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                    for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
       if  (cptcovn>0) {          
         fprintf(ficresp, "\n#********** Variable ");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         fprintf(ficresp, "**********\n#");            savm=oldm;
       }            oldm=newm;
       for(i=1; i<=nlstate;i++)          } /* end mult */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        
       fprintf(ficresp, "\n");          s1=s[mw[mi][i]][i];
                s2=s[mw[mi+1][i]][i];
       for(i=(int)agemin; i <= (int)agemax+3; i++){          if( s2 > nlstate){ 
         if(i==(int)agemax+3)            lli=log(out[s1][s2] - savm[s1][s2]);
           printf("Total");          }else{
         else            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           printf("Age %d", i);          }
         for(jk=1; jk <=nlstate ; jk++){          ipmx +=1;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          sw += weight[i];
             pp[jk] += freq[jk][m][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]); */
         for(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
           for(m=-1, pos=0; m <=0 ; m++)      } /* end of individual */
             pos += freq[jk][m][i];    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           if(pp[jk]>=1.e-10)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           else        for(mi=1; mi<= wav[i]-1; mi++){
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(jk=1; jk <=nlstate ; jk++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            }
             pp[jk] += freq[jk][m][i];          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(jk=1,pos=0; jk <=nlstate ; jk++)            for (kk=1; kk<=cptcovage;kk++) {
           pos += pp[jk];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(jk=1; jk <=nlstate ; jk++){            }
           if(pos>=1.e-5)          
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            savm=oldm;
           if( i <= (int) agemax){            oldm=newm;
             if(pos>=1.e-5){          } /* end mult */
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        
               probs[i][jk][j1]= pp[jk]/pos;          s1=s[mw[mi][i]][i];
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          s2=s[mw[mi+1][i]][i];
             }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             else          ipmx +=1;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          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]);*/
                } /* end of wave */
         for(jk=-1; jk <=nlstate+ndeath; jk++)      } /* end of individual */
           for(m=-1; m <=nlstate+ndeath; m++)    } /* End of if */
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         if(i <= (int) agemax)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           fprintf(ficresp,"\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         printf("\n");    return -l;
       }  }
     }  
   }  /*************** log-likelihood *************/
   dateintmean=dateintsum/k2cpt;  double funcone( double *x)
    {
   fclose(ficresp);    /* Same as likeli but slower because of a lot of printf and if */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    int i, ii, j, k, mi, d, kk;
   free_vector(pp,1,nlstate);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
   /* End of Freq */    double lli; /* Individual log likelihood */
 }    double llt;
     int s1, s2;
 /************ Prevalence ********************/    double bbh, survp;
 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)    /*extern weight */
 {  /* Some frequencies */    /* We are differentiating ll according to initial status */
      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    /*for(i=1;i<imx;i++) 
   double ***freq; /* Frequencies */      printf(" %d\n",s[4][i]);
   double *pp;    */
   double pos, k2;    cov[1]=1.;
   
   pp=vector(1,nlstate);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   j1=0;      for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
   j=cptcoveff;          for (j=1;j<=nlstate+ndeath;j++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              savm[ii][j]=(ii==j ? 1.0 : 0.0);
  for(k1=1; k1<=j;k1++){          }
     for(i1=1; i1<=ncodemax[k1];i1++){        for(d=0; d<dh[mi][i]; d++){
       j1++;          newm=savm;
            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (i=-1; i<=nlstate+ndeath; i++)            for (kk=1; kk<=cptcovage;kk++) {
         for (jk=-1; jk<=nlstate+ndeath; jk++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for(m=agemin; m <= agemax+3; m++)          }
             freq[i][jk][m]=0;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                             1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (i=1; i<=imx; i++) {          savm=oldm;
         bool=1;          oldm=newm;
         if  (cptcovn>0) {        } /* end mult */
           for (z1=1; z1<=cptcoveff; z1++)        
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        s1=s[mw[mi][i]][i];
               bool=0;        s2=s[mw[mi+1][i]][i];
         }        bbh=(double)bh[mi][i]/(double)stepm; 
         if (bool==1) {        /* bias is positive if real duration
           for(m=firstpass; m<=lastpass; m++){         * is higher than the multiple of stepm and negative otherwise.
             k2=anint[m][i]+(mint[m][i]/12.);         */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        if( s2 > nlstate && (mle <5) ){  /* Jackson */
               if(agev[m][i]==0) agev[m][i]=agemax+1;          lli=log(out[s1][s2] - savm[s1][s2]);
               if(agev[m][i]==1) agev[m][i]=agemax+2;        } else if (mle==1){
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */        } else if(mle==2){
             }          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 */
           }        } 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(i=(int)agemin; i <= (int)agemax+3; i++){          lli=log(out[s1][s2]); /* Original formula */
           for(jk=1; jk <=nlstate ; jk++){        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          lli=log(out[s1][s2]); /* Original formula */
               pp[jk] += freq[jk][m][i];        } /* End of if */
           }        ipmx +=1;
           for(jk=1; jk <=nlstate ; jk++){        sw += weight[i];
             for(m=-1, pos=0; m <=0 ; m++)        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             pos += freq[jk][m][i];  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         }        if(globpr){
                  fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
          for(jk=1; jk <=nlstate ; jk++){   %10.6f %10.6f %10.6f ", \
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
              pp[jk] += freq[jk][m][i];                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
          }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                      llt +=ll[k]*gipmx/gsw;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
          for(jk=1; jk <=nlstate ; jk++){                    fprintf(ficresilk," %10.6f\n", -llt);
            if( i <= (int) agemax){        }
              if(pos>=1.e-5){      } /* end of wave */
                probs[i][jk][j1]= pp[jk]/pos;    } /* end of individual */
              }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
            }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
              if(globpr==0){ /* First time we count the contributions and weights */
         }      gipmx=ipmx;
     }      gsw=sw;
   }    }
      return -l;
    }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  char *subdirf(char fileres[])
    {
 }  /* End of Freq */    
     strcpy(tmpout,optionfilefiname);
 /************* Waves Concatenation ***************/    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
 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 tmpout;
 {  }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  
      Death is a valid wave (if date is known).  char *subdirf2(char fileres[], char *preop)
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  {
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    
      and mw[mi+1][i]. dh depends on stepm.    strcpy(tmpout,optionfilefiname);
      */    strcat(tmpout,"/");
     strcat(tmpout,preop);
   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.;*/  }
   char *subdirf3(char fileres[], char *preop, char *preop2)
   int j, k=0,jk, ju, jl;  {
   double sum=0.;    
   jmin=1e+5;    strcpy(tmpout,optionfilefiname);
   jmax=-1;    strcat(tmpout,"/");
   jmean=0.;    strcat(tmpout,preop);
   for(i=1; i<=imx; i++){    strcat(tmpout,preop2);
     mi=0;    strcat(tmpout,fileres);
     m=firstpass;    return tmpout;
     while(s[m][i] <= nlstate){  }
       if(s[m][i]>=1)  
         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 []))
       if(m >=lastpass)  {
         break;    /* This routine should help understanding what is done with 
       else       the selection of individuals/waves and
         m++;       to check the exact contribution to the likelihood.
     }/* end while */       Plotting could be done.
     if (s[m][i] > nlstate){     */
       mi++;     /* Death is another wave */    int k;
       /* if(mi==0)  never been interviewed correctly before death */  
          /* Only death is a correct wave */    if(*globpri !=0){ /* Just counts and sums, no printings */
       mw[mi][i]=m;      strcpy(fileresilk,"ilk"); 
     }      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     wav[i]=mi;        printf("Problem with resultfile: %s\n", fileresilk);
     if(mi==0)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      }
   }      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   for(i=1; i<=imx; 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(mi=1; mi<wav[i];mi++){      for(k=1; k<=nlstate; k++) 
       if (stepm <=0)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         dh[mi][i]=1;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       else{    }
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {    *fretone=(*funcone)(p);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    if(*globpri !=0){
           if(j==0) j=1;  /* Survives at least one month after exam */      fclose(ficresilk);
           k=k+1;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           if (j >= jmax) jmax=j;      fflush(fichtm); 
           if (j <= jmin) jmin=j;    } 
           sum=sum+j;    return;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */  }
           }  
         }  
         else{  /*********** Maximum Likelihood Estimation ***************/
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
           if (j >= jmax) jmax=j;  {
           else if (j <= jmin)jmin=j;    int i,j, iter;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    double **xi;
           sum=sum+j;    double fret;
         }    double fretone; /* Only one call to likelihood */
         jk= j/stepm;    char filerespow[FILENAMELENGTH];
         jl= j -jk*stepm;    xi=matrix(1,npar,1,npar);
         ju= j -(jk+1)*stepm;    for (i=1;i<=npar;i++)
         if(jl <= -ju)      for (j=1;j<=npar;j++)
           dh[mi][i]=jk;        xi[i][j]=(i==j ? 1.0 : 0.0);
         else    printf("Powell\n");  fprintf(ficlog,"Powell\n");
           dh[mi][i]=jk+1;    strcpy(filerespow,"pow"); 
         if(dh[mi][i]==0)    strcat(filerespow,fileres);
           dh[mi][i]=1; /* At least one step */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", filerespow);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   }    }
   jmean=sum/k;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    for (i=1;i<=nlstate;i++)
  }      for(j=1;j<=nlstate+ndeath;j++)
 /*********** Tricode ****************************/        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 void tricode(int *Tvar, int **nbcode, int imx)    fprintf(ficrespow,"\n");
 {  
   int Ndum[20],ij=1, k, j, i;    powell(p,xi,npar,ftol,&iter,&fret,func);
   int cptcode=0;  
   cptcoveff=0;    fclose(ficrespow);
      printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   for (k=0; k<19; k++) Ndum[k]=0;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   for (k=1; k<=7; k++) ncodemax[k]=0;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  }
     for (i=1; i<=imx; i++) {  
       ij=(int)(covar[Tvar[j]][i]);  /**** Computes Hessian and covariance matrix ***/
       Ndum[ij]++;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  {
       if (ij > cptcode) cptcode=ij;    double  **a,**y,*x,pd;
     }    double **hess;
     int i, j,jk;
     for (i=0; i<=cptcode; i++) {    int *indx;
       if(Ndum[i]!=0) ncodemax[j]++;  
     }    double hessii(double p[], double delta, int theta, double delti[]);
     ij=1;    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) ;
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {    hess=matrix(1,npar,1,npar);
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;    printf("\nCalculation of the hessian matrix. Wait...\n");
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
           ij++;    for (i=1;i<=npar;i++){
         }      printf("%d",i);fflush(stdout);
         if (ij > ncodemax[j]) break;      fprintf(ficlog,"%d",i);fflush(ficlog);
       }        hess[i][i]=hessii(p,ftolhess,i,delti);
     }      /*printf(" %f ",p[i]);*/
   }        /*printf(" %lf ",hess[i][i]);*/
     }
  for (k=0; k<19; k++) Ndum[k]=0;    
     for (i=1;i<=npar;i++) {
  for (i=1; i<=ncovmodel-2; i++) {      for (j=1;j<=npar;j++)  {
       ij=Tvar[i];        if (j>i) { 
       Ndum[ij]++;          printf(".%d%d",i,j);fflush(stdout);
     }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j);
  ij=1;          hess[j][i]=hess[i][j];    
  for (i=1; i<=10; i++) {          /*printf(" %lf ",hess[i][j]);*/
    if((Ndum[i]!=0) && (i<=ncovcol)){        }
      Tvaraff[ij]=i;      }
      ij++;    }
    }    printf("\n");
  }    fprintf(ficlog,"\n");
    
     cptcoveff=ij-1;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
 /*********** Health Expectancies ****************/    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    x=vector(1,npar);
 {    indx=ivector(1,npar);
   /* Health expectancies */    for (i=1;i<=npar;i++)
   int i, j, nhstepm, hstepm, h, nstepm, k;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double age, agelim, hf;    ludcmp(a,npar,indx,&pd);
   double ***p3mat;  
      for (j=1;j<=npar;j++) {
   fprintf(ficreseij,"# Health expectancies\n");      for (i=1;i<=npar;i++) x[i]=0;
   fprintf(ficreseij,"# Age");      x[j]=1;
   for(i=1; i<=nlstate;i++)      lubksb(a,npar,indx,x);
     for(j=1; j<=nlstate;j++)      for (i=1;i<=npar;i++){ 
       fprintf(ficreseij," %1d-%1d",i,j);        matcov[i][j]=x[i];
   fprintf(ficreseij,"\n");      }
     }
   k=1;             /* For example stepm=6 months */  
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */    printf("\n#Hessian matrix#\n");
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */    fprintf(ficlog,"\n#Hessian matrix#\n");
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    for (i=1;i<=npar;i++) { 
      nhstepm is the number of hstepm from age to agelim      for (j=1;j<=npar;j++) { 
      nstepm is the number of stepm from age to agelin.        printf("%.3e ",hess[i][j]);
      Look at hpijx to understand the reason of that which relies in memory size        fprintf(ficlog,"%.3e ",hess[i][j]);
      and note for a fixed period like k years */      }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      printf("\n");
      survival function given by stepm (the optimization length). Unfortunately it      fprintf(ficlog,"\n");
      means that if the survival funtion is printed only each two years of age and if    }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.    /* Recompute Inverse */
   */    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++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /*  printf("\n#Hessian matrix recomputed#\n");
     /* nhstepm age range expressed in number of stepm */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    for (j=1;j<=npar;j++) {
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      for (i=1;i<=npar;i++) x[i]=0;
     /* if (stepm >= YEARM) hstepm=1;*/      x[j]=1;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      lubksb(a,npar,indx,x);
     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        y[i][j]=x[i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        printf("%.3e ",y[i][j]);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          fprintf(ficlog,"%.3e ",y[i][j]);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      }
     for(i=1; i<=nlstate;i++)      printf("\n");
       for(j=1; j<=nlstate;j++)      fprintf(ficlog,"\n");
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    }
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    */
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/  
         }    free_matrix(a,1,npar,1,npar);
     fprintf(ficreseij,"%3.0f",age );    free_matrix(y,1,npar,1,npar);
     for(i=1; i<=nlstate;i++)    free_vector(x,1,npar);
       for(j=1; j<=nlstate;j++){    free_ivector(indx,1,npar);
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    free_matrix(hess,1,npar,1,npar);
       }  
     fprintf(ficreseij,"\n");  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
   }  
 }  /*************** hessian matrix ****************/
   double hessii( double x[], double delta, int theta, double delti[])
 /************ Variance ******************/  {
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    int i;
 {    int l=1, lmax=20;
   /* Variance of health expectancies */    double k1,k2;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double p2[NPARMAX+1];
   double **newm;    double res;
   double **dnewm,**doldm;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   int i, j, nhstepm, hstepm, h, nstepm, kk;    double fx;
   int k, cptcode;    int k=0,kmax=10;
   double *xp;    double l1;
   double **gp, **gm;  
   double ***gradg, ***trgradg;    fx=func(x);
   double ***p3mat;    for (i=1;i<=npar;i++) p2[i]=x[i];
   double age,agelim, hf;    for(l=0 ; l <=lmax; l++){
   int theta;      l1=pow(10,l);
       delts=delt;
    fprintf(ficresvij,"# Covariances of life expectancies\n");      for(k=1 ; k <kmax; k=k+1){
   fprintf(ficresvij,"# Age");        delt = delta*(l1*k);
   for(i=1; i<=nlstate;i++)        p2[theta]=x[theta] +delt;
     for(j=1; j<=nlstate;j++)        k1=func(p2)-fx;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        p2[theta]=x[theta]-delt;
   fprintf(ficresvij,"\n");        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
   xp=vector(1,npar);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   dnewm=matrix(1,nlstate,1,npar);        
   doldm=matrix(1,nlstate,1,nlstate);  #ifdef DEBUG
          printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   kk=1;             /* For example stepm=6 months */        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);
   hstepm=kk*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */  #endif
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
      nhstepm is the number of hstepm from age to agelim          k=kmax;
      nstepm is the number of stepm from age to agelin.        }
      Look at hpijx to understand the reason of that which relies in memory size        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
      and note for a fixed period like k years */          k=kmax; l=lmax*10.;
   /* 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        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
      means that if the survival funtion is printed only each two years of age and if          delts=delt;
      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.      }
   */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */    delti[theta]=delts;
   agelim = AGESUP;    return res; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  double hessij( double x[], double delti[], int thetai,int thetaj)
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  {
     gp=matrix(0,nhstepm,1,nlstate);    int i;
     gm=matrix(0,nhstepm,1,nlstate);    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
     for(theta=1; theta <=npar; theta++){    double p2[NPARMAX+1];
       for(i=1; i<=npar; i++){ /* Computes gradient */    int k;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    fx=func(x);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for (k=1; k<=2; k++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
       if (popbased==1) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         for(i=1; i<=nlstate;i++)      k1=func(p2)-fx;
           prlim[i][i]=probs[(int)age][i][ij];    
       }      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(j=1; j<= nlstate; j++){      k2=func(p2)-fx;
         for(h=0; h<=nhstepm; h++){    
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      p2[thetai]=x[thetai]-delti[thetai]/k;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         }      k3=func(p2)-fx;
       }    
          p2[thetai]=x[thetai]-delti[thetai]/k;
       for(i=1; i<=npar; i++) /* Computes gradient */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      k4=func(p2)-fx;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  #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);
       if (popbased==1) {      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         for(i=1; i<=nlstate;i++)  #endif
           prlim[i][i]=probs[(int)age][i][ij];    }
       }    return res;
   }
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  /************** Inverse of matrix **************/
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  void ludcmp(double **a, int n, int *indx, double *d) 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  { 
         }    int i,imax,j,k; 
       }    double big,dum,sum,temp; 
     double *vv; 
       for(j=1; j<= nlstate; j++)   
         for(h=0; h<=nhstepm; h++){    vv=vector(1,n); 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    *d=1.0; 
         }    for (i=1;i<=n;i++) { 
     } /* End theta */      big=0.0; 
       for (j=1;j<=n;j++) 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        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(j=1; j<=nlstate;j++)    } 
         for(theta=1; theta <=npar; theta++)    for (j=1;j<=n;j++) { 
           trgradg[h][j][theta]=gradg[h][theta][j];      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     for(i=1;i<=nlstate;i++)        a[i][j]=sum; 
       for(j=1;j<=nlstate;j++)      } 
         vareij[i][j][(int)age] =0.;      big=0.0; 
       for (i=j;i<=n;i++) { 
     for(h=0;h<=nhstepm;h++){        sum=a[i][j]; 
       for(k=0;k<=nhstepm;k++){        for (k=1;k<j;k++) 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          sum -= a[i][k]*a[k][j]; 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        a[i][j]=sum; 
         for(i=1;i<=nlstate;i++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           for(j=1;j<=nlstate;j++)          big=dum; 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          imax=i; 
       }        } 
     }      } 
       if (j != imax) { 
     fprintf(ficresvij,"%.0f ",age );        for (k=1;k<=n;k++) { 
     for(i=1; i<=nlstate;i++)          dum=a[imax][k]; 
       for(j=1; j<=nlstate;j++){          a[imax][k]=a[j][k]; 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          a[j][k]=dum; 
       }        } 
     fprintf(ficresvij,"\n");        *d = -(*d); 
     free_matrix(gp,0,nhstepm,1,nlstate);        vv[imax]=vv[j]; 
     free_matrix(gm,0,nhstepm,1,nlstate);      } 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      indx[j]=imax; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if (j != n) { 
   } /* End age */        dum=1.0/(a[j][j]); 
          for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   free_vector(xp,1,npar);      } 
   free_matrix(doldm,1,nlstate,1,npar);    } 
   free_matrix(dnewm,1,nlstate,1,nlstate);    free_vector(vv,1,n);  /* Doesn't work */
   ;
 }  } 
   
 /************ Variance of prevlim ******************/  void lubksb(double **a, int n, int *indx, double b[]) 
 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)  { 
 {    int i,ii=0,ip,j; 
   /* Variance of prevalence limit */    double sum; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/   
   double **newm;    for (i=1;i<=n;i++) { 
   double **dnewm,**doldm;      ip=indx[i]; 
   int i, j, nhstepm, hstepm;      sum=b[ip]; 
   int k, cptcode;      b[ip]=b[i]; 
   double *xp;      if (ii) 
   double *gp, *gm;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double **gradg, **trgradg;      else if (sum) ii=i; 
   double age,agelim;      b[i]=sum; 
   int theta;    } 
        for (i=n;i>=1;i--) { 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      sum=b[i]; 
   fprintf(ficresvpl,"# Age");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   for(i=1; i<=nlstate;i++)      b[i]=sum/a[i][i]; 
       fprintf(ficresvpl," %1d-%1d",i,i);    } 
   fprintf(ficresvpl,"\n");  } 
   
   xp=vector(1,npar);  /************ Frequencies ********************/
   dnewm=matrix(1,nlstate,1,npar);  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)
   doldm=matrix(1,nlstate,1,nlstate);  {  /* Some frequencies */
      
   hstepm=1*YEARM; /* Every year of age */    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    int first;
   agelim = AGESUP;    double ***freq; /* Frequencies */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double *pp, **prop;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     if (stepm >= YEARM) hstepm=1;    FILE *ficresp;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    char fileresp[FILENAMELENGTH];
     gradg=matrix(1,npar,1,nlstate);    
     gp=vector(1,nlstate);    pp=vector(1,nlstate);
     gm=vector(1,nlstate);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
     for(theta=1; theta <=npar; theta++){    strcat(fileresp,fileres);
       for(i=1; i<=npar; i++){ /* Computes gradient */    if((ficresp=fopen(fileresp,"w"))==NULL) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      printf("Problem with prevalence resultfile: %s\n", fileresp);
       }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      exit(0);
       for(i=1;i<=nlstate;i++)    }
         gp[i] = prlim[i][i];    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
        j1=0;
       for(i=1; i<=npar; i++) /* Computes gradient */    
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    j=cptcoveff;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];    first=1;
   
       for(i=1;i<=nlstate;i++)    for(k1=1; k1<=j;k1++){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      for(i1=1; i1<=ncodemax[k1];i1++){
     } /* End theta */        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     trgradg =matrix(1,nlstate,1,npar);          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
     for(j=1; j<=nlstate;j++)          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       for(theta=1; theta <=npar; theta++)            for(m=iagemin; m <= iagemax+3; m++)
         trgradg[j][theta]=gradg[theta][j];              freq[i][jk][m]=0;
   
     for(i=1;i<=nlstate;i++)      for (i=1; i<=nlstate; i++)  
       varpl[i][(int)age] =0.;        for(m=iagemin; m <= iagemax+3; m++)
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          prop[i][m]=0;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        
     for(i=1;i<=nlstate;i++)        dateintsum=0;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        k2cpt=0;
         for (i=1; i<=imx; i++) {
     fprintf(ficresvpl,"%.0f ",age );          bool=1;
     for(i=1; i<=nlstate;i++)          if  (cptcovn>0) {
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            for (z1=1; z1<=cptcoveff; z1++) 
     fprintf(ficresvpl,"\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     free_vector(gp,1,nlstate);                bool=0;
     free_vector(gm,1,nlstate);          }
     free_matrix(gradg,1,npar,1,nlstate);          if (bool==1){
     free_matrix(trgradg,1,nlstate,1,npar);            for(m=firstpass; m<=lastpass; m++){
   } /* End age */              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   free_vector(xp,1,npar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   free_matrix(doldm,1,nlstate,1,npar);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   free_matrix(dnewm,1,nlstate,1,nlstate);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 if (m<lastpass) {
 }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 /************ Variance of one-step probabilities  ******************/                }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)                
 {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   int i, j;                  dateintsum=dateintsum+k2;
   int k=0, cptcode;                  k2cpt++;
   double **dnewm,**doldm;                }
   double *xp;                /*}*/
   double *gp, *gm;            }
   double **gradg, **trgradg;          }
   double age,agelim, cov[NCOVMAX];        }
   int theta;         
   char fileresprob[FILENAMELENGTH];        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
   strcpy(fileresprob,"prob");        if  (cptcovn>0) {
   strcat(fileresprob,fileres);          fprintf(ficresp, "\n#********** Variable "); 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("Problem with resultfile: %s\n", fileresprob);          fprintf(ficresp, "**********\n#");
   }        }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        for(i=1; i<=nlstate;i++) 
            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
   xp=vector(1,npar);        
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for(i=iagemin; i <= iagemax+3; i++){
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          if(i==iagemax+3){
              fprintf(ficlog,"Total");
   cov[1]=1;          }else{
   for (age=bage; age<=fage; age ++){            if(first==1){
     cov[2]=age;              first=0;
     gradg=matrix(1,npar,1,9);              printf("See log file for details...\n");
     trgradg=matrix(1,9,1,npar);            }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            fprintf(ficlog,"Age %d", i);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          }
              for(jk=1; jk <=nlstate ; jk++){
     for(theta=1; theta <=npar; theta++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       for(i=1; i<=npar; i++)              pp[jk] += freq[jk][m][i]; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
                for(jk=1; jk <=nlstate ; jk++){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            for(m=-1, pos=0; m <=0 ; m++)
                  pos += freq[jk][m][i];
       k=0;            if(pp[jk]>=1.e-10){
       for(i=1; i<= (nlstate+ndeath); i++){              if(first==1){
         for(j=1; j<=(nlstate+ndeath);j++){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
            k=k+1;              }
           gp[k]=pmmij[i][j];              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         }            }else{
       }              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for(i=1; i<=npar; i++)              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            }
              }
   
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          for(jk=1; jk <=nlstate ; jk++){
       k=0;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for(i=1; i<=(nlstate+ndeath); i++){              pp[jk] += freq[jk][m][i];
         for(j=1; j<=(nlstate+ndeath);j++){          }       
           k=k+1;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
           gm[k]=pmmij[i][j];            pos += pp[jk];
         }            posprop += prop[jk][i];
       }          }
                for(jk=1; jk <=nlstate ; jk++){
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            if(pos>=1.e-5){
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                if(first==1)
     }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            }else{
       for(theta=1; theta <=npar; theta++)              if(first==1)
       trgradg[j][theta]=gradg[theta][j];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);            if( i <= iagemax){
               if(pos>=1.e-5){
      pmij(pmmij,cov,ncovmodel,x,nlstate);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
      k=0;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
      for(i=1; i<=(nlstate+ndeath); i++){              }
        for(j=1; j<=(nlstate+ndeath);j++){              else
          k=k+1;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
          gm[k]=pmmij[i][j];            }
         }          }
      }          
                for(jk=-1; jk <=nlstate+ndeath; jk++)
      /*printf("\n%d ",(int)age);            for(m=-1; m <=nlstate+ndeath; m++)
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              if(freq[jk][m][i] !=0 ) {
                      if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
      }*/              }
           if(i <= iagemax)
   fprintf(ficresprob,"\n%d ",(int)age);            fprintf(ficresp,"\n");
           if(first==1)
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            printf("Others in log...\n");
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          fprintf(ficlog,"\n");
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        }
   }      }
     }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    dateintmean=dateintsum/k2cpt; 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));   
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fclose(ficresp);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
 }    free_vector(pp,1,nlstate);
  free_vector(xp,1,npar);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 fclose(ficresprob);    /* End of Freq */
   }
 }  
   /************ Prevalence ********************/
 /******************* Printing html file ***********/  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)
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  {  
  int lastpass, int stepm, int weightopt, char model[],\    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \       in each health status at the date of interview (if between dateprev1 and dateprev2).
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\       We still use firstpass and lastpass as another selection.
  char version[], int popforecast ){    */
   int jj1, k1, i1, cpt;   
   FILE *fichtm;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   /*char optionfilehtm[FILENAMELENGTH];*/    double ***freq; /* Frequencies */
     double *pp, **prop;
   strcpy(optionfilehtm,optionfile);    double pos,posprop; 
   strcat(optionfilehtm,".htm");    double  y2; /* in fractional years */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    int iagemin, iagemax;
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }    iagemin= (int) agemin;
     iagemax= (int) agemax;
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    /*pp=vector(1,nlstate);*/
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    prop=matrix(1,nlstate,iagemin,iagemax+3); 
 \n    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 Total number of observations=%d <br>\n    j1=0;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    
 <hr  size=\"2\" color=\"#EC5E5E\">    j=cptcoveff;
  <ul><li>Outputs files<br>\n    if (cptcovn<1) {j=1;ncodemax[1]=1;}
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    for(k1=1; k1<=j;k1++){
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      for(i1=1; i1<=ncodemax[k1];i1++){
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n        j1++;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n        
  - 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);        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
  fprintf(fichtm,"\n            prop[i][m]=0.0;
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n       
  - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>\n        for (i=1; i<=imx; i++) { /* Each individual */
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n          bool=1;
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres);          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
  if(popforecast==1) fprintf(fichtm,"\n              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n                bool=0;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          } 
         <br>",fileres,fileres,fileres,fileres);          if (bool==1) { 
  else            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
    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);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
 fprintf(fichtm," <li>Graphs</li><p>");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
  m=cptcoveff;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                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) { 
  jj1=0;                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
  for(k1=1; k1<=m;k1++){                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
    for(i1=1; i1<=ncodemax[k1];i1++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
        jj1++;                } 
        if (cptcovn > 0) {              }
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            } /* end selection of waves */
          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\">");        for(i=iagemin; i <= iagemax+3; i++){  
        }          
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                posprop += prop[jk][i]; 
        for(cpt=1; cpt<nlstate;cpt++){          } 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(jk=1; jk <=nlstate ; jk++){     
        }            if( i <=  iagemax){ 
     for(cpt=1; cpt<=nlstate;cpt++) {              if(posprop>=1.e-5){ 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident                probs[i][jk][j1]= prop[jk][i]/posprop;
 interval) in state (%d): v%s%d%d.gif <br>              } 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              } 
      }          }/* end jk */ 
      for(cpt=1; cpt<=nlstate;cpt++) {        }/* end i */ 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      } /* end i1 */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    } /* end k1 */
      }    
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 health expectancies in states (1) and (2): e%s%d.gif<br>    /*free_vector(pp,1,nlstate);*/
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 fprintf(fichtm,"\n</body>");  }  /* End of prevalence */
    }  
    }  /************* Waves Concatenation ***************/
 fclose(fichtm);  
 }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   {
 /******************* Gnuplot file **************/    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){       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
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
   strcpy(optionfilegnuplot,optionfilefiname);       */
   strcat(optionfilegnuplot,".gp.txt");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    int i, mi, m;
     printf("Problem with file %s",optionfilegnuplot);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   }       double sum=0., jmean=0.;*/
     int first;
 #ifdef windows    int j, k=0,jk, ju, jl;
     fprintf(ficgp,"cd \"%s\" \n",pathc);    double sum=0.;
 #endif    first=0;
 m=pow(2,cptcoveff);    jmin=1e+5;
      jmax=-1;
  /* 1eme*/    jmean=0.;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for(i=1; i<=imx; i++){
    for (k1=1; k1<= m ; k1 ++) {      mi=0;
       m=firstpass;
 #ifdef windows      while(s[m][i] <= nlstate){
     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);        if(s[m][i]>=1)
 #endif          mw[++mi][i]=m;
 #ifdef unix        if(m >=lastpass)
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          break;
 #endif        else
           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\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);           /* Only death is a correct wave */
     for (i=1; i<= nlstate ; i ++) {        mw[mi][i]=m;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      wav[i]=mi;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      if(mi==0){
      for (i=1; i<= nlstate ; i ++) {        if(first==0){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          first=1;
 }          }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        if(first==1){
 #ifdef unix          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
 fprintf(ficgp,"\nset ter gif small size 400,300");        }
 #endif      } /* end mi==0 */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    } /* End individuals */
    }  
   }    for(i=1; i<=imx; i++){
   /*2 eme*/      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
   for (k1=1; k1<= m ; k1 ++) {          dh[mi][i]=1;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);        else{
              if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     for (i=1; i<= nlstate+1 ; i ++) {            if (agedc[i] < 2*AGESUP) {
       k=2*i;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              if(j==0) j=1;  /* Survives at least one month after exam */
       for (j=1; j<= nlstate+1 ; j ++) {              else if(j<0){
   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)");                j=1; /* Careful Patch */
 }                  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 (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                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,"\" t\"LE in state (%d)\" w l ,",i-1);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              }
       for (j=1; j<= nlstate+1 ; j ++) {              k=k+1;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              if (j >= jmax) jmax=j;
         else fprintf(ficgp," \%%*lf (\%%*lf)");              if (j <= jmin) jmin=j;
 }                sum=sum+j;
       fprintf(ficgp,"\" t\"\" w l 0,");              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       for (j=1; j<= nlstate+1 ; j ++) {            }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          else{
 }              j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       else fprintf(ficgp,"\" t\"\" w l 0,");            k=k+1;
     }            if (j >= jmax) jmax=j;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            else if (j <= jmin)jmin=j;
   }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
              /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   /*3eme*/            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]);
   for (k1=1; k1<= m ; k1 ++) {              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]);
     for (cpt=1; cpt<= nlstate ; cpt ++) {            }
       k=2+nlstate*(cpt-1);            sum=sum+j;
       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);          }
       for (i=1; i< nlstate ; i ++) {          jk= j/stepm;
         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);          jl= j -jk*stepm;
       }          ju= j -(jk+1)*stepm;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     }            if(jl==0){
     }              dh[mi][i]=jk;
                bh[mi][i]=0;
   /* CV preval stat */            }else{ /* We want a negative bias in order to only have interpolation ie
     for (k1=1; k1<= m ; k1 ++) {                    * at the price of an extra matrix product in likelihood */
     for (cpt=1; cpt<nlstate ; cpt ++) {              dh[mi][i]=jk+1;
       k=3;              bh[mi][i]=ju;
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);            }
           }else{
       for (i=1; i< nlstate ; i ++)            if(jl <= -ju){
         fprintf(ficgp,"+$%d",k+i+1);              dh[mi][i]=jk;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              bh[mi][i]=jl;       /* bias is positive if real duration
                                         * is higher than the multiple of stepm and negative otherwise.
       l=3+(nlstate+ndeath)*cpt;                                   */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            }
       for (i=1; i< nlstate ; i ++) {            else{
         l=3+(nlstate+ndeath)*cpt;              dh[mi][i]=jk+1;
         fprintf(ficgp,"+$%d",l+i+1);              bh[mi][i]=ju;
       }            }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              if(dh[mi][i]==0){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              dh[mi][i]=1; /* At least one step */
     }              bh[mi][i]=ju; /* At least one step */
   }                /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
              }
   /* proba elementaires */          } /* end if mle */
    for(i=1,jk=1; i <=nlstate; i++){        }
     for(k=1; k <=(nlstate+ndeath); k++){      } /* end wave */
       if (k != i) {    }
         for(j=1; j <=ncovmodel; j++){    jmean=sum/k;
            printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           jk++;   }
           fprintf(ficgp,"\n");  
         }  /*********** Tricode ****************************/
       }  void tricode(int *Tvar, int **nbcode, int imx)
     }  {
     }    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
     for(jk=1; jk <=m; jk++) {    int cptcode=0;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    cptcoveff=0; 
    i=1;   
    for(k2=1; k2<=nlstate; k2++) {    for (k=0; k<maxncov; k++) Ndum[k]=0;
      k3=i;    for (k=1; k<=7; k++) ncodemax[k]=0;
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
 ij=1;                                 modality*/ 
         for(j=3; j <=ncovmodel; j++) {        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        Ndum[ij]++; /*store the modality */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
             ij++;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
           }                                         Tvar[j]. If V=sex and male is 0 and 
           else                                         female is 1, then  cptcode=1.*/
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      }
         }  
           fprintf(ficgp,")/(1");      for (i=0; i<=cptcode; i++) {
                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 */
         for(k1=1; k1 <=nlstate; k1++){        }
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
 ij=1;      ij=1; 
           for(j=3; j <=ncovmodel; j++){      for (i=1; i<=ncodemax[j]; i++) {
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for (k=0; k<= maxncov; k++) {
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          if (Ndum[k] != 0) {
             ij++;            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; */
           else            
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            ij++;
           }          }
           fprintf(ficgp,")");          if (ij > ncodemax[j]) break; 
         }        }  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      } 
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    }  
         i=i+ncovmodel;  
        }   for (k=0; k< maxncov; k++) Ndum[k]=0;
      }  
    }   for (i=1; i<=ncovmodel-2; i++) { 
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    }     ij=Tvar[i];
         Ndum[ij]++;
   fclose(ficgp);   }
 }  /* end gnuplot */  
    ij=1;
    for (i=1; i<= maxncov; i++) {
 /*************** Moving average **************/     if((Ndum[i]!=0) && (i<=ncovcol)){
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){       Tvaraff[ij]=i; /*For printing */
        ij++;
   int i, cpt, cptcod;     }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)   }
       for (i=1; i<=nlstate;i++)   
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)   cptcoveff=ij-1; /*Number of simple covariates*/
           mobaverage[(int)agedeb][i][cptcod]=0.;  }
      
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  /*********** Health Expectancies ****************/
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  {
           }    /* Health expectancies */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         }    double age, agelim, hf;
       }    double ***p3mat,***varhe;
     }    double **dnewm,**doldm;
        double *xp;
 }    double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
 /************** 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){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
      xp=vector(1,npar);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    dnewm=matrix(1,nlstate*nlstate,1,npar);
   int *popage;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    
   double *popeffectif,*popcount;    fprintf(ficreseij,"# Health expectancies\n");
   double ***p3mat;    fprintf(ficreseij,"# Age");
   char fileresf[FILENAMELENGTH];    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
  agelim=AGESUP;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    fprintf(ficreseij,"\n");
   
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   strcpy(fileresf,"f");    else  hstepm=estepm;   
   strcat(fileresf,fileres);    /* We compute the life expectancy from trapezoids spaced every estepm months
   if((ficresf=fopen(fileresf,"w"))==NULL) {     * This is mainly to measure the difference between two models: for example
     printf("Problem with forecast resultfile: %s\n", fileresf);     * if stepm=24 months pijx are given only every 2 years and by summing them
   }     * we are calculating an estimate of the Life Expectancy assuming a linear 
   printf("Computing forecasting: result on file '%s' \n", fileresf);     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;     * 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 
   if (mobilav==1) {     * hypothesis. A more precise result, taking into account a more precise
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * curvature will be obtained if estepm is as small as stepm. */
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   stepsize=(int) (stepm+YEARM-1)/YEARM;       nhstepm is the number of hstepm from age to agelim 
   if (stepm<=12) stepsize=1;       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
   agelim=AGESUP;       and note for a fixed period like estepm months */
      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   hstepm=1;       survival function given by stepm (the optimization length). Unfortunately it
   hstepm=hstepm/stepm;       means that if the survival funtion is printed only each two years of age and if
   yp1=modf(dateintmean,&yp);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   anprojmean=yp;       results. So we changed our mind and took the option of the best precision.
   yp2=modf((yp1*12),&yp);    */
   mprojmean=yp;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;    agelim=AGESUP;
   if(jprojmean==0) jprojmean=1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   if(mprojmean==0) jprojmean=1;      /* nhstepm age range expressed in number of stepm */
        nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        /* if (stepm >= YEARM) hstepm=1;*/
   for(cptcov=1;cptcov<=i2;cptcov++){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k=k+1;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       fprintf(ficresf,"\n#******");      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       for(j=1;j<=cptcoveff;j++) {      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       fprintf(ficresf,"******\n");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       fprintf(ficresf,"# StartingAge FinalAge");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);   
        
            hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  
         fprintf(ficresf,"\n");      /* Computing Variances of health expectancies */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
        for(theta=1; theta <=npar; theta++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(i=1; i<=npar; i++){ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           nhstepm = nhstepm/hstepm;        }
                  hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           oldm=oldms;savm=savms;        cptj=0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(j=1; j<= nlstate; j++){
                  for(i=1; i<=nlstate; i++){
           for (h=0; h<=nhstepm; h++){            cptj=cptj+1;
             if (h==(int) (calagedate+YEARM*cpt)) {            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }            }
             for(j=1; j<=nlstate+ndeath;j++) {          }
               kk1=0.;kk2=0;        }
               for(i=1; i<=nlstate;i++) {                     
                 if (mobilav==1)       
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        for(i=1; i<=npar; i++) 
                 else {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                 }        
                        cptj=0;
               }        for(j=1; j<= nlstate; j++){
               if (h==(int)(calagedate+12*cpt)){          for(i=1;i<=nlstate;i++){
                 fprintf(ficresf," %.3f", kk1);            cptj=cptj+1;
                                    for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
               }  
             }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
         }        }
       }        for(j=1; j<= nlstate*nlstate; j++)
     }          for(h=0; h<=nhstepm-1; h++){
   }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                  }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       } 
      
   fclose(ficresf);  /* End theta */
 }  
 /************** Forecasting ******************/       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  
         for(h=0; h<=nhstepm-1; h++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        for(j=1; j<=nlstate*nlstate;j++)
   int *popage;          for(theta=1; theta <=npar; theta++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            trgradg[h][j][theta]=gradg[h][theta][j];
   double *popeffectif,*popcount;       
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];       for(i=1;i<=nlstate*nlstate;i++)
         for(j=1;j<=nlstate*nlstate;j++)
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          varhe[i][j][(int)age] =0.;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   agelim=AGESUP;       printf("%d|",(int)age);fflush(stdout);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(h=0;h<=nhstepm-1;h++){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(k=0;k<=nhstepm-1;k++){
            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   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] += doldm[i][j]*hf*hf;
     printf("Problem with forecast resultfile: %s\n", filerespop);        }
   }      }
   printf("Computing forecasting: result on file '%s' \n", filerespop);      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   if (mobilav==1) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            
     movingaverage(agedeb, fage, ageminpar, mobaverage);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   }  
           }
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;      fprintf(ficreseij,"%3.0f",age );
        cptj=0;
   agelim=AGESUP;      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
   hstepm=1;          cptj++;
   hstepm=hstepm/stepm;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
          }
   if (popforecast==1) {      fprintf(ficreseij,"\n");
     if((ficpop=fopen(popfile,"r"))==NULL) {     
       printf("Problem with population file : %s\n",popfile);exit(0);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     popage=ivector(0,AGESUP);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     popeffectif=vector(0,AGESUP);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     popcount=vector(0,AGESUP);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        }
     i=1;      printf("\n");
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    fprintf(ficlog,"\n");
      
     imx=i;    free_vector(xp,1,npar);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   for(cptcov=1;cptcov<=i2;cptcov++){  }
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;  /************ Variance ******************/
       fprintf(ficrespop,"\n#******");  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(j=1;j<=cptcoveff;j++) {  {
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* Variance of health expectancies */
       }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       fprintf(ficrespop,"******\n");    /* double **newm;*/
       fprintf(ficrespop,"# Age");    double **dnewm,**doldm;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    double **dnewmp,**doldmp;
       if (popforecast==1)  fprintf(ficrespop," [Population]");    int i, j, nhstepm, hstepm, h, nstepm ;
          int k, cptcode;
       for (cpt=0; cpt<=0;cpt++) {    double *xp;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      double **gp, **gm;  /* for var eij */
            double ***gradg, ***trgradg; /*for var eij */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    double **gradgp, **trgradgp; /* for var p point j */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double *gpp, *gmp; /* for var p point j */
           nhstepm = nhstepm/hstepm;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
              double ***p3mat;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double age,agelim, hf;
           oldm=oldms;savm=savms;    double ***mobaverage;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int theta;
            char digit[4];
           for (h=0; h<=nhstepm; h++){    char digitp[25];
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    char fileresprobmorprev[FILENAMELENGTH];
             }  
             for(j=1; j<=nlstate+ndeath;j++) {    if(popbased==1){
               kk1=0.;kk2=0;      if(mobilav!=0)
               for(i=1; i<=nlstate;i++) {                      strcpy(digitp,"-populbased-mobilav-");
                 if (mobilav==1)      else strcpy(digitp,"-populbased-nomobil-");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    }
                 else {    else 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      strcpy(digitp,"-stablbased-");
                 }  
               }    if (mobilav!=0) {
               if (h==(int)(calagedate+12*cpt)){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                   /*fprintf(ficrespop," %.3f", kk1);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
               }      }
             }    }
             for(i=1; i<=nlstate;i++){  
               kk1=0.;    strcpy(fileresprobmorprev,"prmorprev"); 
                 for(j=1; j<=nlstate;j++){    sprintf(digit,"%-d",ij);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                 }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
             }    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      printf("Problem with resultfile: %s\n", fileresprobmorprev);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           }    }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
      fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   /******/    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      for(i=1; i<=nlstate;i++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    }  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficresprobmorprev,"\n");
           nhstepm = nhstepm/hstepm;    fprintf(ficgp,"\n# Routine varevsij");
              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");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           oldm=oldms;savm=savms;  /*   } */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficresvij,"# Age");
             }    for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++) {      for(j=1; j<=nlstate;j++)
               kk1=0.;kk2=0;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
               for(i=1; i<=nlstate;i++) {                  fprintf(ficresvij,"\n");
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }    xp=vector(1,npar);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    dnewm=matrix(1,nlstate,1,npar);
             }    doldm=matrix(1,nlstate,1,nlstate);
           }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }  
       }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
    }    gpp=vector(nlstate+1,nlstate+ndeath);
   }    gmp=vector(nlstate+1,nlstate+ndeath);
      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
     if(estepm < stepm){
   if (popforecast==1) {      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_ivector(popage,0,AGESUP);    }
     free_vector(popeffectif,0,AGESUP);    else  hstepm=estepm;   
     free_vector(popcount,0,AGESUP);    /* For example we decided to compute the life expectancy with the smallest unit */
   }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       nhstepm is the number of hstepm from age to agelim 
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       nstepm is the number of stepm from age to agelin. 
   fclose(ficrespop);       Look at hpijx to understand the reason of that which relies in memory size
 }       and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 /***********************************************/       survival function given by stepm (the optimization length). Unfortunately it
 /**************** Main Program *****************/       means that if the survival funtion is printed every two years of age and if
 /***********************************************/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
 int main(int argc, char *argv[])    */
 {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double agedeb, agefin,hf;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double fret;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   double **xi,tmp,delta;      gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   double dum; /* Dummy variable */  
   double ***p3mat;  
   int *indx;      for(theta=1; theta <=npar; theta++){
   char line[MAXLINE], linepar[MAXLINE];        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   char title[MAXLINE];          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        }
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
         if (popbased==1) {
   char filerest[FILENAMELENGTH];          if(mobilav ==0){
   char fileregp[FILENAMELENGTH];            for(i=1; i<=nlstate;i++)
   char popfile[FILENAMELENGTH];              prlim[i][i]=probs[(int)age][i][ij];
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          }else{ /* mobilav */ 
   int firstobs=1, lastobs=10;            for(i=1; i<=nlstate;i++)
   int sdeb, sfin; /* Status at beginning and end */              prlim[i][i]=mobaverage[(int)age][i][ij];
   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,**adl,*tab;        for(j=1; j<= nlstate; j++){
   int mobilav=0,popforecast=0;          for(h=0; h<=nhstepm; h++){
   int hstepm, nhstepm;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   double bage, fage, age, agelim, agebase;        }
   double ftolpl=FTOL;        /* This for computing probability of death (h=1 means
   double **prlim;           computed over hstepm matrices product = hstepm*stepm months) 
   double *severity;           as a weighted average of prlim.
   double ***param; /* Matrix of parameters */        */
   double  *p;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   double **matcov; /* Matrix of covariance */          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   double ***delti3; /* Scale */            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   double *delti; /* Scale */        }    
   double ***eij, ***vareij;        /* end probability of death */
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   double kk1, kk2;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";        if (popbased==1) {
   char *alph[]={"a","a","b","c","d","e"}, str[4];          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   char z[1]="c", occ;          }else{ /* mobilav */ 
 #include <sys/time.h>            for(i=1; i<=nlstate;i++)
 #include <time.h>              prlim[i][i]=mobaverage[(int)age][i][ij];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          }
          }
   /* long total_usecs;  
   struct timeval start_time, end_time;        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   getcwd(pathcd, size);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   printf("\n%s",version);        }
   if(argc <=1){        /* This for computing probability of death (h=1 means
     printf("\nEnter the parameter file name: ");           computed over hstepm matrices product = hstepm*stepm months) 
     scanf("%s",pathtot);           as a weighted average of prlim.
   }        */
   else{        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     strcpy(pathtot,argv[1]);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        }    
   /*cygwin_split_path(pathtot,path,optionfile);        /* end probability of death */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/        for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          }
   chdir(path);  
   replace(pathc,path);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
 /*-------- arguments in the command line --------*/        }
   
   strcpy(fileres,"r");      } /* End theta */
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
   /*---------arguments file --------*/      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          for(theta=1; theta <=npar; theta++)
     printf("Problem with optionfile %s\n",optionfile);            trgradg[h][j][theta]=gradg[h][theta][j];
     goto end;  
   }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
   strcpy(filereso,"o");          trgradgp[j][theta]=gradgp[theta][j];
   strcat(filereso,fileres);    
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   }      for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
   /* Reads comments: lines beginning with '#' */          vareij[i][j][(int)age] =0.;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      for(h=0;h<=nhstepm;h++){
     fgets(line, MAXLINE, ficpar);        for(k=0;k<=nhstepm;k++){
     puts(line);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     fputs(line,ficparo);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   }          for(i=1;i<=nlstate;i++)
   ungetc(c,ficpar);            for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   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);        }
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);      }
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);    
 while((c=getc(ficpar))=='#' && c!= EOF){      /* pptj */
     ungetc(c,ficpar);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     fgets(line, MAXLINE, ficpar);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     puts(line);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     fputs(line,ficparo);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   }          varppt[j][i]=doldmp[j][i];
   ungetc(c,ficpar);      /* end ppptj */
        /*  x centered again */
          hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   covar=matrix(0,NCOVMAX,1,n);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   cptcovn=0;   
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      if (popbased==1) {
         if(mobilav ==0){
   ncovmodel=2+cptcovn;          for(i=1; i<=nlstate;i++)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            prlim[i][i]=probs[(int)age][i][ij];
          }else{ /* mobilav */ 
   /* Read guess parameters */          for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */            prlim[i][i]=mobaverage[(int)age][i][ij];
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);               
     puts(line);      /* This for computing probability of death (h=1 means
     fputs(line,ficparo);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   }         as a weighted average of prlim.
   ungetc(c,ficpar);      */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     for(i=1; i <=nlstate; i++)          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     for(j=1; j <=nlstate+ndeath-1; j++){      }    
       fscanf(ficpar,"%1d%1d",&i1,&j1);      /* end probability of death */
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(k=1; k<=ncovmodel;k++){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fscanf(ficpar," %lf",&param[i][j][k]);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         printf(" %lf",param[i][j][k]);        for(i=1; i<=nlstate;i++){
         fprintf(ficparo," %lf",param[i][j][k]);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       }        }
       fscanf(ficpar,"\n");      } 
       printf("\n");      fprintf(ficresprobmorprev,"\n");
       fprintf(ficparo,"\n");  
     }      fprintf(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   p=param[1][1];        }
        fprintf(ficresvij,"\n");
   /* Reads comments: lines beginning with '#' */      free_matrix(gp,0,nhstepm,1,nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){      free_matrix(gm,0,nhstepm,1,nlstate);
     ungetc(c,ficpar);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     fgets(line, MAXLINE, ficpar);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     puts(line);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fputs(line,ficparo);    } /* End age */
   }    free_vector(gpp,nlstate+1,nlstate+ndeath);
   ungetc(c,ficpar);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   for(i=1; i <=nlstate; i++){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       fscanf(ficpar,"%1d%1d",&i1,&j1);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       printf("%1d%1d",i,j);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficparo,"%1d%1d",i1,j1);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       for(k=1; k<=ncovmodel;k++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
         fscanf(ficpar,"%le",&delti3[i][j][k]);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
         printf(" %le",delti3[i][j][k]);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
         fprintf(ficparo," %le",delti3[i][j][k]);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
       fscanf(ficpar,"\n");    /*  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);
       printf("\n");  */
       fprintf(ficparo,"\n");  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     }    fprintf(ficgp,"\nset out \"%s%s.png\";replot;",digitp,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   }  
   delti=delti3[1][1];    free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,nlstate);
   /* Reads comments: lines beginning with '#' */    free_matrix(dnewm,1,nlstate,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     ungetc(c,ficpar);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     fgets(line, MAXLINE, ficpar);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     puts(line);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fputs(line,ficparo);    fclose(ficresprobmorprev);
   }    fflush(ficgp);
   ungetc(c,ficpar);    fflush(fichtm); 
    }  /* end varevsij */
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){  /************ Variance of prevlim ******************/
     fscanf(ficpar,"%s",&str);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
     printf("%s",str);  {
     fprintf(ficparo,"%s",str);    /* Variance of prevalence limit */
     for(j=1; j <=i; j++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       fscanf(ficpar," %le",&matcov[i][j]);    double **newm;
       printf(" %.5le",matcov[i][j]);    double **dnewm,**doldm;
       fprintf(ficparo," %.5le",matcov[i][j]);    int i, j, nhstepm, hstepm;
     }    int k, cptcode;
     fscanf(ficpar,"\n");    double *xp;
     printf("\n");    double *gp, *gm;
     fprintf(ficparo,"\n");    double **gradg, **trgradg;
   }    double age,agelim;
   for(i=1; i <=npar; i++)    int theta;
     for(j=i+1;j<=npar;j++)     
       matcov[i][j]=matcov[j][i];    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
        fprintf(ficresvpl,"# Age");
   printf("\n");    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
     /*-------- Rewriting paramater file ----------*/  
      strcpy(rfileres,"r");    /* "Rparameterfile */    xp=vector(1,npar);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    dnewm=matrix(1,nlstate,1,npar);
      strcat(rfileres,".");    /* */    doldm=matrix(1,nlstate,1,nlstate);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    
     if((ficres =fopen(rfileres,"w"))==NULL) {    hstepm=1*YEARM; /* Every year of age */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     }    agelim = AGESUP;
     fprintf(ficres,"#%s\n",version);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
          nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     /*-------- data file ----------*/      if (stepm >= YEARM) hstepm=1;
     if((fic=fopen(datafile,"r"))==NULL)    {      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       printf("Problem with datafile: %s\n", datafile);goto end;      gradg=matrix(1,npar,1,nlstate);
     }      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
     n= lastobs;  
     severity = vector(1,maxwav);      for(theta=1; theta <=npar; theta++){
     outcome=imatrix(1,maxwav+1,1,n);        for(i=1; i<=npar; i++){ /* Computes gradient */
     num=ivector(1,n);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     moisnais=vector(1,n);        }
     annais=vector(1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     moisdc=vector(1,n);        for(i=1;i<=nlstate;i++)
     andc=vector(1,n);          gp[i] = prlim[i][i];
     agedc=vector(1,n);      
     cod=ivector(1,n);        for(i=1; i<=npar; i++) /* Computes gradient */
     weight=vector(1,n);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     mint=matrix(1,maxwav,1,n);        for(i=1;i<=nlstate;i++)
     anint=matrix(1,maxwav,1,n);          gm[i] = prlim[i][i];
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);            for(i=1;i<=nlstate;i++)
     tab=ivector(1,NCOVMAX);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     ncodemax=ivector(1,8);      } /* End theta */
   
     i=1;      trgradg =matrix(1,nlstate,1,npar);
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {      for(j=1; j<=nlstate;j++)
                for(theta=1; theta <=npar; theta++)
         for (j=maxwav;j>=1;j--){          trgradg[j][theta]=gradg[theta][j];
           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);        varpl[i][(int)age] =0.;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
         }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
              for(i=1;i<=nlstate;i++)
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
       fprintf(ficresvpl,"%.0f ",age );
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      free_vector(gp,1,nlstate);
         for (j=ncovcol;j>=1;j--){      free_vector(gm,1,nlstate);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      free_matrix(gradg,1,npar,1,nlstate);
         }      free_matrix(trgradg,1,nlstate,1,npar);
         num[i]=atol(stra);    } /* End age */
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    free_vector(xp,1,npar);
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
         i=i+1;  
       }  }
     }  
     /* printf("ii=%d", ij);  /************ Variance of one-step probabilities  ******************/
        scanf("%d",i);*/  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   imx=i-1; /* Number of individuals */  {
     int i, j=0,  i1, k1, l1, t, tj;
   /* for (i=1; i<=imx; i++){    int k2, l2, j1,  z1;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    int k=0,l, cptcode;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    int first=1, first1;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     }*/    double **dnewm,**doldm;
      double *xp;
   /* for (i=1; i<=imx; i++){    double *gp, *gm;
      if (s[4][i]==9)  s[4][i]=-1;    double **gradg, **trgradg;
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}    double **mu;
   */    double age,agelim, cov[NCOVMAX];
      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   /* Calculation of the number of parameter from char model*/    int theta;
   Tvar=ivector(1,15);    char fileresprob[FILENAMELENGTH];
   Tprod=ivector(1,15);    char fileresprobcov[FILENAMELENGTH];
   Tvaraff=ivector(1,15);    char fileresprobcor[FILENAMELENGTH];
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);          double ***varpij;
      
   if (strlen(model) >1){    strcpy(fileresprob,"prob"); 
     j=0, j1=0, k1=1, k2=1;    strcat(fileresprob,fileres);
     j=nbocc(model,'+');    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     j1=nbocc(model,'*');      printf("Problem with resultfile: %s\n", fileresprob);
     cptcovn=j+1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     cptcovprod=j1;    }
        strcpy(fileresprobcov,"probcov"); 
     strcpy(modelsav,model);    strcat(fileresprobcov,fileres);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Error. Non available option model=%s ",model);      printf("Problem with resultfile: %s\n", fileresprobcov);
       goto end;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }    }
        strcpy(fileresprobcor,"probcor"); 
     for(i=(j+1); i>=1;i--){    strcat(fileresprobcor,fileres);
       cutv(stra,strb,modelsav,'+');    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      printf("Problem with resultfile: %s\n", fileresprobcor);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       /*scanf("%d",i);*/    }
       if (strchr(strb,'*')) {    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         cutv(strd,strc,strb,'*');    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         if (strcmp(strc,"age")==0) {    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           cptcovprod--;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           cutv(strb,stre,strd,'V');    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           Tvar[i]=atoi(stre);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           cptcovage++;    
             Tage[cptcovage]=i;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
             /*printf("stre=%s ", stre);*/    fprintf(ficresprob,"# Age");
         }    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
         else if (strcmp(strd,"age")==0) {    fprintf(ficresprobcov,"# Age");
           cptcovprod--;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           cutv(strb,stre,strc,'V');    fprintf(ficresprobcov,"# Age");
           Tvar[i]=atoi(stre);  
           cptcovage++;  
           Tage[cptcovage]=i;    for(i=1; i<=nlstate;i++)
         }      for(j=1; j<=(nlstate+ndeath);j++){
         else {        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
           cutv(strb,stre,strc,'V');        fprintf(ficresprobcov," p%1d-%1d ",i,j);
           Tvar[i]=ncovcol+k1;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           cutv(strb,strc,strd,'V');      }  
           Tprod[k1]=i;   /* fprintf(ficresprob,"\n");
           Tvard[k1][1]=atoi(strc);    fprintf(ficresprobcov,"\n");
           Tvard[k1][2]=atoi(stre);    fprintf(ficresprobcor,"\n");
           Tvar[cptcovn+k2]=Tvard[k1][1];   */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];   xp=vector(1,npar);
           for (k=1; k<=lastobs;k++)    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           k1++;    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           k2=k2+2;    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
         }    first=1;
       }    fprintf(ficgp,"\n# Routine varprob");
       else {    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    fprintf(fichtm,"\n");
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');    fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       Tvar[i]=atoi(strc);    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");
       }    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");
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    cov[1]=1;
         scanf("%d",i);*/    tj=cptcoveff;
     }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
 }    j1=0;
      for(t=1; t<=tj;t++){
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      for(i1=1; i1<=ncodemax[t];i1++){ 
   printf("cptcovprod=%d ", cptcovprod);        j1++;
   scanf("%d ",i);*/        if  (cptcovn>0) {
     fclose(fic);          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     /*  if(mle==1){*/          fprintf(ficresprob, "**********\n#\n");
     if (weightopt != 1) { /* Maximisation without weights*/          fprintf(ficresprobcov, "\n#********** Variable "); 
       for(i=1;i<=n;i++) weight[i]=1.0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresprobcov, "**********\n#\n");
     /*-calculation of age at interview from date of interview and age at death -*/          
     agev=matrix(1,maxwav,1,imx);          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");
       for(m=2; (m<= maxwav); m++) {          
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          
          anint[m][i]=9999;          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
          s[m][i]=-1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        }          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;          
       }          fprintf(ficresprobcor, "\n#********** Variable ");    
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
     for (i=1; i<=imx; i++)  {        }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        
       for(m=1; (m<= maxwav); m++){        for (age=bage; age<=fage; age ++){ 
         if(s[m][i] >0){          cov[2]=age;
           if (s[m][i] >= nlstate+1) {          for (k=1; k<=cptcovn;k++) {
             if(agedc[i]>0)            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
               if(moisdc[i]!=99 && andc[i]!=9999)          }
                 agev[m][i]=agedc[i];          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/          for (k=1; k<=cptcovprod;k++)
            else {            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
               if (andc[i]!=9999){          
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
               agev[m][i]=-1;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               }          gp=vector(1,(nlstate)*(nlstate+ndeath));
             }          gm=vector(1,(nlstate)*(nlstate+ndeath));
           }      
           else if(s[m][i] !=9){ /* Should no more exist */          for(theta=1; theta <=npar; theta++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            for(i=1; i<=npar; i++)
             if(mint[m][i]==99 || anint[m][i]==9999)              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
               agev[m][i]=1;            
             else if(agev[m][i] <agemin){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
               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);*/            k=0;
             }            for(i=1; i<= (nlstate); i++){
             else if(agev[m][i] >agemax){              for(j=1; j<=(nlstate+ndeath);j++){
               agemax=agev[m][i];                k=k+1;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                gp[k]=pmmij[i][j];
             }              }
             /*agev[m][i]=anint[m][i]-annais[i];*/            }
             /*   agev[m][i] = age[i]+2*m;*/            
           }            for(i=1; i<=npar; i++)
           else { /* =9 */              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
             agev[m][i]=1;      
             s[m][i]=-1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           }            k=0;
         }            for(i=1; i<=(nlstate); i++){
         else /*= 0 Unknown */              for(j=1; j<=(nlstate+ndeath);j++){
           agev[m][i]=1;                k=k+1;
       }                gm[k]=pmmij[i][j];
                  }
     }            }
     for (i=1; i<=imx; i++)  {       
       for(m=1; (m<= maxwav); m++){            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         if (s[m][i] > (nlstate+ndeath)) {              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           printf("Error: Wrong value in nlstate or ndeath\n");            }
           goto end;  
         }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       }            for(theta=1; theta <=npar; theta++)
     }              trgradg[j][theta]=gradg[theta][j];
           
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          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);
     free_vector(severity,1,maxwav);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     free_imatrix(outcome,1,maxwav+1,1,n);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     free_vector(moisnais,1,n);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     free_vector(annais,1,n);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/          pmij(pmmij,cov,ncovmodel,x,nlstate);
     free_vector(moisdc,1,n);          
     free_vector(andc,1,n);          k=0;
           for(i=1; i<=(nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
     wav=ivector(1,imx);              k=k+1;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              mu[k][(int) age]=pmmij[i][j];
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            }
              }
     /* Concatenates waves */          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
       Tcode=ivector(1,100);          /*printf("\n%d ",(int)age);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       ncodemax[1]=1;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                  }*/
    codtab=imatrix(1,100,1,10);  
    h=0;          fprintf(ficresprob,"\n%d ",(int)age);
    m=pow(2,cptcoveff);          fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficresprobcor,"\n%d ",(int)age);
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
        for(j=1; j <= ncodemax[k]; j++){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
            h++;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          }
          }          i=0;
        }          for (k=1; k<=(nlstate);k++){
      }            for (l=1; l<=(nlstate+ndeath);l++){ 
    }              i=i++;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
       codtab[1][2]=1;codtab[2][2]=2; */              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
    /* for(i=1; i <=m ;i++){              for (j=1; j<=i;j++){
       for(k=1; k <=cptcovn; k++){                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       }              }
       printf("\n");            }
       }          }/* end of loop for state */
       scanf("%d",i);*/        } /* end of loop for age */
      
    /* Calculates basic frequencies. Computes observed prevalence at single age        /* Confidence intervalle of pij  */
        and prints on file fileres'p'. */        /*
           fprintf(ficgp,"\nset noparametric;unset label");
              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");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          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);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        */
        
     /* For Powell, parameters are in a vector p[] starting at p[1]        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        first1=1;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     if(mle==1){            if(l2==k2) continue;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            j=(k2-1)*(nlstate+ndeath)+l2;
     }            for (k1=1; k1<=(nlstate);k1++){
                  for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     /*--------- results files --------------*/                if(l1==k1) continue;
     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);                i=(k1-1)*(nlstate+ndeath)+l1;
                  if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
    jk=1;                  if ((int)age %5==0){
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
    for(i=1,jk=1; i <=nlstate; i++){                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
      for(k=1; k <=(nlstate+ndeath); k++){                    mu1=mu[i][(int) age]/stepm*YEARM ;
        if (k != i)                    mu2=mu[j][(int) age]/stepm*YEARM;
          {                    c12=cv12/sqrt(v1*v2);
            printf("%d%d ",i,k);                    /* Computing eigen value of matrix of covariance */
            fprintf(ficres,"%1d%1d ",i,k);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
            for(j=1; j <=ncovmodel; j++){                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
              printf("%f ",p[jk]);                    /* Eigen vectors */
              fprintf(ficres,"%f ",p[jk]);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
              jk++;                    /*v21=sqrt(1.-v11*v11); *//* error */
            }                    v21=(lc1-v1)/cv12*v11;
            printf("\n");                    v12=-v21;
            fprintf(ficres,"\n");                    v22=v11;
          }                    tnalp=v21/v11;
      }                    if(first1==1){
    }                      first1=0;
  if(mle==1){                      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);
     /* Computing hessian and covariance matrix */                    }
     ftolhess=ftol; /* Usually correct */                    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);
     hesscov(matcov, p, npar, delti, ftolhess, func);                    /*printf(fignu*/
  }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     printf("# Scales (for hessian or gradient estimation)\n");                    if(first==1){
      for(i=1,jk=1; i <=nlstate; i++){                      first=0;
       for(j=1; j <=nlstate+ndeath; j++){                      fprintf(ficgp,"\nset parametric;unset label");
         if (j!=i) {                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
           fprintf(ficres,"%1d%1d",i,j);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           printf("%1d%1d",i,j);                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
           for(k=1; k<=ncovmodel;k++){   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
             printf(" %.5e",delti[jk]);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
             fprintf(ficres," %.5e",delti[jk]);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
             jk++;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           }                      fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           printf("\n");                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           fprintf(ficres,"\n");                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
      }                      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",\
                                  mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     k=1;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     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");                    }else{
     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");                      first=0;
     for(i=1;i<=npar;i++){                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
       /*  if (k>nlstate) k=1;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       i1=(i-1)/(ncovmodel*nlstate)+1;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                      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",\
       printf("%s%d%d",alph[k],i1,tab[i]);*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       fprintf(ficres,"%3d",i);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       printf("%3d",i);                    }/* if first */
       for(j=1; j<=i;j++){                  } /* age mod 5 */
         fprintf(ficres," %.5e",matcov[i][j]);                } /* end loop age */
         printf(" %.5e",matcov[i][j]);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       }                first=1;
       fprintf(ficres,"\n");              } /*l12 */
       printf("\n");            } /* k12 */
       k++;          } /*l1 */
     }        }/* k1 */
          } /* loop covariates */
     while((c=getc(ficpar))=='#' && c!= EOF){    }
       ungetc(c,ficpar);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       fgets(line, MAXLINE, ficpar);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       puts(line);    free_vector(xp,1,npar);
       fputs(line,ficparo);    fclose(ficresprob);
     }    fclose(ficresprobcov);
     ungetc(c,ficpar);    fclose(ficresprobcor);
      /*  fclose(ficgp);*/
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&ageminpar,&agemaxpar, &bage, &fage);  }
      
     if (fage <= 2) {  
       bage = ageminpar;  /******************* Printing html file ***********/
       fage = agemaxpar;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     }                    int lastpass, int stepm, int weightopt, char model[],\
                        int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                    int popforecast, int estepm ,\
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);                    double jprev1, double mprev1,double anprev1, \
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);                    double jprev2, double mprev2,double anprev2){
      int jj1, k1, i1, cpt;
     while((c=getc(ficpar))=='#' && c!= EOF){    /*char optionfilehtm[FILENAMELENGTH];*/
     ungetc(c,ficpar);  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
     fgets(line, MAXLINE, ficpar);  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
     puts(line);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
     fputs(line,ficparo);  /*   } */
   }  
   ungetc(c,ficpar);     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 \
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   - Life expectancies by age and initial health status (estepm=%2d months): \
           <a href=\"%s\">%s</a> <br>\n</li>", \
   while((c=getc(ficpar))=='#' && c!= EOF){             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
     ungetc(c,ficpar);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
     fgets(line, MAXLINE, ficpar);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
     puts(line);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     fputs(line,ficparo);  
   }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   ungetc(c,ficpar);  
     m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  
    dateprev2=anprev2+mprev2/12.+jprev2/365.;   jj1=0;
    for(k1=1; k1<=m;k1++){
   fscanf(ficpar,"pop_based=%d\n",&popbased);     for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficparo,"pop_based=%d\n",popbased);         jj1++;
   fprintf(ficres,"pop_based=%d\n",popbased);         if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   while((c=getc(ficpar))=='#' && c!= EOF){         for (cpt=1; cpt<=cptcoveff;cpt++) 
     ungetc(c,ficpar);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     fgets(line, MAXLINE, ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     puts(line);       }
     fputs(line,ficparo);       /* Pij */
   }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   ungetc(c,ficpar);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
   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);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
 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);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
 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);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
 while((c=getc(ficpar))=='#' && c!= EOF){           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
     ungetc(c,ficpar);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
     fgets(line, MAXLINE, ficpar);         }
     puts(line);       for(cpt=1; cpt<=nlstate;cpt++) {
     fputs(line,ficparo);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exo"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   ungetc(c,ficpar);       }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  health expectancies in states (1) and (2): %s%d.png<br>\
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);     } /* end i1 */
    }/* End k1 */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   fprintf(fichtm,"</ul>");
   
 /*------------ gnuplot -------------*/  
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
     - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
 /*------------ free_vector  -------------*/   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
  chdir(path);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
     - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
  free_ivector(wav,1,imx);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);     - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
  free_ivector(num,1,n);           rfileres,rfileres,\
  free_vector(agedc,1,n);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
  /*free_matrix(covar,1,NCOVMAX,1,n);*/           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
  fclose(ficparo);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
  fclose(ficres);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
            subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
 /*--------- index.htm --------*/           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast);  /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - 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 */
   /*--------------- Prevalence limit --------------*/  /*      <br>",fileres,fileres,fileres,fileres); */
    /*  else  */
   strcpy(filerespl,"pl");  /*    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); */
   strcat(filerespl,fileres);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;   m=cptcoveff;
   }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");   jj1=0;
   fprintf(ficrespl,"#Age ");   for(k1=1; k1<=m;k1++){
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);     for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficrespl,"\n");       jj1++;
         if (cptcovn > 0) {
   prlim=matrix(1,nlstate,1,nlstate);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         for (cpt=1; cpt<=cptcoveff;cpt++) 
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       for(cpt=1; cpt<=nlstate;cpt++) {
   k=0;         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
   agebase=ageminpar;  interval) in state (%d): %s%d%d.png <br>\
   agelim=agemaxpar;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"pe"),cpt,jj1,subdirf2(optionfilefiname,"pe"),cpt,jj1);  
   ftolpl=1.e-10;       }
   i1=cptcoveff;     } /* end i1 */
   if (cptcovn < 1){i1=1;}   }/* End k1 */
    fprintf(fichtm,"</ul>");
   for(cptcov=1;cptcov<=i1;cptcov++){   fflush(fichtm);
     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]);*/  /******************* Gnuplot file **************/
         fprintf(ficrespl,"\n#******");  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char path[], double p[]){
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    char dirfileres[132],optfileres[132];
         fprintf(ficrespl,"******\n");    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
            int ng;
         for (age=agebase; age<=agelim; age++){  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  /*     printf("Problem with file %s",optionfilegnuplot); */
           fprintf(ficrespl,"%.0f",age );  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
           for(i=1; i<=nlstate;i++)  /*   } */
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");    /*#ifdef windows */
         }    fprintf(ficgp,"cd \"%s\" \n",path);
       }      /*#endif */
     }    m=pow(2,cptcoveff);
   fclose(ficrespl);  
     strcpy(dirfileres,optionfilefiname);
   /*------------- h Pij x at various ages ------------*/    strcpy(optfileres,"vpl");
     /* 1eme*/
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    for (cpt=1; cpt<= nlstate ; cpt ++) {
   if((ficrespij=fopen(filerespij,"w"))==NULL) {     for (k1=1; k1<= m ; k1 ++) {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   }       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   printf("Computing pij: result on file '%s' \n", filerespij);       fprintf(ficgp,"set xlabel \"Age\" \n\
    set ylabel \"Probability\" \n\
   stepsize=(int) (stepm+YEARM-1)/YEARM;  set ter png small\n\
   /*if (stepm<=24) stepsize=2;*/  set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */       for (i=1; i<= nlstate ; i ++) {
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   k=0;       }
   for(cptcov=1;cptcov<=i1;cptcov++){       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);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       for (i=1; i<= nlstate ; i ++) {
       k=k+1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficrespij,"\n#****** ");         else fprintf(ficgp," \%%*lf (\%%*lf)");
         for(j=1;j<=cptcoveff;j++)       } 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
         fprintf(ficrespij,"******\n");       for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */         else fprintf(ficgp," \%%*lf (\%%*lf)");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       }  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
           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);      /*2 eme*/
           fprintf(ficrespij,"# Age");    
           for(i=1; i<=nlstate;i++)    for (k1=1; k1<= m ; k1 ++) { 
             for(j=1; j<=nlstate+ndeath;j++)      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
               fprintf(ficrespij," %1d-%1d",i,j);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
           fprintf(ficrespij,"\n");      
           for (h=0; h<=nhstepm; h++){      for (i=1; i<= nlstate+1 ; i ++) {
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        k=2*i;
             for(i=1; i<=nlstate;i++)        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
               for(j=1; j<=nlstate+ndeath;j++)        for (j=1; j<= nlstate+1 ; j ++) {
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
             fprintf(ficrespij,"\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
           }        }   
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
           fprintf(ficrespij,"\n");        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         }        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     }        for (j=1; j<= nlstate+1 ; j ++) {
   }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/        }   
         fprintf(ficgp,"\" t\"\" w l 0,");
   fclose(ficrespij);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   /*---------- Forecasting ------------------*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
   if((stepm == 1) && (strcmp(model,".")==0)){        }   
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        else fprintf(ficgp,"\" t\"\" w l 0,");
     free_matrix(mint,1,maxwav,1,n);      }
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    }
     free_vector(weight,1,n);}    
   else{    /*3eme*/
     erreur=108;    
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);    for (k1=1; k1<= m ; k1 ++) { 
   }      for (cpt=1; cpt<= nlstate ; cpt ++) {
          k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
   /*---------- Health expectancies and variances ------------*/        fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   strcpy(filerest,"t");  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
   strcat(filerest,fileres);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   if((ficrest=fopen(filerest,"w"))==NULL) {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
   strcpy(filerese,"e");        */
   strcat(filerese,fileres);        for (i=1; i< nlstate ; i ++) {
   if((ficreseij=fopen(filerese,"w"))==NULL) {          fprintf(ficgp," ,\"%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);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          
   }        } 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      }
     }
  strcpy(fileresv,"v");    
   strcat(fileresv,fileres);    /* CV preval stable (period) */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    for (k1=1; k1<= m ; k1 ++) { 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      for (cpt=1; cpt<=nlstate ; cpt ++) {
   }        k=3;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   k=0;  set ter png small\nset size 0.65,0.65\n\
   for(cptcov=1;cptcov<=i1;cptcov++){  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        
       k=k+1;        for (i=1; i< nlstate ; i ++)
       fprintf(ficrest,"\n#****** ");          fprintf(ficgp,"+$%d",k+i+1);
       for(j=1;j<=cptcoveff;j++)        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        
       fprintf(ficrest,"******\n");        l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
       fprintf(ficreseij,"\n#****** ");        for (i=1; i< nlstate ; i ++) {
       for(j=1;j<=cptcoveff;j++)          l=3+(nlstate+ndeath)*cpt;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"+$%d",l+i+1);
       fprintf(ficreseij,"******\n");        }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       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");    /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      for(k=1; k <=(nlstate+ndeath); k++){
       oldm=oldms;savm=savms;        if (k != i) {
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            for(j=1; j <=ncovmodel; j++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       oldm=oldms;savm=savms;            jk++; 
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            fprintf(ficgp,"\n");
              }
         }
        }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");     }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
       epj=vector(1,nlstate+1);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
       for(age=bage; age <=fage ;age++){         if (ng==2)
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
         if (popbased==1) {         else
           for(i=1; i<=nlstate;i++)           fprintf(ficgp,"\nset title \"Probability\"\n");
             prlim[i][i]=probs[(int)age][i][k];         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
         }         i=1;
                 for(k2=1; k2<=nlstate; k2++) {
         fprintf(ficrest," %4.0f",age);           k3=i;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){           for(k=1; k<=(nlstate+ndeath); k++) {
           for(i=1, epj[j]=0.;i <=nlstate;i++) {             if (k != k2){
             epj[j] += prlim[i][i]*eij[i][j][(int)age];               if(ng==2)
           }                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
           epj[nlstate+1] +=epj[j];               else
         }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
         for(i=1, vepp=0.;i <=nlstate;i++)               ij=1;
           for(j=1;j <=nlstate;j++)               for(j=3; j <=ncovmodel; j++) {
             vepp += vareij[i][j][(int)age];                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
         for(j=1;j <=nlstate;j++){                   ij++;
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));                 }
         }                 else
         fprintf(ficrest,"\n");                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       }               }
     }               fprintf(ficgp,")/(1");
   }               
                for(k1=1; k1 <=nlstate; k1++){   
   fclose(ficreseij);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   fclose(ficresvij);                 ij=1;
   fclose(ficrest);                 for(j=3; j <=ncovmodel; j++){
   fclose(ficpar);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   free_vector(epj,1,nlstate+1);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                       ij++;
   /*------- Variance limit prevalence------*/                     }
                    else
   strcpy(fileresvpl,"vpl");                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   strcat(fileresvpl,fileres);                 }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                 fprintf(ficgp,")");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);               }
     exit(0);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   }               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);               i=i+ncovmodel;
              }
   k=0;           } /* end k */
   for(cptcov=1;cptcov<=i1;cptcov++){         } /* end k2 */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       } /* end jk */
       k=k+1;     } /* end ng */
       fprintf(ficresvpl,"\n#****** ");     fflush(ficgp); 
       for(j=1;j<=cptcoveff;j++)  }  /* end gnuplot */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\n");  
        /*************** Moving average **************/
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
       oldm=oldms;savm=savms;  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    int i, cpt, cptcod;
     }    int modcovmax =1;
  }    int mobilavrange, mob;
     double age;
   fclose(ficresvpl);  
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   /*---------- End : free ----------------*/                             a covariate has 2 modalities */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      if(mobilav==1) mobilavrange=5; /* default */
        else mobilavrange=mobilav;
        for (age=bage; age<=fage; age++)
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        for (i=1; i<=nlstate;i++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      /* We keep the original values on the extreme ages bage, fage and for 
           fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   free_matrix(matcov,1,npar,1,npar);         we use a 5 terms etc. until the borders are no more concerned. 
   free_vector(delti,1,npar);      */ 
   free_matrix(agev,1,maxwav,1,imx);      for (mob=3;mob <=mobilavrange;mob=mob+2){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
   if(erreur >0)            for (cptcod=1;cptcod<=modcovmax;cptcod++){
     printf("End of Imach with error or warning %d\n",erreur);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   else   printf("End of Imach\n");                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                    mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/                }
   /*printf("Total time was %d uSec.\n", total_usecs);*/              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   /*------ End -----------*/            }
           }
         }/* end age */
  end:      }/* end mob */
 #ifdef windows    }else return -1;
   /* chdir(pathcd);*/    return 0;
 #endif  }/* End movingaverage */
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/  /************** Forecasting ******************/
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  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){
  strcpy(plotcmd,GNUPLOTPROGRAM);    /* proj1, year, month, day of starting projection 
  strcat(plotcmd," ");       agemin, agemax range of age
  strcat(plotcmd,optionfilegnuplot);       dateprev1 dateprev2 range of dates during which prevalence is computed
  system(plotcmd);       anproj2 year of en of projection (same day and month as proj1).
     */
 #ifdef windows    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   while (z[0] != 'q') {    int *popage;
     /* chdir(path); */    double agec; /* generic age */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     scanf("%s",z);    double *popeffectif,*popcount;
     if (z[0] == 'c') system("./imach");    double ***p3mat;
     else if (z[0] == 'e') system(optionfilehtm);    double ***mobaverage;
     else if (z[0] == 'g') system(plotcmd);    char fileresf[FILENAMELENGTH];
     else if (z[0] == 'q') exit(0);  
   }    agelim=AGESUP;
 #endif    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);
     
     /*  replace(pathc,path);*/
   
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, path,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Localtime at start %s\nLocal time at end   %s",strstart, strtend); 
     /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
   
     printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(ficgp);
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
     chdir(path);
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
   

Removed from v.1.35  
changed lines
  Added in v.1.88


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>