Diff for /imach/src/imach.c between versions 1.42 and 1.90

version 1.42, 2002/05/21 18:44:41 version 1.90, 2003/06/24 12:34:15
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.90  2003/06/24 12:34:15  brouard
      (Module): Some bugs corrected for windows. Also, when
   This program computes Healthy Life Expectancies from    mle=-1 a template is output in file "or"mypar.txt with the design
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    of the covariance matrix to be input.
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.89  2003/06/24 12:30:52  brouard
   case of a health survey which is our main interest) -2- at least a    (Module): Some bugs corrected for windows. Also, when
   second wave of interviews ("longitudinal") which measure each change    mle=-1 a template is output in file "or"mypar.txt with the design
   (if any) in individual health status.  Health expectancies are    of the covariance matrix to be input.
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.88  2003/06/23 17:54:56  brouard
   Maximum Likelihood of the parameters involved in the model.  The    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Revision 1.87  2003/06/18 12:26:01  brouard
   conditional to be observed in state i at the first wave. Therefore    Version 0.96
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.86  2003/06/17 20:04:08  brouard
   complex model than "constant and age", you should modify the program    (Module): Change position of html and gnuplot routines and added
   where the markup *Covariates have to be included here again* invites    routine fileappend.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
   The advantage of this computer programme, compared to a simple    current date of interview. It may happen when the death was just
   multinomial logistic model, is clear when the delay between waves is not    prior to the death. In this case, dh was negative and likelihood
   identical for each individual. Also, if a individual missed an    was wrong (infinity). We still send an "Error" but patch by
   intermediate interview, the information is lost, but taken into    assuming that the date of death was just one stepm after the
   account using an interpolation or extrapolation.      interview.
     (Repository): Because some people have very long ID (first column)
   hPijx is the probability to be observed in state i at age x+h    we changed int to long in num[] and we added a new lvector for
   conditional to the observed state i at age x. The delay 'h' can be    memory allocation. But we also truncated to 8 characters (left
   split into an exact number (nh*stepm) of unobserved intermediate    truncation)
   states. This elementary transition (by month or quarter trimester,    (Repository): No more line truncation errors.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.84  2003/06/13 21:44:43  brouard
   and the contribution of each individual to the likelihood is simply    * imach.c (Repository): Replace "freqsummary" at a correct
   hPijx.    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
   Also this programme outputs the covariance matrix of the parameters but also    parcimony.
   of the life expectancies. It also computes the prevalence limits.    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.83  2003/06/10 13:39:11  lievre
            Institut national d'études démographiques, Paris.    *** empty log message ***
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.82  2003/06/05 15:57:20  brouard
   It is copyrighted identically to a GNU software product, ie programme and    Add log in  imach.c and  fullversion number is now printed.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .  */
   **********************************************************************/  /*
       Interpolated Markov Chain
 #include <math.h>  
 #include <stdio.h>    Short summary of the programme:
 #include <stdlib.h>    
 #include <unistd.h>    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define MAXLINE 256    first survey ("cross") where individuals from different ages are
 #define GNUPLOTPROGRAM "gnuplot"    interviewed on their health status or degree of disability (in the
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    case of a health survey which is our main interest) -2- at least a
 #define FILENAMELENGTH 80    second wave of interviews ("longitudinal") which measure each change
 /*#define DEBUG*/    (if any) in individual health status.  Health expectancies are
 #define windows    computed from the time spent in each health state according to a
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    model. More health states you consider, more time is necessary to reach the
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    probability to be observed in state j at the second wave
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define NINTERVMAX 8    'age' is age and 'sex' is a covariate. If you want to have a more
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    complex model than "constant and age", you should modify the program
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    where the markup *Covariates have to be included here again* invites
 #define NCOVMAX 8 /* Maximum number of covariates */    you to do it.  More covariates you add, slower the
 #define MAXN 20000    convergence.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    The advantage of this computer programme, compared to a simple
 #define AGEBASE 40    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 int erreur; /* Error number */    account using an interpolation or extrapolation.  
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    hPijx is the probability to be observed in state i at age x+h
 int npar=NPARMAX;    conditional to the observed state i at age x. The delay 'h' can be
 int nlstate=2; /* Number of live states */    split into an exact number (nh*stepm) of unobserved intermediate
 int ndeath=1; /* Number of dead states */    states. This elementary transition (by month, quarter,
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    semester or year) is modelled as a multinomial logistic.  The hPx
 int popbased=0;    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 int *wav; /* Number of waves for this individuual 0 is possible */    hPijx.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Also this programme outputs the covariance matrix of the parameters but also
 int mle, weightopt;    of the life expectancies. It also computes the stable prevalence. 
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 double jmean; /* Mean space between 2 waves */             Institut national d'études démographiques, Paris.
 double **oldm, **newm, **savm; /* Working pointers to matrices */    This software have been partly granted by Euro-REVES, a concerted action
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    from the European Union.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    It is copyrighted identically to a GNU software product, ie programme and
 FILE *ficgp,*ficresprob,*ficpop;    software can be distributed freely for non commercial use. Latest version
 FILE *ficreseij;    can be accessed at http://euroreves.ined.fr/imach .
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   char fileresv[FILENAMELENGTH];    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
  FILE  *ficresvpl;    
   char fileresvpl[FILENAMELENGTH];    **********************************************************************/
   /*
 #define NR_END 1    main
 #define FREE_ARG char*    read parameterfile
 #define FTOL 1.0e-10    read datafile
     concatwav
 #define NRANSI    freqsummary
 #define ITMAX 200    if (mle >= 1)
       mlikeli
 #define TOL 2.0e-4    print results files
     if mle==1 
 #define CGOLD 0.3819660       computes hessian
 #define ZEPS 1.0e-10    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);        begin-prev-date,...
     open gnuplot file
 #define GOLD 1.618034    open html file
 #define GLIMIT 100.0    stable prevalence
 #define TINY 1.0e-20     for age prevalim()
     h Pij x
 static double maxarg1,maxarg2;    variance of p varprob
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    forecasting if prevfcast==1 prevforecast call prevalence()
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    health expectancies
      Variance-covariance of DFLE
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    prevalence()
 #define rint(a) floor(a+0.5)     movingaverage()
     varevsij() 
 static double sqrarg;    if popbased==1 varevsij(,popbased)
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    total life expectancies
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Variance of stable prevalence
    end
 int imx;  */
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  
   
 int estepm;   
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  #include <math.h>
   #include <stdio.h>
 int m,nb;  #include <stdlib.h>
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #include <unistd.h>
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;  #include <sys/time.h>
 double dateintmean=0;  #include <time.h>
   #include "timeval.h"
 double *weight;  
 int **s; /* Status */  #define MAXLINE 256
 double *agedc, **covar, idx;  #define GNUPLOTPROGRAM "gnuplot"
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  /*#define DEBUG*/
 double ftolhess; /* Tolerance for computing hessian */  /*#define windows*/
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 /**************** split *************************/  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    char *s;                             /* pointer */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    int  l1, l2;                         /* length counters */  
   #define NINTERVMAX 8
    l1 = strlen( path );                 /* length of path */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #ifdef windows  #define NCOVMAX 8 /* Maximum number of covariates */
    s = strrchr( path, '\\' );           /* find last / */  #define MAXN 20000
 #else  #define YEARM 12. /* Number of months per year */
    s = strrchr( path, '/' );            /* find last / */  #define AGESUP 130
 #endif  #define AGEBASE 40
    if ( s == NULL ) {                   /* no directory, so use current */  #ifdef unix
 #if     defined(__bsd__)                /* get current working directory */  #define DIRSEPARATOR '/'
       extern char       *getwd( );  #define ODIRSEPARATOR '\\'
   #else
       if ( getwd( dirc ) == NULL ) {  #define DIRSEPARATOR '\\'
 #else  #define ODIRSEPARATOR '/'
       extern char       *getcwd( );  #endif
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  /* $Id$ */
 #endif  /* $State$ */
          return( GLOCK_ERROR_GETCWD );  
       }  char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
       strcpy( name, path );             /* we've got it */  char fullversion[]="$Revision$ $Date$"; 
    } else {                             /* strip direcotry from path */  int erreur; /* Error number */
       s++;                              /* after this, the filename */  int nvar;
       l2 = strlen( s );                 /* length of filename */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int npar=NPARMAX;
       strcpy( name, s );                /* save file name */  int nlstate=2; /* Number of live states */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  int ndeath=1; /* Number of dead states */
       dirc[l1-l2] = 0;                  /* add zero */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    }  int popbased=0;
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows  int *wav; /* Number of waves for this individuual 0 is possible */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int maxwav; /* Maxim number of waves */
 #else  int jmin, jmax; /* min, max spacing between 2 waves */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int gipmx, gsw; /* Global variables on the number of contributions 
 #endif                     to the likelihood and the sum of weights (done by funcone)*/
    s = strrchr( name, '.' );            /* find last / */  int mle, weightopt;
    s++;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
    strcpy(ext,s);                       /* save extension */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    l1= strlen( name);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
    l2= strlen( s)+1;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
    strncpy( finame, name, l1-l2);  double jmean; /* Mean space between 2 waves */
    finame[l1-l2]= 0;  double **oldm, **newm, **savm; /* Working pointers to matrices */
    return( 0 );                         /* we're done */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 }  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
   int globpr; /* Global variable for printing or not */
 /******************************************/  double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
 void replace(char *s, char*t)  double sw; /* Sum of weights */
 {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   int i;  FILE *ficresilk;
   int lg=20;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   i=0;  FILE *ficresprobmorprev;
   lg=strlen(t);  FILE *fichtm; /* Html File */
   for(i=0; i<= lg; i++) {  FILE *ficreseij;
     (s[i] = t[i]);  char filerese[FILENAMELENGTH];
     if (t[i]== '\\') s[i]='/';  FILE  *ficresvij;
   }  char fileresv[FILENAMELENGTH];
 }  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 int nbocc(char *s, char occ)  char title[MAXLINE];
 {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   int i,j=0;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   int lg=20;  char tmpout[FILENAMELENGTH]; 
   i=0;  char command[FILENAMELENGTH];
   lg=strlen(s);  int  outcmd=0;
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   }  char lfileres[FILENAMELENGTH];
   return j;  char filelog[FILENAMELENGTH]; /* Log file */
 }  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 void cutv(char *u,char *v, char*t, char occ)  char popfile[FILENAMELENGTH];
 {  
   int i,lg,j,p=0;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {  #define NR_END 1
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #define FREE_ARG char*
   }  #define FTOL 1.0e-10
   
   lg=strlen(t);  #define NRANSI 
   for(j=0; j<p; j++) {  #define ITMAX 200 
     (u[j] = t[j]);  
   }  #define TOL 2.0e-4 
      u[p]='\0';  
   #define CGOLD 0.3819660 
    for(j=0; j<= lg; j++) {  #define ZEPS 1.0e-10 
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   }  
 }  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 /********************** nrerror ********************/  #define TINY 1.0e-20 
   
 void nrerror(char error_text[])  static double maxarg1,maxarg2;
 {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   fprintf(stderr,"ERREUR ...\n");  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   fprintf(stderr,"%s\n",error_text);    
   exit(1);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 }  #define rint(a) floor(a+0.5)
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  static double sqrarg;
 {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   double *v;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  int imx; 
   return v-nl+NR_END;  int stepm;
 }  /* Stepm, step in month: minimum step interpolation*/
   
 /************************ free vector ******************/  int estepm;
 void free_vector(double*v, int nl, int nh)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 {  
   free((FREE_ARG)(v+nl-NR_END));  int m,nb;
 }  long *num;
   int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 /************************ivector *******************************/  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 int *ivector(long nl,long nh)  double **pmmij, ***probs;
 {  double dateintmean=0;
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  double *weight;
   if (!v) nrerror("allocation failure in ivector");  int **s; /* Status */
   return v-nl+NR_END;  double *agedc, **covar, idx;
 }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
 /******************free ivector **************************/  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 void free_ivector(int *v, long nl, long nh)  double ftolhess; /* Tolerance for computing hessian */
 {  
   free((FREE_ARG)(v+nl-NR_END));  /**************** split *************************/
 }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 /******************* imatrix *******************************/    char  *ss;                            /* pointer */
 int **imatrix(long nrl, long nrh, long ncl, long nch)    int   l1, l2;                         /* length counters */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    l1 = strlen(path );                   /* length of path */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   int **m;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      if ( ss == NULL ) {                   /* no directory, so use current */
   /* allocate pointers to rows */      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   if (!m) nrerror("allocation failure 1 in matrix()");      /* get current working directory */
   m += NR_END;      /*    extern  char* getcwd ( char *buf , int len);*/
   m -= nrl;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
          return( GLOCK_ERROR_GETCWD );
        }
   /* allocate rows and set pointers to them */      strcpy( name, path );               /* we've got it */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    } else {                              /* strip direcotry from path */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      ss++;                               /* after this, the filename */
   m[nrl] += NR_END;      l2 = strlen( ss );                  /* length of filename */
   m[nrl] -= ncl;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
        strcpy( name, ss );         /* save file name */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
        dirc[l1-l2] = 0;                    /* add zero */
   /* return pointer to array of pointers to rows */    }
   return m;    l1 = strlen( dirc );                  /* length of directory */
 }    /*#ifdef windows
     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 /****************** free_imatrix *************************/  #else
 void free_imatrix(m,nrl,nrh,ncl,nch)    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
       int **m;  #endif
       long nch,ncl,nrh,nrl;    */
      /* free an int matrix allocated by imatrix() */    ss = strrchr( name, '.' );            /* find last / */
 {    ss++;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    strcpy(ext,ss);                       /* save extension */
   free((FREE_ARG) (m+nrl-NR_END));    l1= strlen( name);
 }    l2= strlen(ss)+1;
     strncpy( finame, name, l1-l2);
 /******************* matrix *******************************/    finame[l1-l2]= 0;
 double **matrix(long nrl, long nrh, long ncl, long nch)    return( 0 );                          /* we're done */
 {  }
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  
   /******************************************/
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  void replace_back_to_slash(char *s, char*t)
   m += NR_END;  {
   m -= nrl;    int i;
     int lg=0;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    i=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    lg=strlen(t);
   m[nrl] += NR_END;    for(i=0; i<= lg; i++) {
   m[nrl] -= ncl;      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    }
   return m;  }
 }  
   int nbocc(char *s, char occ)
 /*************************free matrix ************************/  {
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    int i,j=0;
 {    int lg=20;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    i=0;
   free((FREE_ARG)(m+nrl-NR_END));    lg=strlen(s);
 }    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 /******************* ma3x *******************************/    }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    return j;
 {  }
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  void cutv(char *u,char *v, char*t, char occ)
   {
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    /* cuts string t into u and v where u is ended by char occ excluding it
   if (!m) nrerror("allocation failure 1 in matrix()");       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   m += NR_END;       gives u="abcedf" and v="ghi2j" */
   m -= nrl;    int i,lg,j,p=0;
     i=0;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    for(j=0; j<=strlen(t)-1; j++) {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   m[nrl] += NR_END;    }
   m[nrl] -= ncl;  
     lg=strlen(t);
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    for(j=0; j<p; j++) {
       (u[j] = t[j]);
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    }
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");       u[p]='\0';
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;     for(j=0; j<= lg; j++) {
   for (j=ncl+1; j<=nch; j++)      if (j>=(p+1))(v[j-p-1] = t[j]);
     m[nrl][j]=m[nrl][j-1]+nlay;    }
    }
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /********************** nrerror ********************/
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  void nrerror(char error_text[])
   }  {
   return m;    fprintf(stderr,"ERREUR ...\n");
 }    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
 /*************************free ma3x ************************/  }
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  /*********************** vector *******************/
 {  double *vector(int nl, int nh)
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    double *v;
   free((FREE_ARG)(m+nrl-NR_END));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /***************** f1dim *************************/  }
 extern int ncom;  
 extern double *pcom,*xicom;  /************************ free vector ******************/
 extern double (*nrfunc)(double []);  void free_vector(double*v, int nl, int nh)
    {
 double f1dim(double x)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   int j;  
   double f;  /************************ivector *******************************/
   double *xt;  int *ivector(long nl,long nh)
    {
   xt=vector(1,ncom);    int *v;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   f=(*nrfunc)(xt);    if (!v) nrerror("allocation failure in ivector");
   free_vector(xt,1,ncom);    return v-nl+NR_END;
   return f;  }
 }  
   /******************free ivector **************************/
 /*****************brent *************************/  void free_ivector(int *v, long nl, long nh)
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  {
 {    free((FREE_ARG)(v+nl-NR_END));
   int iter;  }
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  /************************lvector *******************************/
   double ftemp;  long *lvector(long nl,long nh)
   double p,q,r,tol1,tol2,u,v,w,x,xm;  {
   double e=0.0;    long *v;
      v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   a=(ax < cx ? ax : cx);    if (!v) nrerror("allocation failure in ivector");
   b=(ax > cx ? ax : cx);    return v-nl+NR_END;
   x=w=v=bx;  }
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  /******************free lvector **************************/
     xm=0.5*(a+b);  void free_lvector(long *v, long nl, long nh)
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  {
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    free((FREE_ARG)(v+nl-NR_END));
     printf(".");fflush(stdout);  }
 #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);  /******************* imatrix *******************************/
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 #endif       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  { 
       *xmin=x;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       return fx;    int **m; 
     }    
     ftemp=fu;    /* allocate pointers to rows */ 
     if (fabs(e) > tol1) {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       r=(x-w)*(fx-fv);    if (!m) nrerror("allocation failure 1 in matrix()"); 
       q=(x-v)*(fx-fw);    m += NR_END; 
       p=(x-v)*q-(x-w)*r;    m -= nrl; 
       q=2.0*(q-r);    
       if (q > 0.0) p = -p;    
       q=fabs(q);    /* allocate rows and set pointers to them */ 
       etemp=e;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       e=d;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m[nrl] += NR_END; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl] -= ncl; 
       else {    
         d=p/q;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         u=x+d;    
         if (u-a < tol2 || b-u < tol2)    /* return pointer to array of pointers to rows */ 
           d=SIGN(tol1,xm-x);    return m; 
       }  } 
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  /****************** free_imatrix *************************/
     }  void free_imatrix(m,nrl,nrh,ncl,nch)
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));        int **m;
     fu=(*f)(u);        long nch,ncl,nrh,nrl; 
     if (fu <= fx) {       /* free an int matrix allocated by imatrix() */ 
       if (u >= x) a=x; else b=x;  { 
       SHFT(v,w,x,u)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         SHFT(fv,fw,fx,fu)    free((FREE_ARG) (m+nrl-NR_END)); 
         } else {  } 
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /******************* matrix *******************************/
             v=w;  double **matrix(long nrl, long nrh, long ncl, long nch)
             w=u;  {
             fv=fw;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
             fw=fu;    double **m;
           } else if (fu <= fv || v == x || v == w) {  
             v=u;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
             fv=fu;    if (!m) nrerror("allocation failure 1 in matrix()");
           }    m += NR_END;
         }    m -= nrl;
   }  
   nrerror("Too many iterations in brent");    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   *xmin=x;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   return fx;    m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /****************** mnbrak ***********************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
             double (*func)(double))     */
 {  }
   double ulim,u,r,q, dum;  
   double fu;  /*************************free matrix ************************/
    void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   *fa=(*func)(*ax);  {
   *fb=(*func)(*bx);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   if (*fb > *fa) {    free((FREE_ARG)(m+nrl-NR_END));
     SHFT(dum,*ax,*bx,dum)  }
       SHFT(dum,*fb,*fa,dum)  
       }  /******************* ma3x *******************************/
   *cx=(*bx)+GOLD*(*bx-*ax);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   *fc=(*func)(*cx);  {
   while (*fb > *fc) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     r=(*bx-*ax)*(*fb-*fc);    double ***m;
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    if (!m) nrerror("allocation failure 1 in matrix()");
     ulim=(*bx)+GLIMIT*(*cx-*bx);    m += NR_END;
     if ((*bx-u)*(u-*cx) > 0.0) {    m -= nrl;
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       fu=(*func)(u);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       if (fu < *fc) {    m[nrl] += NR_END;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    m[nrl] -= ncl;
           SHFT(*fb,*fc,fu,(*func)(u))  
           }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;    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()");
     } else {    m[nrl][ncl] += NR_END;
       u=(*cx)+GOLD*(*cx-*bx);    m[nrl][ncl] -= nll;
       fu=(*func)(u);    for (j=ncl+1; j<=nch; j++) 
     }      m[nrl][j]=m[nrl][j-1]+nlay;
     SHFT(*ax,*bx,*cx,u)    
       SHFT(*fa,*fb,*fc,fu)    for (i=nrl+1; i<=nrh; i++) {
       }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 }      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
 /*************** linmin ************************/    }
     return m; 
 int ncom;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 double *pcom,*xicom;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 double (*nrfunc)(double []);    */
    }
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  /*************************free ma3x ************************/
   double brent(double ax, double bx, double cx,  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
                double (*f)(double), double tol, double *xmin);  {
   double f1dim(double x);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    free((FREE_ARG)(m[nrl]+ncl-NR_END));
               double *fc, double (*func)(double));    free((FREE_ARG)(m+nrl-NR_END));
   int j;  }
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  /***************** f1dim *************************/
    extern int ncom; 
   ncom=n;  extern double *pcom,*xicom;
   pcom=vector(1,n);  extern double (*nrfunc)(double []); 
   xicom=vector(1,n);   
   nrfunc=func;  double f1dim(double x) 
   for (j=1;j<=n;j++) {  { 
     pcom[j]=p[j];    int j; 
     xicom[j]=xi[j];    double f;
   }    double *xt; 
   ax=0.0;   
   xx=1.0;    xt=vector(1,ncom); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    f=(*nrfunc)(xt); 
 #ifdef DEBUG    free_vector(xt,1,ncom); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    return f; 
 #endif  } 
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  /*****************brent *************************/
     p[j] += xi[j];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   }  { 
   free_vector(xicom,1,n);    int iter; 
   free_vector(pcom,1,n);    double a,b,d,etemp;
 }    double fu,fv,fw,fx;
     double ftemp;
 /*************** powell ************************/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    double e=0.0; 
             double (*func)(double []))   
 {    a=(ax < cx ? ax : cx); 
   void linmin(double p[], double xi[], int n, double *fret,    b=(ax > cx ? ax : cx); 
               double (*func)(double []));    x=w=v=bx; 
   int i,ibig,j;    fw=fv=fx=(*f)(x); 
   double del,t,*pt,*ptt,*xit;    for (iter=1;iter<=ITMAX;iter++) { 
   double fp,fptt;      xm=0.5*(a+b); 
   double *xits;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   pt=vector(1,n);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   ptt=vector(1,n);      printf(".");fflush(stdout);
   xit=vector(1,n);      fprintf(ficlog,".");fflush(ficlog);
   xits=vector(1,n);  #ifdef DEBUG
   *fret=(*func)(p);      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);
   for (j=1;j<=n;j++) pt[j]=p[j];      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);
   for (*iter=1;;++(*iter)) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     fp=(*fret);  #endif
     ibig=0;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     del=0.0;        *xmin=x; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);        return fx; 
     for (i=1;i<=n;i++)      } 
       printf(" %d %.12f",i, p[i]);      ftemp=fu;
     printf("\n");      if (fabs(e) > tol1) { 
     for (i=1;i<=n;i++) {        r=(x-w)*(fx-fv); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        q=(x-v)*(fx-fw); 
       fptt=(*fret);        p=(x-v)*q-(x-w)*r; 
 #ifdef DEBUG        q=2.0*(q-r); 
       printf("fret=%lf \n",*fret);        if (q > 0.0) p = -p; 
 #endif        q=fabs(q); 
       printf("%d",i);fflush(stdout);        etemp=e; 
       linmin(p,xit,n,fret,func);        e=d; 
       if (fabs(fptt-(*fret)) > del) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         del=fabs(fptt-(*fret));          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         ibig=i;        else { 
       }          d=p/q; 
 #ifdef DEBUG          u=x+d; 
       printf("%d %.12e",i,(*fret));          if (u-a < tol2 || b-u < tol2) 
       for (j=1;j<=n;j++) {            d=SIGN(tol1,xm-x); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);        } 
         printf(" x(%d)=%.12e",j,xit[j]);      } else { 
       }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for(j=1;j<=n;j++)      } 
         printf(" p=%.12e",p[j]);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       printf("\n");      fu=(*f)(u); 
 #endif      if (fu <= fx) { 
     }        if (u >= x) a=x; else b=x; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        SHFT(v,w,x,u) 
 #ifdef DEBUG          SHFT(fv,fw,fx,fu) 
       int k[2],l;          } else { 
       k[0]=1;            if (u < x) a=u; else b=u; 
       k[1]=-1;            if (fu <= fw || w == x) { 
       printf("Max: %.12e",(*func)(p));              v=w; 
       for (j=1;j<=n;j++)              w=u; 
         printf(" %.12e",p[j]);              fv=fw; 
       printf("\n");              fw=fu; 
       for(l=0;l<=1;l++) {            } else if (fu <= fv || v == x || v == w) { 
         for (j=1;j<=n;j++) {              v=u; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];              fv=fu; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);            } 
         }          } 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    } 
       }    nrerror("Too many iterations in brent"); 
 #endif    *xmin=x; 
     return fx; 
   } 
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  /****************** mnbrak ***********************/
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       return;              double (*func)(double)) 
     }  { 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    double ulim,u,r,q, dum;
     for (j=1;j<=n;j++) {    double fu; 
       ptt[j]=2.0*p[j]-pt[j];   
       xit[j]=p[j]-pt[j];    *fa=(*func)(*ax); 
       pt[j]=p[j];    *fb=(*func)(*bx); 
     }    if (*fb > *fa) { 
     fptt=(*func)(ptt);      SHFT(dum,*ax,*bx,dum) 
     if (fptt < fp) {        SHFT(dum,*fb,*fa,dum) 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        } 
       if (t < 0.0) {    *cx=(*bx)+GOLD*(*bx-*ax); 
         linmin(p,xit,n,fret,func);    *fc=(*func)(*cx); 
         for (j=1;j<=n;j++) {    while (*fb > *fc) { 
           xi[j][ibig]=xi[j][n];      r=(*bx-*ax)*(*fb-*fc); 
           xi[j][n]=xit[j];      q=(*bx-*cx)*(*fb-*fa); 
         }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 #ifdef DEBUG        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         for(j=1;j<=n;j++)      if ((*bx-u)*(u-*cx) > 0.0) { 
           printf(" %.12e",xit[j]);        fu=(*func)(u); 
         printf("\n");      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 #endif        fu=(*func)(u); 
       }        if (fu < *fc) { 
     }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   }            SHFT(*fb,*fc,fu,(*func)(u)) 
 }            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 /**** Prevalence limit ****************/        u=ulim; 
         fu=(*func)(u); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      } else { 
 {        u=(*cx)+GOLD*(*cx-*bx); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        fu=(*func)(u); 
      matrix by transitions matrix until convergence is reached */      } 
       SHFT(*ax,*bx,*cx,u) 
   int i, ii,j,k;        SHFT(*fa,*fb,*fc,fu) 
   double min, max, maxmin, maxmax,sumnew=0.;        } 
   double **matprod2();  } 
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  /*************** linmin ************************/
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   int ncom; 
   for (ii=1;ii<=nlstate+ndeath;ii++)  double *pcom,*xicom;
     for (j=1;j<=nlstate+ndeath;j++){  double (*nrfunc)(double []); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);   
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
    cov[1]=1.;    double brent(double ax, double bx, double cx, 
                   double (*f)(double), double tol, double *xmin); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double f1dim(double x); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     newm=savm;                double *fc, double (*func)(double)); 
     /* Covariates have to be included here again */    int j; 
      cov[2]=agefin;    double xx,xmin,bx,ax; 
      double fx,fb,fa;
       for (k=1; k<=cptcovn;k++) {   
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    ncom=n; 
         /*      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]]);*/    pcom=vector(1,n); 
       }    xicom=vector(1,n); 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    nrfunc=func; 
       for (k=1; k<=cptcovprod;k++)    for (j=1;j<=n;j++) { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    } 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    ax=0.0; 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    xx=1.0; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     savm=oldm;  #ifdef DEBUG
     oldm=newm;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     maxmax=0.;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for(j=1;j<=nlstate;j++){  #endif
       min=1.;    for (j=1;j<=n;j++) { 
       max=0.;      xi[j] *= xmin; 
       for(i=1; i<=nlstate; i++) {      p[j] += xi[j]; 
         sumnew=0;    } 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    free_vector(xicom,1,n); 
         prlim[i][j]= newm[i][j]/(1-sumnew);    free_vector(pcom,1,n); 
         max=FMAX(max,prlim[i][j]);  } 
         min=FMIN(min,prlim[i][j]);  
       }  /*************** powell ************************/
       maxmin=max-min;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       maxmax=FMAX(maxmax,maxmin);              double (*func)(double [])) 
     }  { 
     if(maxmax < ftolpl){    void linmin(double p[], double xi[], int n, double *fret, 
       return prlim;                double (*func)(double [])); 
     }    int i,ibig,j; 
   }    double del,t,*pt,*ptt,*xit;
 }    double fp,fptt;
     double *xits;
 /*************** transition probabilities ***************/    pt=vector(1,n); 
     ptt=vector(1,n); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    xit=vector(1,n); 
 {    xits=vector(1,n); 
   double s1, s2;    *fret=(*func)(p); 
   /*double t34;*/    for (j=1;j<=n;j++) pt[j]=p[j]; 
   int i,j,j1, nc, ii, jj;    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
     for(i=1; i<= nlstate; i++){      ibig=0; 
     for(j=1; j<i;j++){      del=0.0; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         /*s2 += param[i][j][nc]*cov[nc];*/      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      fprintf(ficrespow,"%d %.12f",*iter,*fret);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      for (i=1;i<=n;i++) {
       }        printf(" %d %.12f",i, p[i]);
       ps[i][j]=s2;        fprintf(ficlog," %d %.12lf",i, p[i]);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        fprintf(ficrespow," %.12lf", p[i]);
     }      }
     for(j=i+1; j<=nlstate+ndeath;j++){      printf("\n");
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      fprintf(ficlog,"\n");
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      fprintf(ficrespow,"\n");
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      for (i=1;i<=n;i++) { 
       }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       ps[i][j]=s2;        fptt=(*fret); 
     }  #ifdef DEBUG
   }        printf("fret=%lf \n",*fret);
     /*ps[3][2]=1;*/        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
   for(i=1; i<= nlstate; i++){        printf("%d",i);fflush(stdout);
      s1=0;        fprintf(ficlog,"%d",i);fflush(ficlog);
     for(j=1; j<i; j++)        linmin(p,xit,n,fret,func); 
       s1+=exp(ps[i][j]);        if (fabs(fptt-(*fret)) > del) { 
     for(j=i+1; j<=nlstate+ndeath; j++)          del=fabs(fptt-(*fret)); 
       s1+=exp(ps[i][j]);          ibig=i; 
     ps[i][i]=1./(s1+1.);        } 
     for(j=1; j<i; j++)  #ifdef DEBUG
       ps[i][j]= exp(ps[i][j])*ps[i][i];        printf("%d %.12e",i,(*fret));
     for(j=i+1; j<=nlstate+ndeath; j++)        fprintf(ficlog,"%d %.12e",i,(*fret));
       ps[i][j]= exp(ps[i][j])*ps[i][i];        for (j=1;j<=n;j++) {
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   } /* end i */          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        }
     for(jj=1; jj<= nlstate+ndeath; jj++){        for(j=1;j<=n;j++) {
       ps[ii][jj]=0;          printf(" p=%.12e",p[j]);
       ps[ii][ii]=1;          fprintf(ficlog," p=%.12e",p[j]);
     }        }
   }        printf("\n");
         fprintf(ficlog,"\n");
   #endif
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      } 
     for(jj=1; jj<= nlstate+ndeath; jj++){      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
      printf("%lf ",ps[ii][jj]);  #ifdef DEBUG
    }        int k[2],l;
     printf("\n ");        k[0]=1;
     }        k[1]=-1;
     printf("\n ");printf("%lf ",cov[2]);*/        printf("Max: %.12e",(*func)(p));
 /*        fprintf(ficlog,"Max: %.12e",(*func)(p));
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        for (j=1;j<=n;j++) {
   goto end;*/          printf(" %.12e",p[j]);
     return ps;          fprintf(ficlog," %.12e",p[j]);
 }        }
         printf("\n");
 /**************** Product of 2 matrices ******************/        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)          for (j=1;j<=n;j++) {
 {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   /* in, b, out are matrice of pointers which should have been initialized          }
      before: only the contents of out is modified. The function returns          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      a pointer to pointers identical to out */          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   long i, j, k;        }
   for(i=nrl; i<= nrh; i++)  #endif
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
   return out;        free_vector(ptt,1,n); 
 }        free_vector(pt,1,n); 
         return; 
       } 
 /************* Higher Matrix Product ***************/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        ptt[j]=2.0*p[j]-pt[j]; 
 {        xit[j]=p[j]-pt[j]; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        pt[j]=p[j]; 
      duration (i.e. until      } 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      fptt=(*func)(ptt); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      if (fptt < fp) { 
      (typically every 2 years instead of every month which is too big).        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
      Model is determined by parameters x and covariates have to be        if (t < 0.0) { 
      included manually here.          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
      */            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
   int i, j, d, h, k;          }
   double **out, cov[NCOVMAX];  #ifdef DEBUG
   double **newm;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   /* Hstepm could be zero and should return the unit matrix */          for(j=1;j<=n;j++){
   for (i=1;i<=nlstate+ndeath;i++)            printf(" %.12e",xit[j]);
     for (j=1;j<=nlstate+ndeath;j++){            fprintf(ficlog," %.12e",xit[j]);
       oldm[i][j]=(i==j ? 1.0 : 0.0);          }
       po[i][j][0]=(i==j ? 1.0 : 0.0);          printf("\n");
     }          fprintf(ficlog,"\n");
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #endif
   for(h=1; h <=nhstepm; h++){        }
     for(d=1; d <=hstepm; d++){      } 
       newm=savm;    } 
       /* Covariates have to be included here again */  } 
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /**** Prevalence limit (stable prevalence)  ****************/
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  {
       for (k=1; k<=cptcovprod;k++)    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       matrix by transitions matrix until convergence is reached */
   
     int i, ii,j,k;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    double min, max, maxmin, maxmax,sumnew=0.;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    double **matprod2();
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    double **out, cov[NCOVMAX], **pmij();
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    double **newm;
       savm=oldm;    double agefin, delaymax=50 ; /* Max number of years to converge */
       oldm=newm;  
     }    for (ii=1;ii<=nlstate+ndeath;ii++)
     for(i=1; i<=nlstate+ndeath; i++)      for (j=1;j<=nlstate+ndeath;j++){
       for(j=1;j<=nlstate+ndeath;j++) {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         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]);  
          */     cov[1]=1.;
       }   
   } /* end h */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   return po;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 }      newm=savm;
       /* Covariates have to be included here again */
        cov[2]=agefin;
 /*************** log-likelihood *************/    
 double func( double *x)        for (k=1; k<=cptcovn;k++) {
 {          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int i, ii, j, k, mi, d, kk;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        }
   double **out;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double sw; /* Sum of weights */        for (k=1; k<=cptcovprod;k++)
   double lli; /* Individual log likelihood */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   long ipmx;  
   /*extern weight */        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   /* We are differentiating ll according to initial status */        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   /*for(i=1;i<imx;i++)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     printf(" %d\n",s[4][i]);  
   */      savm=oldm;
   cov[1]=1.;      oldm=newm;
       maxmax=0.;
   for(k=1; k<=nlstate; k++) ll[k]=0.;      for(j=1;j<=nlstate;j++){
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        min=1.;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        max=0.;
     for(mi=1; mi<= wav[i]-1; mi++){        for(i=1; i<=nlstate; i++) {
       for (ii=1;ii<=nlstate+ndeath;ii++)          sumnew=0;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       for(d=0; d<dh[mi][i]; d++){          prlim[i][j]= newm[i][j]/(1-sumnew);
         newm=savm;          max=FMAX(max,prlim[i][j]);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          min=FMIN(min,prlim[i][j]);
         for (kk=1; kk<=cptcovage;kk++) {        }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        maxmin=max-min;
         }        maxmax=FMAX(maxmax,maxmin);
              }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      if(maxmax < ftolpl){
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        return prlim;
         savm=oldm;      }
         oldm=newm;    }
          }
          
       } /* end mult */  /*************** transition probabilities ***************/ 
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  {
       ipmx +=1;    double s1, s2;
       sw += weight[i];    /*double t34;*/
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    int i,j,j1, nc, ii, jj;
     } /* end of wave */  
   } /* end of individual */      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          /*s2 += param[i][j][nc]*cov[nc];*/
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   return -l;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 }        }
         ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 /*********** Maximum Likelihood Estimation ***************/      }
       for(j=i+1; j<=nlstate+ndeath;j++){
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 {          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   int i,j, iter;          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   double **xi,*delti;        }
   double fret;        ps[i][j]=s2;
   xi=matrix(1,npar,1,npar);      }
   for (i=1;i<=npar;i++)    }
     for (j=1;j<=npar;j++)      /*ps[3][2]=1;*/
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");    for(i=1; i<= nlstate; i++){
   powell(p,xi,npar,ftol,&iter,&fret,func);       s1=0;
       for(j=1; j<i; j++)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        s1+=exp(ps[i][j]);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
 }      ps[i][i]=1./(s1+1.);
       for(j=1; j<i; j++)
 /**** Computes Hessian and covariance matrix ***/        ps[i][j]= exp(ps[i][j])*ps[i][i];
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      for(j=i+1; j<=nlstate+ndeath; j++)
 {        ps[i][j]= exp(ps[i][j])*ps[i][i];
   double  **a,**y,*x,pd;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   double **hess;    } /* end i */
   int i, j,jk;  
   int *indx;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
   double hessii(double p[], double delta, int theta, double delti[]);        ps[ii][jj]=0;
   double hessij(double p[], double delti[], int i, int j);        ps[ii][ii]=1;
   void lubksb(double **a, int npar, int *indx, double b[]) ;      }
   void ludcmp(double **a, int npar, int *indx, double *d) ;    }
   
   hess=matrix(1,npar,1,npar);  
     /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   printf("\nCalculation of the hessian matrix. Wait...\n");      for(jj=1; jj<= nlstate+ndeath; jj++){
   for (i=1;i<=npar;i++){       printf("%lf ",ps[ii][jj]);
     printf("%d",i);fflush(stdout);     }
     hess[i][i]=hessii(p,ftolhess,i,delti);      printf("\n ");
     /*printf(" %f ",p[i]);*/      }
     /*printf(" %lf ",hess[i][i]);*/      printf("\n ");printf("%lf ",cov[2]);*/
   }  /*
      for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for (i=1;i<=npar;i++) {    goto end;*/
     for (j=1;j<=npar;j++)  {      return ps;
       if (j>i) {  }
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);  /**************** Product of 2 matrices ******************/
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       }  {
     }    /* 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(...) */
   printf("\n");    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");       a pointer to pointers identical to out */
      long i, j, k;
   a=matrix(1,npar,1,npar);    for(i=nrl; i<= nrh; i++)
   y=matrix(1,npar,1,npar);      for(k=ncolol; k<=ncoloh; k++)
   x=vector(1,npar);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   indx=ivector(1,npar);          out[i][k] +=in[i][j]*b[j][k];
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    return out;
   ludcmp(a,npar,indx,&pd);  }
   
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /************* Higher Matrix Product ***************/
     x[j]=1;  
     lubksb(a,npar,indx,x);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for (i=1;i<=npar;i++){  {
       matcov[i][j]=x[i];    /* Computes the transition matrix starting at age 'age' over 
     }       'nhstepm*hstepm*stepm' months (i.e. until
   }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
   printf("\n#Hessian matrix#\n");       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   for (i=1;i<=npar;i++) {       (typically every 2 years instead of every month which is too big 
     for (j=1;j<=npar;j++) {       for the memory).
       printf("%.3e ",hess[i][j]);       Model is determined by parameters x and covariates have to be 
     }       included manually here. 
     printf("\n");  
   }       */
   
   /* Recompute Inverse */    int i, j, d, h, k;
   for (i=1;i<=npar;i++)    double **out, cov[NCOVMAX];
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    double **newm;
   ludcmp(a,npar,indx,&pd);  
     /* Hstepm could be zero and should return the unit matrix */
   /*  printf("\n#Hessian matrix recomputed#\n");    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   for (j=1;j<=npar;j++) {        oldm[i][j]=(i==j ? 1.0 : 0.0);
     for (i=1;i<=npar;i++) x[i]=0;        po[i][j][0]=(i==j ? 1.0 : 0.0);
     x[j]=1;      }
     lubksb(a,npar,indx,x);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for (i=1;i<=npar;i++){    for(h=1; h <=nhstepm; h++){
       y[i][j]=x[i];      for(d=1; d <=hstepm; d++){
       printf("%.3e ",y[i][j]);        newm=savm;
     }        /* Covariates have to be included here again */
     printf("\n");        cov[1]=1.;
   }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   */        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
   free_matrix(a,1,npar,1,npar);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   free_matrix(y,1,npar,1,npar);        for (k=1; k<=cptcovprod;k++)
   free_vector(x,1,npar);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
 /*************** hessian matrix ****************/        savm=oldm;
 double hessii( double x[], double delta, int theta, double delti[])        oldm=newm;
 {      }
   int i;      for(i=1; i<=nlstate+ndeath; i++)
   int l=1, lmax=20;        for(j=1;j<=nlstate+ndeath;j++) {
   double k1,k2;          po[i][j][h]=newm[i][j];
   double p2[NPARMAX+1];          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   double res;           */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        }
   double fx;    } /* end h */
   int k=0,kmax=10;    return po;
   double l1;  }
   
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];  /*************** log-likelihood *************/
   for(l=0 ; l <=lmax; l++){  double func( double *x)
     l1=pow(10,l);  {
     delts=delt;    int i, ii, j, k, mi, d, kk;
     for(k=1 ; k <kmax; k=k+1){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       delt = delta*(l1*k);    double **out;
       p2[theta]=x[theta] +delt;    double sw; /* Sum of weights */
       k1=func(p2)-fx;    double lli; /* Individual log likelihood */
       p2[theta]=x[theta]-delt;    int s1, s2;
       k2=func(p2)-fx;    double bbh, survp;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    long ipmx;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    /*extern weight */
          /* We are differentiating ll according to initial status */
 #ifdef DEBUG    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       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);    /*for(i=1;i<imx;i++) 
 #endif      printf(" %d\n",s[4][i]);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    cov[1]=1.;
         k=kmax;  
       }    for(k=1; k<=nlstate; k++) ll[k]=0.;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;    if(mle==1){
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         delts=delt;        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   delti[theta]=delts;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   return res;            }
            for(d=0; d<dh[mi][i]; d++){
 }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 double hessij( double x[], double delti[], int thetai,int thetaj)            for (kk=1; kk<=cptcovage;kk++) {
 {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i;            }
   int l=1, l1, lmax=20;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double k1,k2,k3,k4,res,fx;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double p2[NPARMAX+1];            savm=oldm;
   int k;            oldm=newm;
           } /* end mult */
   fx=func(x);        
   for (k=1; k<=2; k++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     for (i=1;i<=npar;i++) p2[i]=x[i];          /* But now since version 0.9 we anticipate for bias and large stepm.
     p2[thetai]=x[thetai]+delti[thetai]/k;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     k1=func(p2)-fx;           * 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
     p2[thetai]=x[thetai]+delti[thetai]/k;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * probability in order to take into account the bias as a fraction of the way
     k2=func(p2)-fx;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
             * -stepm/2 to stepm/2 .
     p2[thetai]=x[thetai]-delti[thetai]/k;           * For stepm=1 the results are the same as for previous versions of Imach.
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * For stepm > 1 the results are less biased than in previous versions. 
     k3=func(p2)-fx;           */
            s1=s[mw[mi][i]][i];
     p2[thetai]=x[thetai]-delti[thetai]/k;          s2=s[mw[mi+1][i]][i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          bbh=(double)bh[mi][i]/(double)stepm; 
     k4=func(p2)-fx;          /* bias is positive if real duration
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */           * is higher than the multiple of stepm and negative otherwise.
 #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);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 #endif          if( s2 > nlstate){ 
   }            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   return res;               to the likelihood is the probability to die between last step unit time and current 
 }               step unit time, which is also the differences between probability to die before dh 
                and probability to die before dh-stepm . 
 /************** Inverse of matrix **************/               In version up to 0.92 likelihood was computed
 void ludcmp(double **a, int n, int *indx, double *d)          as if date of death was unknown. Death was treated as any other
 {          health state: the date of the interview describes the actual state
   int i,imax,j,k;          and not the date of a change in health state. The former idea was
   double big,dum,sum,temp;          to consider that at each interview the state was recorded
   double *vv;          (healthy, disable or death) and IMaCh was corrected; but when we
            introduced the exact date of death then we should have modified
   vv=vector(1,n);          the contribution of an exact death to the likelihood. This new
   *d=1.0;          contribution is smaller and very dependent of the step unit
   for (i=1;i<=n;i++) {          stepm. It is no more the probability to die between last interview
     big=0.0;          and month of death but the probability to survive from last
     for (j=1;j<=n;j++)          interview up to one month before death multiplied by the
       if ((temp=fabs(a[i][j])) > big) big=temp;          probability to die within a month. Thanks to Chris
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          Jackson for correcting this bug.  Former versions increased
     vv[i]=1.0/big;          mortality artificially. The bad side is that we add another loop
   }          which slows down the processing. The difference can be up to 10%
   for (j=1;j<=n;j++) {          lower mortality.
     for (i=1;i<j;i++) {            */
       sum=a[i][j];            lli=log(out[s1][s2] - savm[s1][s2]);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          }else{
       a[i][j]=sum;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }            /*  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 */
     big=0.0;          } 
     for (i=j;i<=n;i++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       sum=a[i][j];          /*if(lli ==000.0)*/
       for (k=1;k<j;k++)          /*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); */
         sum -= a[i][k]*a[k][j];          ipmx +=1;
       a[i][j]=sum;          sw += weight[i];
       if ( (dum=vv[i]*fabs(sum)) >= big) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         big=dum;        } /* end of wave */
         imax=i;      } /* end of individual */
       }    }  else if(mle==2){
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if (j != imax) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for (k=1;k<=n;k++) {        for(mi=1; mi<= wav[i]-1; mi++){
         dum=a[imax][k];          for (ii=1;ii<=nlstate+ndeath;ii++)
         a[imax][k]=a[j][k];            for (j=1;j<=nlstate+ndeath;j++){
         a[j][k]=dum;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       *d = -(*d);            }
       vv[imax]=vv[j];          for(d=0; d<=dh[mi][i]; d++){
     }            newm=savm;
     indx[j]=imax;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (a[j][j] == 0.0) a[j][j]=TINY;            for (kk=1; kk<=cptcovage;kk++) {
     if (j != n) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       dum=1.0/(a[j][j]);            }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   free_vector(vv,1,n);  /* Doesn't work */            oldm=newm;
 ;          } /* end mult */
 }        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 void lubksb(double **a, int n, int *indx, double b[])          /* 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 
   int i,ii=0,ip,j;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double sum;           * 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
   for (i=1;i<=n;i++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     ip=indx[i];           * probability in order to take into account the bias as a fraction of the way
     sum=b[ip];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     b[ip]=b[i];           * -stepm/2 to stepm/2 .
     if (ii)           * For stepm=1 the results are the same as for previous versions of Imach.
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];           * For stepm > 1 the results are less biased than in previous versions. 
     else if (sum) ii=i;           */
     b[i]=sum;          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
   for (i=n;i>=1;i--) {          bbh=(double)bh[mi][i]/(double)stepm; 
     sum=b[i];          /* bias is positive if real duration
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];           * is higher than the multiple of stepm and negative otherwise.
     b[i]=sum/a[i][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 */
 }          /* 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 */
 /************ Frequencies ********************/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 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)          /*if(lli ==000.0)*/
 {  /* Some frequencies */          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
            ipmx +=1;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          sw += weight[i];
   double ***freq; /* Frequencies */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double *pp;        } /* end of wave */
   double pos, k2, dateintsum=0,k2cpt=0;      } /* end of individual */
   FILE *ficresp;    }  else if(mle==3){  /* exponential inter-extrapolation */
   char fileresp[FILENAMELENGTH];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   pp=vector(1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (ii=1;ii<=nlstate+ndeath;ii++)
   strcpy(fileresp,"p");            for (j=1;j<=nlstate+ndeath;j++){
   strcat(fileresp,fileres);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((ficresp=fopen(fileresp,"w"))==NULL) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("Problem with prevalence resultfile: %s\n", fileresp);            }
     exit(0);          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   j1=0;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   j=cptcoveff;            }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(k1=1; k1<=j;k1++){            savm=oldm;
     for(i1=1; i1<=ncodemax[k1];i1++){            oldm=newm;
       j1++;          } /* end mult */
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        
         scanf("%d", i);*/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       for (i=-1; i<=nlstate+ndeath; i++)            /* But now since version 0.9 we anticipate for bias and large stepm.
         for (jk=-1; jk<=nlstate+ndeath; jk++)             * If stepm is larger than one month (smallest stepm) and if the exact delay 
           for(m=agemin; m <= agemax+3; m++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
             freq[i][jk][m]=0;           * 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
       dateintsum=0;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       k2cpt=0;           * probability in order to take into account the bias as a fraction of the way
       for (i=1; i<=imx; i++) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         bool=1;           * -stepm/2 to stepm/2 .
         if  (cptcovn>0) {           * For stepm=1 the results are the same as for previous versions of Imach.
           for (z1=1; z1<=cptcoveff; z1++)           * For stepm > 1 the results are less biased than in previous versions. 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           */
               bool=0;          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
         if (bool==1) {          bbh=(double)bh[mi][i]/(double)stepm; 
           for(m=firstpass; m<=lastpass; m++){          /* bias is positive if real duration
             k2=anint[m][i]+(mint[m][i]/12.);           * is higher than the multiple of stepm and negative otherwise.
             if ((k2>=dateprev1) && (k2<=dateprev2)) {           */
               if(agev[m][i]==0) agev[m][i]=agemax+1;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
               if(agev[m][i]==1) agev[m][i]=agemax+2;          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 */
               if (m<lastpass) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          /*if(lli ==000.0)*/
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
               }          ipmx +=1;
                        sw += weight[i];
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                 dateintsum=dateintsum+k2;        } /* end of wave */
                 k2cpt++;      } /* end of individual */
               }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
             }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
                    for (j=1;j<=nlstate+ndeath;j++){
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if  (cptcovn>0) {            }
         fprintf(ficresp, "\n#********** Variable ");          for(d=0; d<dh[mi][i]; d++){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            newm=savm;
         fprintf(ficresp, "**********\n#");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
       for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);            }
       fprintf(ficresp, "\n");          
                  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=(int)agemin; i <= (int)agemax+3; i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if(i==(int)agemax+3)            savm=oldm;
           printf("Total");            oldm=newm;
         else          } /* end mult */
           printf("Age %d", i);        
         for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          s2=s[mw[mi+1][i]][i];
             pp[jk] += freq[jk][m][i];          if( s2 > nlstate){ 
         }            lli=log(out[s1][s2] - savm[s1][s2]);
         for(jk=1; jk <=nlstate ; jk++){          }else{
           for(m=-1, pos=0; m <=0 ; m++)            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             pos += freq[jk][m][i];          }
           if(pp[jk]>=1.e-10)          ipmx +=1;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          sw += weight[i];
           else          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         }        } /* end of wave */
       } /* end of individual */
         for(jk=1; jk <=nlstate ; jk++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             pp[jk] += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
         for(jk=1,pos=0; jk <=nlstate ; jk++)            for (j=1;j<=nlstate+ndeath;j++){
           pos += pp[jk];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(jk=1; jk <=nlstate ; jk++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           if(pos>=1.e-5)            }
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          for(d=0; d<dh[mi][i]; d++){
           else            newm=savm;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           if( i <= (int) agemax){            for (kk=1; kk<=cptcovage;kk++) {
             if(pos>=1.e-5){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            }
               probs[i][jk][j1]= pp[jk]/pos;          
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             else            savm=oldm;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            oldm=newm;
           }          } /* end mult */
         }        
                  s1=s[mw[mi][i]][i];
         for(jk=-1; jk <=nlstate+ndeath; jk++)          s2=s[mw[mi+1][i]][i];
           for(m=-1; m <=nlstate+ndeath; m++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          ipmx +=1;
         if(i <= (int) agemax)          sw += weight[i];
           fprintf(ficresp,"\n");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         printf("\n");          /*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 */
     }      } /* end of individual */
   }    } /* End of if */
   dateintmean=dateintsum/k2cpt;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   fclose(ficresp);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    return -l;
   free_vector(pp,1,nlstate);  }
    
   /* End of Freq */  /*************** log-likelihood *************/
 }  double funcone( double *x)
   {
 /************ Prevalence ********************/    /* Same as likeli but slower because of a lot of printf and if */
 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)    int i, ii, j, k, mi, d, kk;
 {  /* Some frequencies */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    double lli; /* Individual log likelihood */
   double ***freq; /* Frequencies */    double llt;
   double *pp;    int s1, s2;
   double pos, k2;    double bbh, survp;
     /*extern weight */
   pp=vector(1,nlstate);    /* We are differentiating ll according to initial status */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      /*for(i=1;i<imx;i++) 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      printf(" %d\n",s[4][i]);
   j1=0;    */
      cov[1]=1.;
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    for(k=1; k<=nlstate; k++) ll[k]=0.;
    
   for(k1=1; k1<=j;k1++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i1=1; i1<=ncodemax[k1];i1++){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       j1++;      for(mi=1; mi<= wav[i]-1; mi++){
              for (ii=1;ii<=nlstate+ndeath;ii++)
       for (i=-1; i<=nlstate+ndeath; i++)            for (j=1;j<=nlstate+ndeath;j++){
         for (jk=-1; jk<=nlstate+ndeath; jk++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=agemin; m <= agemax+3; m++)            savm[ii][j]=(ii==j ? 1.0 : 0.0);
             freq[i][jk][m]=0;          }
              for(d=0; d<dh[mi][i]; d++){
       for (i=1; i<=imx; i++) {          newm=savm;
         bool=1;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if  (cptcovn>0) {          for (kk=1; kk<=cptcovage;kk++) {
           for (z1=1; z1<=cptcoveff; z1++)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          }
               bool=0;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (bool==1) {          savm=oldm;
           for(m=firstpass; m<=lastpass; m++){          oldm=newm;
             k2=anint[m][i]+(mint[m][i]/12.);        } /* end mult */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        
               if(agev[m][i]==0) agev[m][i]=agemax+1;        s1=s[mw[mi][i]][i];
               if(agev[m][i]==1) agev[m][i]=agemax+2;        s2=s[mw[mi+1][i]][i];
               if (m<lastpass) {        bbh=(double)bh[mi][i]/(double)stepm; 
                 if (calagedate>0)        /* bias is positive if real duration
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];         * is higher than the multiple of stepm and negative otherwise.
                 else         */
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        if( s2 > nlstate && (mle <5) ){  /* Jackson */
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          lli=log(out[s1][s2] - savm[s1][s2]);
               }        } else if (mle==1){
             }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           }        } 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 */
       for(i=(int)agemin; i <= (int)agemax+3; i++){          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         for(jk=1; jk <=nlstate ; jk++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          lli=log(out[s1][s2]); /* Original formula */
             pp[jk] += freq[jk][m][i];        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
         }          lli=log(out[s1][s2]); /* Original formula */
         for(jk=1; jk <=nlstate ; jk++){        } /* End of if */
           for(m=-1, pos=0; m <=0 ; m++)        ipmx +=1;
             pos += freq[jk][m][i];        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]); */
         for(jk=1; jk <=nlstate ; jk++){        if(globpr){
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
             pp[jk] += freq[jk][m][i];   %10.6f %10.6f %10.6f ", \
         }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                          2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                    llt +=ll[k]*gipmx/gsw;
         for(jk=1; jk <=nlstate ; jk++){                fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           if( i <= (int) agemax){          }
             if(pos>=1.e-5){          fprintf(ficresilk," %10.6f\n", -llt);
               probs[i][jk][j1]= pp[jk]/pos;        }
             }      } /* end of wave */
           }    } /* 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;
      }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    return -l;
   free_vector(pp,1,nlstate);  }
    
 }  /* End of Freq */  char *subdirf(char fileres[])
   {
 /************* Waves Concatenation ***************/    
     strcpy(tmpout,optionfilefiname);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    strcat(tmpout,"/"); /* Add to the right */
 {    strcat(tmpout,fileres);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    return tmpout;
      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  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  char *subdirf2(char fileres[], char *preop)
      and mw[mi+1][i]. dh depends on stepm.  {
      */    
     strcpy(tmpout,optionfilefiname);
   int i, mi, m;    strcat(tmpout,"/");
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    strcat(tmpout,preop);
      double sum=0., jmean=0.;*/    strcat(tmpout,fileres);
     return tmpout;
   int j, k=0,jk, ju, jl;  }
   double sum=0.;  char *subdirf3(char fileres[], char *preop, char *preop2)
   jmin=1e+5;  {
   jmax=-1;    
   jmean=0.;    strcpy(tmpout,optionfilefiname);
   for(i=1; i<=imx; i++){    strcat(tmpout,"/");
     mi=0;    strcat(tmpout,preop);
     m=firstpass;    strcat(tmpout,preop2);
     while(s[m][i] <= nlstate){    strcat(tmpout,fileres);
       if(s[m][i]>=1)    return tmpout;
         mw[++mi][i]=m;  }
       if(m >=lastpass)  
         break;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       else  {
         m++;    /* This routine should help understanding what is done with 
     }/* end while */       the selection of individuals/waves and
     if (s[m][i] > nlstate){       to check the exact contribution to the likelihood.
       mi++;     /* Death is another wave */       Plotting could be done.
       /* if(mi==0)  never been interviewed correctly before death */     */
          /* Only death is a correct wave */    int k;
       mw[mi][i]=m;  
     }    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
     wav[i]=mi;      strcat(fileresilk,fileres);
     if(mi==0)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        printf("Problem with resultfile: %s\n", fileresilk);
   }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
   for(i=1; i<=imx; 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");
     for(mi=1; mi<wav[i];mi++){      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       if (stepm <=0)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         dh[mi][i]=1;      for(k=1; k<=nlstate; k++) 
       else{        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         if (s[mw[mi+1][i]][i] > nlstate) {      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           if (agedc[i] < 2*AGESUP) {    }
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */    *fretone=(*funcone)(p);
           k=k+1;    if(*globpri !=0){
           if (j >= jmax) jmax=j;      fclose(ficresilk);
           if (j <= jmin) jmin=j;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           sum=sum+j;      fflush(fichtm); 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    } 
           }    return;
         }  }
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;  /*********** Maximum Likelihood Estimation ***************/
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  {
           sum=sum+j;    int i,j, iter;
         }    double **xi;
         jk= j/stepm;    double fret;
         jl= j -jk*stepm;    double fretone; /* Only one call to likelihood */
         ju= j -(jk+1)*stepm;    char filerespow[FILENAMELENGTH];
         if(jl <= -ju)    xi=matrix(1,npar,1,npar);
           dh[mi][i]=jk;    for (i=1;i<=npar;i++)
         else      for (j=1;j<=npar;j++)
           dh[mi][i]=jk+1;        xi[i][j]=(i==j ? 1.0 : 0.0);
         if(dh[mi][i]==0)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
           dh[mi][i]=1; /* At least one step */    strcpy(filerespow,"pow"); 
       }    strcat(filerespow,fileres);
     }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", filerespow);
   jmean=sum/k;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    }
  }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
 /*********** Tricode ****************************/    for (i=1;i<=nlstate;i++)
 void tricode(int *Tvar, int **nbcode, int imx)      for(j=1;j<=nlstate+ndeath;j++)
 {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   int Ndum[20],ij=1, k, j, i;    fprintf(ficrespow,"\n");
   int cptcode=0;  
   cptcoveff=0;    powell(p,xi,npar,ftol,&iter,&fret,func);
    
   for (k=0; k<19; k++) Ndum[k]=0;    fclose(ficrespow);
   for (k=1; k<=7; k++) ncodemax[k]=0;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for (i=1; i<=imx; i++) {  
       ij=(int)(covar[Tvar[j]][i]);  }
       Ndum[ij]++;  
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  /**** Computes Hessian and covariance matrix ***/
       if (ij > cptcode) cptcode=ij;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     }  {
     double  **a,**y,*x,pd;
     for (i=0; i<=cptcode; i++) {    double **hess;
       if(Ndum[i]!=0) ncodemax[j]++;    int i, j,jk;
     }    int *indx;
     ij=1;  
     double hessii(double p[], double delta, int theta, double delti[]);
     double hessij(double p[], double delti[], int i, int j);
     for (i=1; i<=ncodemax[j]; i++) {    void lubksb(double **a, int npar, int *indx, double b[]) ;
       for (k=0; k<=19; k++) {    void ludcmp(double **a, int npar, int *indx, double *d) ;
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;    hess=matrix(1,npar,1,npar);
            
           ij++;    printf("\nCalculation of the hessian matrix. Wait...\n");
         }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         if (ij > ncodemax[j]) break;    for (i=1;i<=npar;i++){
       }        printf("%d",i);fflush(stdout);
     }      fprintf(ficlog,"%d",i);fflush(ficlog);
   }        hess[i][i]=hessii(p,ftolhess,i,delti);
       /*printf(" %f ",p[i]);*/
  for (k=0; k<19; k++) Ndum[k]=0;      /*printf(" %lf ",hess[i][i]);*/
     }
  for (i=1; i<=ncovmodel-2; i++) {    
       ij=Tvar[i];    for (i=1;i<=npar;i++) {
       Ndum[ij]++;      for (j=1;j<=npar;j++)  {
     }        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
  ij=1;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
  for (i=1; i<=10; i++) {          hess[i][j]=hessij(p,delti,i,j);
    if((Ndum[i]!=0) && (i<=ncovcol)){          hess[j][i]=hess[i][j];    
      Tvaraff[ij]=i;          /*printf(" %lf ",hess[i][j]);*/
      ij++;        }
    }      }
  }    }
      printf("\n");
     cptcoveff=ij-1;    fprintf(ficlog,"\n");
 }  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 /*********** Health Expectancies ****************/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
 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 )    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
 {    x=vector(1,npar);
   /* Health expectancies */    indx=ivector(1,npar);
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    for (i=1;i<=npar;i++)
   double age, agelim, hf;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double ***p3mat,***varhe;    ludcmp(a,npar,indx,&pd);
   double **dnewm,**doldm;  
   double *xp;    for (j=1;j<=npar;j++) {
   double **gp, **gm;      for (i=1;i<=npar;i++) x[i]=0;
   double ***gradg, ***trgradg;      x[j]=1;
   int theta;      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        matcov[i][j]=x[i];
   xp=vector(1,npar);      }
   dnewm=matrix(1,nlstate*2,1,npar);    }
   doldm=matrix(1,nlstate*2,1,nlstate*2);  
      printf("\n#Hessian matrix#\n");
   fprintf(ficreseij,"# Health expectancies\n");    fprintf(ficlog,"\n#Hessian matrix#\n");
   fprintf(ficreseij,"# Age");    for (i=1;i<=npar;i++) { 
   for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++) { 
     for(j=1; j<=nlstate;j++)        printf("%.3e ",hess[i][j]);
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        fprintf(ficlog,"%.3e ",hess[i][j]);
   fprintf(ficreseij,"\n");      }
       printf("\n");
   if(estepm < stepm){      fprintf(ficlog,"\n");
     printf ("Problem %d lower than %d\n",estepm, stepm);    }
   }  
   else  hstepm=estepm;      /* Recompute Inverse */
   /* We compute the life expectancy from trapezoids spaced every estepm months    for (i=1;i<=npar;i++)
    * This is mainly to measure the difference between two models: for example      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
    * if stepm=24 months pijx are given only every 2 years and by summing them    ludcmp(a,npar,indx,&pd);
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according    /*  printf("\n#Hessian matrix recomputed#\n");
    * to the curvature of the survival function. If, for the same date, we  
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    for (j=1;j<=npar;j++) {
    * to compare the new estimate of Life expectancy with the same linear      for (i=1;i<=npar;i++) x[i]=0;
    * hypothesis. A more precise result, taking into account a more precise      x[j]=1;
    * curvature will be obtained if estepm is as small as stepm. */      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   /* For example we decided to compute the life expectancy with the smallest unit */        y[i][j]=x[i];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        printf("%.3e ",y[i][j]);
      nhstepm is the number of hstepm from age to agelim        fprintf(ficlog,"%.3e ",y[i][j]);
      nstepm is the number of stepm from age to agelin.      }
      Look at hpijx to understand the reason of that which relies in memory size      printf("\n");
      and note for a fixed period like estepm months */      fprintf(ficlog,"\n");
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    }
      survival function given by stepm (the optimization length). Unfortunately it    */
      means that if the survival funtion is printed only each two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    free_matrix(a,1,npar,1,npar);
      results. So we changed our mind and took the option of the best precision.    free_matrix(y,1,npar,1,npar);
   */    free_vector(x,1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     /* nhstepm age range expressed in number of stepm */  }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  /*************** hessian matrix ****************/
     /* if (stepm >= YEARM) hstepm=1;*/  double hessii( double x[], double delta, int theta, double delti[])
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    int l=1, lmax=20;
     gp=matrix(0,nhstepm,1,nlstate*2);    double k1,k2;
     gm=matrix(0,nhstepm,1,nlstate*2);    double p2[NPARMAX+1];
     double res;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    double fx;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      int k=0,kmax=10;
      double l1;
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
     /* Computing Variances of health expectancies */    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
      for(theta=1; theta <=npar; theta++){      delts=delt;
       for(i=1; i<=npar; i++){      for(k=1 ; k <kmax; k=k+1){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        delt = delta*(l1*k);
       }        p2[theta]=x[theta] +delt;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          k1=func(p2)-fx;
          p2[theta]=x[theta]-delt;
       cptj=0;        k2=func(p2)-fx;
       for(j=1; j<= nlstate; j++){        /*res= (k1-2.0*fx+k2)/delt/delt; */
         for(i=1; i<=nlstate; i++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           cptj=cptj+1;        
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){  #ifdef DEBUG
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           }        fprintf(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);
         }  #endif
       }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
              if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                k=kmax;
       for(i=1; i<=npar; i++)        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            k=kmax; l=lmax*10.;
              }
       cptj=0;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for(j=1; j<= nlstate; j++){          delts=delt;
         for(i=1;i<=nlstate;i++){        }
           cptj=cptj+1;      }
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    }
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    delti[theta]=delts;
           }    return res; 
         }    
       }  }
        
      double hessij( double x[], double delti[], int thetai,int thetaj)
   {
       for(j=1; j<= nlstate*2; j++)    int i;
         for(h=0; h<=nhstepm-1; h++){    int l=1, l1, lmax=20;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double k1,k2,k3,k4,res,fx;
         }    double p2[NPARMAX+1];
     int k;
      }  
        fx=func(x);
 /* End theta */    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      for(h=0; h<=nhstepm-1; h++)      k1=func(p2)-fx;
       for(j=1; j<=nlstate*2;j++)    
         for(theta=1; theta <=npar; theta++)      p2[thetai]=x[thetai]+delti[thetai]/k;
         trgradg[h][j][theta]=gradg[h][theta][j];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
     
      for(i=1;i<=nlstate*2;i++)      p2[thetai]=x[thetai]-delti[thetai]/k;
       for(j=1;j<=nlstate*2;j++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         varhe[i][j][(int)age] =0.;      k3=func(p2)-fx;
     
      printf("%d||",(int)age);fflush(stdout);      p2[thetai]=x[thetai]-delti[thetai]/k;
     for(h=0;h<=nhstepm-1;h++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(k=0;k<=nhstepm-1;k++){      k4=func(p2)-fx;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  #ifdef DEBUG
         for(i=1;i<=nlstate*2;i++)      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
           for(j=1;j<=nlstate*2;j++)      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);
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  #endif
       }    }
     }    return res;
   }
        
     /* Computing expectancies */  /************** Inverse of matrix **************/
     for(i=1; i<=nlstate;i++)  void ludcmp(double **a, int n, int *indx, double *d) 
       for(j=1; j<=nlstate;j++)  { 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    int i,imax,j,k; 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    double big,dum,sum,temp; 
              double *vv; 
 /* 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]);*/   
     vv=vector(1,n); 
         }    *d=1.0; 
     for (i=1;i<=n;i++) { 
     fprintf(ficreseij,"%3.0f",age );      big=0.0; 
     cptj=0;      for (j=1;j<=n;j++) 
     for(i=1; i<=nlstate;i++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
       for(j=1; j<=nlstate;j++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         cptj++;      vv[i]=1.0/big; 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    } 
       }    for (j=1;j<=n;j++) { 
     fprintf(ficreseij,"\n");      for (i=1;i<j;i++) { 
            sum=a[i][j]; 
     free_matrix(gm,0,nhstepm,1,nlstate*2);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     free_matrix(gp,0,nhstepm,1,nlstate*2);        a[i][j]=sum; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      } 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      big=0.0; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=j;i<=n;i++) { 
   }        sum=a[i][j]; 
   free_vector(xp,1,npar);        for (k=1;k<j;k++) 
   free_matrix(dnewm,1,nlstate*2,1,npar);          sum -= a[i][k]*a[k][j]; 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        a[i][j]=sum; 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
 }          big=dum; 
           imax=i; 
 /************ Variance ******************/        } 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)      } 
 {      if (j != imax) { 
   /* Variance of health expectancies */        for (k=1;k<=n;k++) { 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          dum=a[imax][k]; 
   double **newm;          a[imax][k]=a[j][k]; 
   double **dnewm,**doldm;          a[j][k]=dum; 
   int i, j, nhstepm, hstepm, h, nstepm ;        } 
   int k, cptcode;        *d = -(*d); 
   double *xp;        vv[imax]=vv[j]; 
   double **gp, **gm;      } 
   double ***gradg, ***trgradg;      indx[j]=imax; 
   double ***p3mat;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   double age,agelim, hf;      if (j != n) { 
   int theta;        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
    fprintf(ficresvij,"# Covariances of life expectancies\n");      } 
   fprintf(ficresvij,"# Age");    } 
   for(i=1; i<=nlstate;i++)    free_vector(vv,1,n);  /* Doesn't work */
     for(j=1; j<=nlstate;j++)  ;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  } 
   fprintf(ficresvij,"\n");  
   void lubksb(double **a, int n, int *indx, double b[]) 
   xp=vector(1,npar);  { 
   dnewm=matrix(1,nlstate,1,npar);    int i,ii=0,ip,j; 
   doldm=matrix(1,nlstate,1,nlstate);    double sum; 
     
   if(estepm < stepm){    for (i=1;i<=n;i++) { 
     printf ("Problem %d lower than %d\n",estepm, stepm);      ip=indx[i]; 
   }      sum=b[ip]; 
   else  hstepm=estepm;        b[ip]=b[i]; 
   /* For example we decided to compute the life expectancy with the smallest unit */      if (ii) 
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
      nhstepm is the number of hstepm from age to agelim      else if (sum) ii=i; 
      nstepm is the number of stepm from age to agelin.      b[i]=sum; 
      Look at hpijx to understand the reason of that which relies in memory size    } 
      and note for a fixed period like k years */    for (i=n;i>=1;i--) { 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      sum=b[i]; 
      survival function given by stepm (the optimization length). Unfortunately it      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
      means that if the survival funtion is printed only each two years of age and if      b[i]=sum/a[i][i]; 
      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 stepm=6 & estepm=24 , = 24/6 months = 4 */  /************ Frequencies ********************/
   agelim = AGESUP;  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)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  {  /* Some frequencies */
     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 */    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int first;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double ***freq; /* Frequencies */
     gp=matrix(0,nhstepm,1,nlstate);    double *pp, **prop;
     gm=matrix(0,nhstepm,1,nlstate);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
     for(theta=1; theta <=npar; theta++){    char fileresp[FILENAMELENGTH];
       for(i=1; i<=npar; i++){ /* Computes gradient */    
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    pp=vector(1,nlstate);
       }    prop=matrix(1,nlstate,iagemin,iagemax+3);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      strcpy(fileresp,"p");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
       if (popbased==1) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
         for(i=1; i<=nlstate;i++)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           prlim[i][i]=probs[(int)age][i][ij];      exit(0);
       }    }
      freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
       for(j=1; j<= nlstate; j++){    j1=0;
         for(h=0; h<=nhstepm; h++){    
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    j=cptcoveff;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         }  
       }    first=1;
      
       for(i=1; i<=npar; i++) /* Computes gradient */    for(k1=1; k1<=j;k1++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for(i1=1; i1<=ncodemax[k1];i1++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          j1++;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
            scanf("%d", i);*/
       if (popbased==1) {        for (i=-1; i<=nlstate+ndeath; i++)  
         for(i=1; i<=nlstate;i++)          for (jk=-1; jk<=nlstate+ndeath; jk++)  
           prlim[i][i]=probs[(int)age][i][ij];            for(m=iagemin; m <= iagemax+3; m++)
       }              freq[i][jk][m]=0;
   
       for(j=1; j<= nlstate; j++){      for (i=1; i<=nlstate; i++)  
         for(h=0; h<=nhstepm; h++){        for(m=iagemin; m <= iagemax+3; m++)
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          prop[i][m]=0;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        
         }        dateintsum=0;
       }        k2cpt=0;
         for (i=1; i<=imx; i++) {
       for(j=1; j<= nlstate; j++)          bool=1;
         for(h=0; h<=nhstepm; h++){          if  (cptcovn>0) {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            for (z1=1; z1<=cptcoveff; z1++) 
         }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     } /* End theta */                bool=0;
           }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
     for(h=0; h<=nhstepm; h++)              k2=anint[m][i]+(mint[m][i]/12.);
       for(j=1; j<=nlstate;j++)              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         for(theta=1; theta <=npar; theta++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           trgradg[h][j][theta]=gradg[h][theta][j];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                if (m<lastpass) {
     for(i=1;i<=nlstate;i++)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       for(j=1;j<=nlstate;j++)                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         vareij[i][j][(int)age] =0.;                }
                 
     for(h=0;h<=nhstepm;h++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       for(k=0;k<=nhstepm;k++){                  dateintsum=dateintsum+k2;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);                  k2cpt++;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);                }
         for(i=1;i<=nlstate;i++)                /*}*/
           for(j=1;j<=nlstate;j++)            }
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          }
       }        }
     }         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)        if  (cptcovn>0) {
       for(j=1; j<=nlstate;j++){          fprintf(ficresp, "\n#********** Variable "); 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresp, "**********\n#");
     fprintf(ficresvij,"\n");        }
     free_matrix(gp,0,nhstepm,1,nlstate);        for(i=1; i<=nlstate;i++) 
     free_matrix(gm,0,nhstepm,1,nlstate);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        fprintf(ficresp, "\n");
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=iagemin; i <= iagemax+3; i++){
   } /* End age */          if(i==iagemax+3){
              fprintf(ficlog,"Total");
   free_vector(xp,1,npar);          }else{
   free_matrix(doldm,1,nlstate,1,npar);            if(first==1){
   free_matrix(dnewm,1,nlstate,1,nlstate);              first=0;
               printf("See log file for details...\n");
 }            }
             fprintf(ficlog,"Age %d", i);
 /************ Variance of prevlim ******************/          }
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          for(jk=1; jk <=nlstate ; jk++){
 {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   /* Variance of prevalence limit */              pp[jk] += freq[jk][m][i]; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          }
   double **newm;          for(jk=1; jk <=nlstate ; jk++){
   double **dnewm,**doldm;            for(m=-1, pos=0; m <=0 ; m++)
   int i, j, nhstepm, hstepm;              pos += freq[jk][m][i];
   int k, cptcode;            if(pp[jk]>=1.e-10){
   double *xp;              if(first==1){
   double *gp, *gm;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   double **gradg, **trgradg;              }
   double age,agelim;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   int theta;            }else{
                  if(first==1)
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficresvpl,"# Age");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   for(i=1; i<=nlstate;i++)            }
       fprintf(ficresvpl," %1d-%1d",i,i);          }
   fprintf(ficresvpl,"\n");  
           for(jk=1; jk <=nlstate ; jk++){
   xp=vector(1,npar);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   dnewm=matrix(1,nlstate,1,npar);              pp[jk] += freq[jk][m][i];
   doldm=matrix(1,nlstate,1,nlstate);          }       
            for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   hstepm=1*YEARM; /* Every year of age */            pos += pp[jk];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            posprop += prop[jk][i];
   agelim = AGESUP;          }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for(jk=1; jk <=nlstate ; jk++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            if(pos>=1.e-5){
     if (stepm >= YEARM) hstepm=1;              if(first==1)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     gradg=matrix(1,npar,1,nlstate);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     gp=vector(1,nlstate);            }else{
     gm=vector(1,nlstate);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     for(theta=1; theta <=npar; theta++){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(i=1; i<=npar; i++){ /* Computes gradient */            }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            if( i <= iagemax){
       }              if(pos>=1.e-5){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       for(i=1;i<=nlstate;i++)                /*probs[i][jk][j1]= pp[jk]/pos;*/
         gp[i] = prlim[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]);*/
                  }
       for(i=1; i<=npar; i++) /* Computes gradient */              else
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            }
       for(i=1;i<=nlstate;i++)          }
         gm[i] = prlim[i][i];          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
       for(i=1;i<=nlstate;i++)            for(m=-1; m <=nlstate+ndeath; m++)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];              if(freq[jk][m][i] !=0 ) {
     } /* End theta */              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     trgradg =matrix(1,nlstate,1,npar);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
     for(j=1; j<=nlstate;j++)          if(i <= iagemax)
       for(theta=1; theta <=npar; theta++)            fprintf(ficresp,"\n");
         trgradg[j][theta]=gradg[theta][j];          if(first==1)
             printf("Others in log...\n");
     for(i=1;i<=nlstate;i++)          fprintf(ficlog,"\n");
       varpl[i][(int)age] =0.;        }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    }
     for(i=1;i<=nlstate;i++)    dateintmean=dateintsum/k2cpt; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */   
     fclose(ficresp);
     fprintf(ficresvpl,"%.0f ",age );    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     for(i=1; i<=nlstate;i++)    free_vector(pp,1,nlstate);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     fprintf(ficresvpl,"\n");    /* End of Freq */
     free_vector(gp,1,nlstate);  }
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);  /************ Prevalence ********************/
     free_matrix(trgradg,1,nlstate,1,npar);  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)
   } /* End age */  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   free_vector(xp,1,npar);       in each health status at the date of interview (if between dateprev1 and dateprev2).
   free_matrix(doldm,1,nlstate,1,npar);       We still use firstpass and lastpass as another selection.
   free_matrix(dnewm,1,nlstate,1,nlstate);    */
    
 }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
 /************ Variance of one-step probabilities  ******************/    double *pp, **prop;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    double pos,posprop; 
 {    double  y2; /* in fractional years */
   int i, j, i1, k1, j1, z1;    int iagemin, iagemax;
   int k=0, cptcode;  
   double **dnewm,**doldm;    iagemin= (int) agemin;
   double *xp;    iagemax= (int) agemax;
   double *gp, *gm;    /*pp=vector(1,nlstate);*/
   double **gradg, **trgradg;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   double age,agelim, cov[NCOVMAX];    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   int theta;    j1=0;
   char fileresprob[FILENAMELENGTH];    
     j=cptcoveff;
   strcpy(fileresprob,"prob");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   strcat(fileresprob,fileres);    
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    for(k1=1; k1<=j;k1++){
     printf("Problem with resultfile: %s\n", fileresprob);      for(i1=1; i1<=ncodemax[k1];i1++){
   }        j1++;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);        
          for (i=1; i<=nlstate; i++)  
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");          for(m=iagemin; m <= iagemax+3; m++)
   fprintf(ficresprob,"# Age");            prop[i][m]=0.0;
   for(i=1; i<=nlstate;i++)       
     for(j=1; j<=(nlstate+ndeath);j++)        for (i=1; i<=imx; i++) { /* Each individual */
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);          bool=1;
           if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   fprintf(ficresprob,"\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
           } 
   xp=vector(1,npar);          if (bool==1) { 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   cov[1]=1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   j=cptcoveff;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   if (cptcovn<1) {j=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); 
   j1=0;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   for(k1=1; k1<=1;k1++){                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     for(i1=1; i1<=ncodemax[k1];i1++){                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     j1++;                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
     if  (cptcovn>0) {              }
       fprintf(ficresprob, "\n#********** Variable ");            } /* end selection of waves */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          }
       fprintf(ficresprob, "**********\n#");        }
     }        for(i=iagemin; i <= iagemax+3; i++){  
              
       for (age=bage; age<=fage; age ++){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         cov[2]=age;            posprop += prop[jk][i]; 
         for (k=1; k<=cptcovn;k++) {          } 
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  
                    for(jk=1; jk <=nlstate ; jk++){     
         }            if( i <=  iagemax){ 
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];              if(posprop>=1.e-5){ 
         for (k=1; k<=cptcovprod;k++)                probs[i][jk][j1]= prop[jk][i]/posprop;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              } 
                    } 
         gradg=matrix(1,npar,1,9);          }/* end jk */ 
         trgradg=matrix(1,9,1,npar);        }/* end i */ 
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      } /* end i1 */
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    } /* end k1 */
        
         for(theta=1; theta <=npar; theta++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           for(i=1; i<=npar; i++)    /*free_vector(pp,1,nlstate);*/
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
            }  /* End of prevalence */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
            /************* Waves Concatenation ***************/
           k=0;  
           for(i=1; i<= (nlstate+ndeath); i++){  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)
             for(j=1; j<=(nlstate+ndeath);j++){  {
               k=k+1;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
               gp[k]=pmmij[i][j];       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
           }       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.
           for(i=1; i<=npar; i++)       */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);  
        int i, mi, m;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           k=0;       double sum=0., jmean=0.;*/
           for(i=1; i<=(nlstate+ndeath); i++){    int first;
             for(j=1; j<=(nlstate+ndeath);j++){    int j, k=0,jk, ju, jl;
               k=k+1;    double sum=0.;
               gm[k]=pmmij[i][j];    first=0;
             }    jmin=1e+5;
           }    jmax=-1;
          jmean=0.;
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    for(i=1; i<=imx; i++){
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        mi=0;
         }      m=firstpass;
       while(s[m][i] <= nlstate){
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        if(s[m][i]>=1)
           for(theta=1; theta <=npar; theta++)          mw[++mi][i]=m;
             trgradg[j][theta]=gradg[theta][j];        if(m >=lastpass)
                  break;
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        else
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          m++;
              }/* end while */
         pmij(pmmij,cov,ncovmodel,x,nlstate);      if (s[m][i] > nlstate){
                mi++;     /* Death is another wave */
         k=0;        /* if(mi==0)  never been interviewed correctly before death */
         for(i=1; i<=(nlstate+ndeath); i++){           /* Only death is a correct wave */
           for(j=1; j<=(nlstate+ndeath);j++){        mw[mi][i]=m;
             k=k+1;      }
             gm[k]=pmmij[i][j];  
           }      wav[i]=mi;
         }      if(mi==0){
              if(first==0){
      /*printf("\n%d ",(int)age);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          first=1;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        }
      }*/        if(first==1){
           fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
         fprintf(ficresprob,"\n%d ",(int)age);        }
       } /* end mi==0 */
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    } /* End individuals */
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));  
      for(i=1; i<=imx; i++){
       }      for(mi=1; mi<wav[i];mi++){
     }        if (stepm <=0)
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          dh[mi][i]=1;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        else{
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            if (agedc[i] < 2*AGESUP) {
   }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   free_vector(xp,1,npar);              if(j==0) j=1;  /* Survives at least one month after exam */
   fclose(ficresprob);              else if(j<0){
                  printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 }                j=1; /* Careful Patch */
                 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);
 /******************* Printing html file ***********/                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]);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \                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);
  int lastpass, int stepm, int weightopt, char model[],\              }
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \              k=k+1;
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\              if (j >= jmax) jmax=j;
  char version[], int popforecast, int estepm ){              if (j <= jmin) jmin=j;
   int jj1, k1, i1, cpt;              sum=sum+j;
   FILE *fichtm;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   /*char optionfilehtm[FILENAMELENGTH];*/              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
   strcpy(optionfilehtm,optionfile);          }
   strcat(optionfilehtm,".htm");          else{
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     printf("Problem with %s \n",optionfilehtm), exit(0);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   }            k=k+1;
             if (j >= jmax) jmax=j;
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n            else if (j <= jmin)jmin=j;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 \n            /*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]);*/
 Total number of observations=%d <br>\n            if(j<0){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n              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]);
 <hr  size=\"2\" color=\"#EC5E5E\">              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]);
  <ul><li>Outputs files<br>\n            }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n            sum=sum+j;
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n          }
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          jk= j/stepm;
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n          jl= j -jk*stepm;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n          ju= j -(jk+1)*stepm;
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
  fprintf(fichtm,"\n              dh[mi][i]=jk;
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n              bh[mi][i]=0;
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n            }else{ /* We want a negative bias in order to only have interpolation ie
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n                    * at the price of an extra matrix product in likelihood */
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n              dh[mi][i]=jk+1;
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);              bh[mi][i]=ju;
             }
  if(popforecast==1) fprintf(fichtm,"\n          }else{
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n            if(jl <= -ju){
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n              dh[mi][i]=jk;
         <br>",fileres,fileres,fileres,fileres);              bh[mi][i]=jl;       /* bias is positive if real duration
  else                                   * is higher than the multiple of stepm and negative otherwise.
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);                                   */
 fprintf(fichtm," <li>Graphs</li><p>");            }
             else{
  m=cptcoveff;              dh[mi][i]=jk+1;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              bh[mi][i]=ju;
             }
  jj1=0;            if(dh[mi][i]==0){
  for(k1=1; k1<=m;k1++){              dh[mi][i]=1; /* At least one step */
    for(i1=1; i1<=ncodemax[k1];i1++){              bh[mi][i]=ju; /* At least one step */
        jj1++;              /*  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);*/
        if (cptcovn > 0) {            }
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          } /* end if mle */
          for (cpt=1; cpt<=cptcoveff;cpt++)        }
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      } /* end wave */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    }
        }    jmean=sum/k;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.png<br>    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 <img src=\"pe%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
        for(cpt=1; cpt<nlstate;cpt++){   }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.png<br>  
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  /*********** Tricode ****************************/
        }  void tricode(int *Tvar, int **nbcode, int imx)
     for(cpt=1; cpt<=nlstate;cpt++) {  {
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    
 interval) in state (%d): v%s%d%d.png <br>    int Ndum[20],ij=1, k, j, i, maxncov=19;
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      int cptcode=0;
      }    cptcoveff=0; 
      for(cpt=1; cpt<=nlstate;cpt++) {   
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    for (k=0; k<maxncov; k++) Ndum[k]=0;
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    for (k=1; k<=7; k++) ncodemax[k]=0;
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 health expectancies in states (1) and (2): e%s%d.png<br>      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                                 modality*/ 
 fprintf(fichtm,"\n</body>");        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
    }        Ndum[ij]++; /*store the modality */
    }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 fclose(fichtm);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
 }                                         Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
 /******************* Gnuplot file **************/      }
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
       for (i=0; i<=cptcode; i++) {
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        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 */
       }
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".gp.txt");      ij=1; 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      for (i=1; i<=ncodemax[j]; i++) {
     printf("Problem with file %s",optionfilegnuplot);        for (k=0; k<= maxncov; k++) {
   }          if (Ndum[k] != 0) {
             nbcode[Tvar[j]][ij]=k; 
 #ifdef windows            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     fprintf(ficgp,"cd \"%s\" \n",pathc);            
 #endif            ij++;
 m=pow(2,cptcoveff);          }
            if (ij > ncodemax[j]) break; 
  /* 1eme*/        }  
   for (cpt=1; cpt<= nlstate ; cpt ++) {      } 
    for (k1=1; k1<= m ; k1 ++) {    }  
   
 #ifdef windows   for (k=0; k< maxncov; k++) Ndum[k]=0;
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);  
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);   for (i=1; i<=ncovmodel-2; i++) { 
 #endif     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
 #ifdef unix     ij=Tvar[i];
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);     Ndum[ij]++;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);   }
 #endif  
    ij=1;
 for (i=1; i<= nlstate ; i ++) {   for (i=1; i<= maxncov; i++) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");     if((Ndum[i]!=0) && (i<=ncovcol)){
   else fprintf(ficgp," \%%*lf (\%%*lf)");       Tvaraff[ij]=i; /*For printing */
 }       ij++;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);     }
     for (i=1; i<= nlstate ; i ++) {   }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");   
   else fprintf(ficgp," \%%*lf (\%%*lf)");   cptcoveff=ij-1; /*Number of simple covariates*/
 }  }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {  /*********** Health Expectancies ****************/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  {
 #ifdef unix    /* Health expectancies */
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
 #endif    double age, agelim, hf;
    }    double ***p3mat,***varhe;
   }    double **dnewm,**doldm;
   /*2 eme*/    double *xp;
     double **gp, **gm;
   for (k1=1; k1<= m ; k1 ++) {    double ***gradg, ***trgradg;
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n\n",strtok(optionfile, "."),k1);    int theta;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);  
        varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     for (i=1; i<= nlstate+1 ; i ++) {    xp=vector(1,npar);
       k=2*i;    dnewm=matrix(1,nlstate*nlstate,1,npar);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {    
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficreseij,"# Health expectancies\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficreseij,"# Age");
 }      for(i=1; i<=nlstate;i++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      for(j=1; j<=nlstate;j++)
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficreseij,"\n");
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    if(estepm < stepm){
         else fprintf(ficgp," \%%*lf (\%%*lf)");      printf ("Problem %d lower than %d\n",estepm, stepm);
 }      }
       fprintf(ficgp,"\" t\"\" w l 0,");    else  hstepm=estepm;   
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /* We compute the life expectancy from trapezoids spaced every estepm months
       for (j=1; j<= nlstate+1 ; j ++) {     * This is mainly to measure the difference between two models: for example
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");     * if stepm=24 months pijx are given only every 2 years and by summing them
   else fprintf(ficgp," \%%*lf (\%%*lf)");     * we are calculating an estimate of the Life Expectancy assuming a linear 
 }       * progression in between and thus overestimating or underestimating according
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");     * to the curvature of the survival function. If, for the same date, we 
       else fprintf(ficgp,"\" t\"\" w l 0,");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     }     * to compare the new estimate of Life expectancy with the same linear 
   }     * hypothesis. A more precise result, taking into account a more precise
       * curvature will be obtained if estepm is as small as stepm. */
   /*3eme*/  
     /* For example we decided to compute the life expectancy with the smallest unit */
   for (k1=1; k1<= m ; k1 ++) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     for (cpt=1; cpt<= nlstate ; cpt ++) {       nhstepm is the number of hstepm from age to agelim 
       k=2+nlstate*(2*cpt-2);       nstepm is the number of stepm from age to agelin. 
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);       and note for a fixed period like estepm months */
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");       survival function given by stepm (the optimization length). Unfortunately it
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);       means that if the survival funtion is printed only each two years of age and if
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");       results. So we changed our mind and took the option of the best precision.
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 */  
       for (i=1; i< nlstate ; i ++) {    agelim=AGESUP;
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* nhstepm age range expressed in number of stepm */
       }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   }      /* if (stepm >= YEARM) hstepm=1;*/
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   /* CV preval stat */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for (k1=1; k1<= m ; k1 ++) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     for (cpt=1; cpt<nlstate ; cpt ++) {      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       k=3;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
       fprintf(ficgp,"set out \"p%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       for (i=1; i< nlstate ; i ++)      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
         fprintf(ficgp,"+$%d",k+i+1);   
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
            hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      /* Computing Variances of health expectancies */
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;       for(theta=1; theta <=npar; theta++){
         fprintf(ficgp,"+$%d",l+i+1);        for(i=1; i<=npar; i++){ 
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          }
     }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }      
          cptj=0;
   /* proba elementaires */        for(j=1; j<= nlstate; j++){
    for(i=1,jk=1; i <=nlstate; i++){          for(i=1; i<=nlstate; i++){
     for(k=1; k <=(nlstate+ndeath); k++){            cptj=cptj+1;
       if (k != i) {            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         for(j=1; j <=ncovmodel; j++){              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                    }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          }
           jk++;        }
           fprintf(ficgp,"\n");       
         }       
       }        for(i=1; i<=npar; i++) 
     }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
    }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         
    for(jk=1; jk <=m; jk++) {        cptj=0;
      fprintf(ficgp,"\nset out \"pe%s%d.png\" \n\n",strtok(optionfile, "."),jk);        for(j=1; j<= nlstate; j++){
      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          for(i=1;i<=nlstate;i++){
      i=1;            cptj=cptj+1;
      for(k2=1; k2<=nlstate; k2++) {            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
        k3=i;  
        for(k=1; k<=(nlstate+ndeath); k++) {              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
          if (k != k2){            }
            fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          }
            ij=1;        }
            for(j=3; j <=ncovmodel; j++) {        for(j=1; j<= nlstate*nlstate; j++)
              if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          for(h=0; h<=nhstepm-1; h++){
                fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                ij++;          }
              }       } 
              else     
                fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  /* End theta */
            }  
            fprintf(ficgp,")/(1");       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
              
            for(k1=1; k1 <=nlstate; k1++){         for(h=0; h<=nhstepm-1; h++)
              fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        for(j=1; j<=nlstate*nlstate;j++)
              ij=1;          for(theta=1; theta <=npar; theta++)
              for(j=3; j <=ncovmodel; j++){            trgradg[h][j][theta]=gradg[h][theta][j];
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       
                  fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
                  ij++;       for(i=1;i<=nlstate*nlstate;i++)
                }        for(j=1;j<=nlstate*nlstate;j++)
                else          varhe[i][j][(int)age] =0.;
                  fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
              }       printf("%d|",(int)age);fflush(stdout);
              fprintf(ficgp,")");       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
            }       for(h=0;h<=nhstepm-1;h++){
            fprintf(ficgp,") t \"p%d%d\" ", k2,k);        for(k=0;k<=nhstepm-1;k++){
            if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
            i=i+ncovmodel;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
          }          for(i=1;i<=nlstate*nlstate;i++)
        }            for(j=1;j<=nlstate*nlstate;j++)
      }              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
    }        }
          }
    fclose(ficgp);      /* Computing expectancies */
 }  /* end gnuplot */      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 /*************** Moving average **************/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***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]);*/
   int i, cpt, cptcod;  
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          }
       for (i=1; i<=nlstate;i++)  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      fprintf(ficreseij,"%3.0f",age );
           mobaverage[(int)agedeb][i][cptcod]=0.;      cptj=0;
          for(i=1; i<=nlstate;i++)
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        for(j=1; j<=nlstate;j++){
       for (i=1; i<=nlstate;i++){          cptj++;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
           for (cpt=0;cpt<=4;cpt++){        }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      fprintf(ficreseij,"\n");
           }     
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 }    }
     printf("\n");
     fprintf(ficlog,"\n");
 /************** 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){    free_vector(xp,1,npar);
      free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   int *popage;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  }
   double *popeffectif,*popcount;  
   double ***p3mat;  /************ Variance ******************/
   char fileresf[FILENAMELENGTH];  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)
   {
  agelim=AGESUP;    /* Variance of health expectancies */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double **dnewm,**doldm;
      double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
   strcpy(fileresf,"f");    int k, cptcode;
   strcat(fileresf,fileres);    double *xp;
   if((ficresf=fopen(fileresf,"w"))==NULL) {    double **gp, **gm;  /* for var eij */
     printf("Problem with forecast resultfile: %s\n", fileresf);    double ***gradg, ***trgradg; /*for var eij */
   }    double **gradgp, **trgradgp; /* for var p point j */
   printf("Computing forecasting: result on file '%s' \n", fileresf);    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    double ***p3mat;
     double age,agelim, hf;
   if (mobilav==1) {    double ***mobaverage;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int theta;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    char digit[4];
   }    char digitp[25];
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    char fileresprobmorprev[FILENAMELENGTH];
   if (stepm<=12) stepsize=1;  
      if(popbased==1){
   agelim=AGESUP;      if(mobilav!=0)
          strcpy(digitp,"-populbased-mobilav-");
   hstepm=1;      else strcpy(digitp,"-populbased-nomobil-");
   hstepm=hstepm/stepm;    }
   yp1=modf(dateintmean,&yp);    else 
   anprojmean=yp;      strcpy(digitp,"-stablbased-");
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;    if (mobilav!=0) {
   yp1=modf((yp2*30.5),&yp);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   jprojmean=yp;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   if(jprojmean==0) jprojmean=1;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   if(mprojmean==0) jprojmean=1;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    }
    
   for(cptcov=1;cptcov<=i2;cptcov++){    strcpy(fileresprobmorprev,"prmorprev"); 
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    sprintf(digit,"%-d",ij);
       k=k+1;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       fprintf(ficresf,"\n#******");    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       for(j=1;j<=cptcoveff;j++) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcat(fileresprobmorprev,fileres);
       }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       fprintf(ficresf,"******\n");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficresf,"# StartingAge FinalAge");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    }
          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);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    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(ficresf,"\n");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      for(i=1; i<=nlstate;i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           nhstepm = nhstepm/hstepm;    }  
              fprintf(ficresprobmorprev,"\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\n# Routine varevsij");
           oldm=oldms;savm=savms;    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");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
          /*   } */
           for (h=0; h<=nhstepm; h++){    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
             }    fprintf(ficresvij,"# Age");
             for(j=1; j<=nlstate+ndeath;j++) {    for(i=1; i<=nlstate;i++)
               kk1=0.;kk2=0;      for(j=1; j<=nlstate;j++)
               for(i=1; i<=nlstate;i++) {                      fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
                 if (mobilav==1)    fprintf(ficresvij,"\n");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {    xp=vector(1,npar);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    dnewm=matrix(1,nlstate,1,npar);
                 }    doldm=matrix(1,nlstate,1,nlstate);
                    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
               }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);    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*/
           }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
       }    }
     }    else  hstepm=estepm;   
   }    /* 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. 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   fclose(ficresf);       Look at hpijx to understand the reason of that which relies in memory size
 }       and note for a fixed period like k years */
 /************** Forecasting ******************/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 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){       survival function given by stepm (the optimization length). Unfortunately it
         means that if the survival funtion is printed every two years of age and if
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   int *popage;       results. So we changed our mind and took the option of the best precision.
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    */
   double *popeffectif,*popcount;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double ***p3mat,***tabpop,***tabpopprev;    agelim = AGESUP;
   char filerespop[FILENAMELENGTH];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   agelim=AGESUP;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      gp=matrix(0,nhstepm,1,nlstate);
        gm=matrix(0,nhstepm,1,nlstate);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
    
        for(theta=1; theta <=npar; theta++){
   strcpy(filerespop,"pop");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   strcat(filerespop,fileres);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        }
     printf("Problem with forecast resultfile: %s\n", filerespop);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
         if (popbased==1) {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   if (mobilav==1) {              prlim[i][i]=probs[(int)age][i][ij];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }else{ /* mobilav */ 
     movingaverage(agedeb, fage, ageminpar, mobaverage);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }
   if (stepm<=12) stepsize=1;    
          for(j=1; j<= nlstate; j++){
   agelim=AGESUP;          for(h=0; h<=nhstepm; h++){
              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   hstepm=1;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   hstepm=hstepm/stepm;          }
          }
   if (popforecast==1) {        /* This for computing probability of death (h=1 means
     if((ficpop=fopen(popfile,"r"))==NULL) {           computed over hstepm matrices product = hstepm*stepm months) 
       printf("Problem with population file : %s\n",popfile);exit(0);           as a weighted average of prlim.
     }        */
     popage=ivector(0,AGESUP);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     popeffectif=vector(0,AGESUP);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     popcount=vector(0,AGESUP);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
            }    
     i=1;          /* end probability of death */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
            for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     imx=i;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   for(cptcov=1;cptcov<=i2;cptcov++){        if (popbased==1) {
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          if(mobilav ==0){
       k=k+1;            for(i=1; i<=nlstate;i++)
       fprintf(ficrespop,"\n#******");              prlim[i][i]=probs[(int)age][i][ij];
       for(j=1;j<=cptcoveff;j++) {          }else{ /* mobilav */ 
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(i=1; i<=nlstate;i++)
       }              prlim[i][i]=mobaverage[(int)age][i][ij];
       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(j=1; j<= nlstate; j++){
                for(h=0; h<=nhstepm; h++){
       for (cpt=0; cpt<=0;cpt++) {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
                  }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        /* This for computing probability of death (h=1 means
           nhstepm = nhstepm/hstepm;           computed over hstepm matrices product = hstepm*stepm months) 
                     as a weighted average of prlim.
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        */
           oldm=oldms;savm=savms;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for(i=1,gmp[j]=0.; i<= nlstate; i++)
                   gmp[j] += prlim[i][i]*p3mat[i][j][1];
           for (h=0; h<=nhstepm; h++){        }    
             if (h==(int) (calagedate+YEARM*cpt)) {        /* end probability of death */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }        for(j=1; j<= nlstate; j++) /* vareij */
             for(j=1; j<=nlstate+ndeath;j++) {          for(h=0; h<=nhstepm; h++){
               kk1=0.;kk2=0;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
               for(i=1; i<=nlstate;i++) {                        }
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                 else {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        }
                 }  
               }      } /* End theta */
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      for(h=0; h<=nhstepm; h++) /* veij */
               }        for(j=1; j<=nlstate;j++)
             }          for(theta=1; theta <=npar; theta++)
             for(i=1; i<=nlstate;i++){            trgradg[h][j][theta]=gradg[h][theta][j];
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        for(theta=1; theta <=npar; theta++)
                 }          trgradgp[j][theta]=gradgp[theta][j];
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    
             }  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      for(i=1;i<=nlstate;i++)
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        for(j=1;j<=nlstate;j++)
           }          vareij[i][j][(int)age] =0.;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }      for(h=0;h<=nhstepm;h++){
       }        for(k=0;k<=nhstepm;k++){
            matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   /******/          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {            for(j=1;j<=nlstate;j++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      }
           nhstepm = nhstepm/hstepm;    
                /* pptj */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           oldm=oldms;savm=savms;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(j=nlstate+1;j<=nlstate+ndeath;j++)
           for (h=0; h<=nhstepm; h++){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
             if (h==(int) (calagedate+YEARM*cpt)) {          varppt[j][i]=doldmp[j][i];
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      /* end ppptj */
             }      /*  x centered again */
             for(j=1; j<=nlstate+ndeath;j++) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
               kk1=0.;kk2=0;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
               for(i=1; i<=nlstate;i++) {                 
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          if (popbased==1) {
               }        if(mobilav ==0){
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          for(i=1; i<=nlstate;i++)
             }            prlim[i][i]=probs[(int)age][i][ij];
           }        }else{ /* mobilav */ 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(i=1; i<=nlstate;i++)
         }            prlim[i][i]=mobaverage[(int)age][i][ij];
       }        }
    }      }
   }               
        /* This for computing probability of death (h=1 means
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
   if (popforecast==1) {      */
     free_ivector(popage,0,AGESUP);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     free_vector(popeffectif,0,AGESUP);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     free_vector(popcount,0,AGESUP);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   }      }    
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /* end probability of death */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   fclose(ficrespop);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
 }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
 /***********************************************/        for(i=1; i<=nlstate;i++){
 /**************** Main Program *****************/          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
 /***********************************************/        }
       } 
 int main(int argc, char *argv[])      fprintf(ficresprobmorprev,"\n");
 {  
       fprintf(ficresvij,"%.0f ",age );
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      for(i=1; i<=nlstate;i++)
   double agedeb, agefin,hf;        for(j=1; j<=nlstate;j++){
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
   double fret;      fprintf(ficresvij,"\n");
   double **xi,tmp,delta;      free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
   double dum; /* Dummy variable */      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   double ***p3mat;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   int *indx;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   char line[MAXLINE], linepar[MAXLINE];    } /* End age */
   char title[MAXLINE];    free_vector(gpp,nlstate+1,nlstate+ndeath);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    free_vector(gmp,nlstate+1,nlstate+ndeath);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
      free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   char filerest[FILENAMELENGTH];    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   char fileregp[FILENAMELENGTH];  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   char popfile[FILENAMELENGTH];  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   int firstobs=1, lastobs=10;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   int sdeb, sfin; /* Status at beginning and end */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   int c,  h , cpt,l;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   int ju,jl, mi;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    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);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    /*  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);
   int mobilav=0,popforecast=0;  */
   int hstepm, nhstepm;  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
   double bage, fage, age, agelim, agebase;    free_vector(xp,1,npar);
   double ftolpl=FTOL;    free_matrix(doldm,1,nlstate,1,nlstate);
   double **prlim;    free_matrix(dnewm,1,nlstate,1,npar);
   double *severity;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double ***param; /* Matrix of parameters */    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   double  *p;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double **matcov; /* Matrix of covariance */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   double ***delti3; /* Scale */    fclose(ficresprobmorprev);
   double *delti; /* Scale */    fflush(ficgp);
   double ***eij, ***vareij;    fflush(fichtm); 
   double **varpl; /* Variances of prevalence limits by age */  }  /* end varevsij */
   double *epj, vepp;  
   double kk1, kk2;  /************ Variance of prevlim ******************/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  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)
    {
     /* Variance of prevalence limit */
   char version[80]="Imach version 0.8d, May 2002, INED-EUROREVES ";    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   char *alph[]={"a","a","b","c","d","e"}, str[4];    double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   char z[1]="c", occ;    int k, cptcode;
 #include <sys/time.h>    double *xp;
 #include <time.h>    double *gp, *gm;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    double **gradg, **trgradg;
      double age,agelim;
   /* long total_usecs;    int theta;
   struct timeval start_time, end_time;     
      fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    fprintf(ficresvpl,"# Age");
   getcwd(pathcd, size);    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
   printf("\n%s",version);    fprintf(ficresvpl,"\n");
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");    xp=vector(1,npar);
     scanf("%s",pathtot);    dnewm=matrix(1,nlstate,1,npar);
   }    doldm=matrix(1,nlstate,1,nlstate);
   else{    
     strcpy(pathtot,argv[1]);    hstepm=1*YEARM; /* Every year of age */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    agelim = AGESUP;
   /*cygwin_split_path(pathtot,path,optionfile);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   /* cutv(path,optionfile,pathtot,'\\');*/      if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      gradg=matrix(1,npar,1,nlstate);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      gp=vector(1,nlstate);
   chdir(path);      gm=vector(1,nlstate);
   replace(pathc,path);  
       for(theta=1; theta <=npar; theta++){
 /*-------- arguments in the command line --------*/        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   strcpy(fileres,"r");        }
   strcat(fileres, optionfilefiname);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcat(fileres,".txt");    /* Other files have txt extension */        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
   /*---------arguments file --------*/      
         for(i=1; i<=npar; i++) /* Computes gradient */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     printf("Problem with optionfile %s\n",optionfile);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     goto end;        for(i=1;i<=nlstate;i++)
   }          gm[i] = prlim[i][i];
   
   strcpy(filereso,"o");        for(i=1;i<=nlstate;i++)
   strcat(filereso,fileres);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   if((ficparo=fopen(filereso,"w"))==NULL) {      } /* End theta */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }      trgradg =matrix(1,nlstate,1,npar);
   
   /* Reads comments: lines beginning with '#' */      for(j=1; j<=nlstate;j++)
   while((c=getc(ficpar))=='#' && c!= EOF){        for(theta=1; theta <=npar; theta++)
     ungetc(c,ficpar);          trgradg[j][theta]=gradg[theta][j];
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for(i=1;i<=nlstate;i++)
     fputs(line,ficparo);        varpl[i][(int)age] =0.;
   }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   ungetc(c,ficpar);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   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(ficresvpl,"%.0f ",age );
 while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     fgets(line, MAXLINE, ficpar);      fprintf(ficresvpl,"\n");
     puts(line);      free_vector(gp,1,nlstate);
     fputs(line,ficparo);      free_vector(gm,1,nlstate);
   }      free_matrix(gradg,1,npar,1,nlstate);
   ungetc(c,ficpar);      free_matrix(trgradg,1,nlstate,1,npar);
      } /* End age */
      
   covar=matrix(0,NCOVMAX,1,n);    free_vector(xp,1,npar);
   cptcovn=0;    free_matrix(doldm,1,nlstate,1,npar);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    free_matrix(dnewm,1,nlstate,1,nlstate);
   
   ncovmodel=2+cptcovn;  }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
    /************ Variance of one-step probabilities  ******************/
   /* Read guess parameters */  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   /* Reads comments: lines beginning with '#' */  {
   while((c=getc(ficpar))=='#' && c!= EOF){    int i, j=0,  i1, k1, l1, t, tj;
     ungetc(c,ficpar);    int k2, l2, j1,  z1;
     fgets(line, MAXLINE, ficpar);    int k=0,l, cptcode;
     puts(line);    int first=1, first1;
     fputs(line,ficparo);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   }    double **dnewm,**doldm;
   ungetc(c,ficpar);    double *xp;
      double *gp, *gm;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double **gradg, **trgradg;
     for(i=1; i <=nlstate; i++)    double **mu;
     for(j=1; j <=nlstate+ndeath-1; j++){    double age,agelim, cov[NCOVMAX];
       fscanf(ficpar,"%1d%1d",&i1,&j1);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       fprintf(ficparo,"%1d%1d",i1,j1);    int theta;
       printf("%1d%1d",i,j);    char fileresprob[FILENAMELENGTH];
       for(k=1; k<=ncovmodel;k++){    char fileresprobcov[FILENAMELENGTH];
         fscanf(ficpar," %lf",&param[i][j][k]);    char fileresprobcor[FILENAMELENGTH];
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);    double ***varpij;
       }  
       fscanf(ficpar,"\n");    strcpy(fileresprob,"prob"); 
       printf("\n");    strcat(fileresprob,fileres);
       fprintf(ficparo,"\n");    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprob);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    }
     strcpy(fileresprobcov,"probcov"); 
   p=param[1][1];    strcat(fileresprobcov,fileres);
      if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   /* Reads comments: lines beginning with '#' */      printf("Problem with resultfile: %s\n", fileresprobcov);
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    strcpy(fileresprobcor,"probcor"); 
     puts(line);    strcat(fileresprobcor,fileres);
     fputs(line,ficparo);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcor);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   for(i=1; i <=nlstate; i++){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       printf("%1d%1d",i,j);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       fprintf(ficparo,"%1d%1d",i1,j1);    
       for(k=1; k<=ncovmodel;k++){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         fscanf(ficpar,"%le",&delti3[i][j][k]);    fprintf(ficresprob,"# Age");
         printf(" %le",delti3[i][j][k]);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
         fprintf(ficparo," %le",delti3[i][j][k]);    fprintf(ficresprobcov,"# Age");
       }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       fscanf(ficpar,"\n");    fprintf(ficresprobcov,"# Age");
       printf("\n");  
       fprintf(ficparo,"\n");  
     }    for(i=1; i<=nlstate;i++)
   }      for(j=1; j<=(nlstate+ndeath);j++){
   delti=delti3[1][1];        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
   /* Reads comments: lines beginning with '#' */        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   while((c=getc(ficpar))=='#' && c!= EOF){      }  
     ungetc(c,ficpar);   /* fprintf(ficresprob,"\n");
     fgets(line, MAXLINE, ficpar);    fprintf(ficresprobcov,"\n");
     puts(line);    fprintf(ficresprobcor,"\n");
     fputs(line,ficparo);   */
   }   xp=vector(1,npar);
   ungetc(c,ficpar);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   matcov=matrix(1,npar,1,npar);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   for(i=1; i <=npar; i++){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     fscanf(ficpar,"%s",&str);    first=1;
     printf("%s",str);    fprintf(ficgp,"\n# Routine varprob");
     fprintf(ficparo,"%s",str);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     for(j=1; j <=i; j++){    fprintf(fichtm,"\n");
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);    fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       fprintf(ficparo," %.5le",matcov[i][j]);    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");
     fscanf(ficpar,"\n");  
     printf("\n");    cov[1]=1;
     fprintf(ficparo,"\n");    tj=cptcoveff;
   }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   for(i=1; i <=npar; i++)    j1=0;
     for(j=i+1;j<=npar;j++)    for(t=1; t<=tj;t++){
       matcov[i][j]=matcov[j][i];      for(i1=1; i1<=ncodemax[t];i1++){ 
            j1++;
   printf("\n");        if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     /*-------- Rewriting paramater file ----------*/          fprintf(ficresprob, "**********\n#\n");
      strcpy(rfileres,"r");    /* "Rparameterfile */          fprintf(ficresprobcov, "\n#********** Variable "); 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      strcat(rfileres,".");    /* */          fprintf(ficresprobcov, "**********\n#\n");
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          
     if((ficres =fopen(rfileres,"w"))==NULL) {          fprintf(ficgp, "\n#********** Variable "); 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficgp, "**********\n#\n");
     fprintf(ficres,"#%s\n",version);          
              
     /*-------- data file ----------*/          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     if((fic=fopen(datafile,"r"))==NULL)    {          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       printf("Problem with datafile: %s\n", datafile);goto end;          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     }          
           fprintf(ficresprobcor, "\n#********** Variable ");    
     n= lastobs;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     severity = vector(1,maxwav);          fprintf(ficresprobcor, "**********\n#");    
     outcome=imatrix(1,maxwav+1,1,n);        }
     num=ivector(1,n);        
     moisnais=vector(1,n);        for (age=bage; age<=fage; age ++){ 
     annais=vector(1,n);          cov[2]=age;
     moisdc=vector(1,n);          for (k=1; k<=cptcovn;k++) {
     andc=vector(1,n);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     agedc=vector(1,n);          }
     cod=ivector(1,n);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     weight=vector(1,n);          for (k=1; k<=cptcovprod;k++)
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     mint=matrix(1,maxwav,1,n);          
     anint=matrix(1,maxwav,1,n);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     s=imatrix(1,maxwav+1,1,n);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     adl=imatrix(1,maxwav+1,1,n);              gp=vector(1,(nlstate)*(nlstate+ndeath));
     tab=ivector(1,NCOVMAX);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     ncodemax=ivector(1,8);      
           for(theta=1; theta <=npar; theta++){
     i=1;            for(i=1; i<=npar; i++)
     while (fgets(line, MAXLINE, fic) != NULL)    {              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       if ((i >= firstobs) && (i <=lastobs)) {            
                    pmij(pmmij,cov,ncovmodel,xp,nlstate);
         for (j=maxwav;j>=1;j--){            
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            k=0;
           strcpy(line,stra);            for(i=1; i<= (nlstate); i++){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              for(j=1; j<=(nlstate+ndeath);j++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                k=k+1;
         }                gp[k]=pmmij[i][j];
                      }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            
             for(i=1; i<=npar; i++)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            k=0;
         for (j=ncovcol;j>=1;j--){            for(i=1; i<=(nlstate); i++){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);              for(j=1; j<=(nlstate+ndeath);j++){
         }                k=k+1;
         num[i]=atol(stra);                gm[k]=pmmij[i][j];
                      }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            }
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/       
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         i=i+1;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       }          }
     }  
     /* printf("ii=%d", ij);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
        scanf("%d",i);*/            for(theta=1; theta <=npar; theta++)
   imx=i-1; /* Number of individuals */              trgradg[j][theta]=gradg[theta][j];
           
   /* for (i=1; i<=imx; i++){          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     }*/          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    /*  for (i=1; i<=imx; i++){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
      if (s[4][i]==9)  s[4][i]=-1;  
      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]));}*/          pmij(pmmij,cov,ncovmodel,x,nlstate);
            
            k=0;
   /* Calculation of the number of parameter from char model*/          for(i=1; i<=(nlstate); i++){
   Tvar=ivector(1,15);            for(j=1; j<=(nlstate+ndeath);j++){
   Tprod=ivector(1,15);              k=k+1;
   Tvaraff=ivector(1,15);              mu[k][(int) age]=pmmij[i][j];
   Tvard=imatrix(1,15,1,2);            }
   Tage=ivector(1,15);                }
              for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   if (strlen(model) >1){            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     j=0, j1=0, k1=1, k2=1;              varpij[i][j][(int)age] = doldm[i][j];
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');          /*printf("\n%d ",(int)age);
     cptcovn=j+1;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     cptcovprod=j1;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     strcpy(modelsav,model);            }*/
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);          fprintf(ficresprob,"\n%d ",(int)age);
       goto end;          fprintf(ficresprobcov,"\n%d ",(int)age);
     }          fprintf(ficresprobcor,"\n%d ",(int)age);
      
     for(i=(j+1); i>=1;i--){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       cutv(stra,strb,modelsav,'+');            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       /*scanf("%d",i);*/            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       if (strchr(strb,'*')) {          }
         cutv(strd,strc,strb,'*');          i=0;
         if (strcmp(strc,"age")==0) {          for (k=1; k<=(nlstate);k++){
           cptcovprod--;            for (l=1; l<=(nlstate+ndeath);l++){ 
           cutv(strb,stre,strd,'V');              i=i++;
           Tvar[i]=atoi(stre);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
           cptcovage++;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
             Tage[cptcovage]=i;              for (j=1; j<=i;j++){
             /*printf("stre=%s ", stre);*/                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
         else if (strcmp(strd,"age")==0) {              }
           cptcovprod--;            }
           cutv(strb,stre,strc,'V');          }/* end of loop for state */
           Tvar[i]=atoi(stre);        } /* end of loop for age */
           cptcovage++;  
           Tage[cptcovage]=i;        /* Confidence intervalle of pij  */
         }        /*
         else {          fprintf(ficgp,"\nset noparametric;unset label");
           cutv(strb,stre,strc,'V');          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           Tvar[i]=ncovcol+k1;          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           cutv(strb,strc,strd,'V');          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);
           Tprod[k1]=i;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           Tvard[k1][1]=atoi(strc);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           Tvard[k1][2]=atoi(stre);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           Tvar[cptcovn+k2]=Tvard[k1][1];        */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        first1=1;
           k1++;        for (k2=1; k2<=(nlstate);k2++){
           k2=k2+2;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         }            if(l2==k2) continue;
       }            j=(k2-1)*(nlstate+ndeath)+l2;
       else {            for (k1=1; k1<=(nlstate);k1++){
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
        /*  scanf("%d",i);*/                if(l1==k1) continue;
       cutv(strd,strc,strb,'V');                i=(k1-1)*(nlstate+ndeath)+l1;
       Tvar[i]=atoi(strc);                if(i<=j) continue;
       }                for (age=bage; age<=fage; age ++){ 
       strcpy(modelsav,stra);                    if ((int)age %5==0){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         scanf("%d",i);*/                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
 }                    mu1=mu[i][(int) age]/stepm*YEARM ;
                      mu2=mu[j][(int) age]/stepm*YEARM;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                    c12=cv12/sqrt(v1*v2);
   printf("cptcovprod=%d ", cptcovprod);                    /* Computing eigen value of matrix of covariance */
   scanf("%d ",i);*/                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     fclose(fic);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
     /*  if(mle==1){*/                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     if (weightopt != 1) { /* Maximisation without weights*/                    /*v21=sqrt(1.-v11*v11); *//* error */
       for(i=1;i<=n;i++) weight[i]=1.0;                    v21=(lc1-v1)/cv12*v11;
     }                    v12=-v21;
     /*-calculation of age at interview from date of interview and age at death -*/                    v22=v11;
     agev=matrix(1,maxwav,1,imx);                    tnalp=v21/v11;
                     if(first1==1){
     for (i=1; i<=imx; i++) {                      first1=0;
       for(m=2; (m<= maxwav); m++) {                      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);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                    }
          anint[m][i]=9999;                    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);
          s[m][i]=-1;                    /*printf(fignu*/
        }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       }                    if(first==1){
     }                      first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
     for (i=1; i<=imx; 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);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       for(m=1; (m<= maxwav); m++){                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
         if(s[m][i] >0){   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
           if (s[m][i] >= nlstate+1) {  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
             if(agedc[i]>0)                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
               if(moisdc[i]!=99 && andc[i]!=9999)                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 agev[m][i]=agedc[i];                      fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
            else {                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
               if (andc[i]!=9999){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
               agev[m][i]=-1;                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
               }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
             }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           }                    }else{
           else if(s[m][i] !=9){ /* Should no more exist */                      first=0;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
             if(mint[m][i]==99 || anint[m][i]==9999)                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
               agev[m][i]=1;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
             else if(agev[m][i] <agemin){                      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",\
               agemin=agev[m][i];                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
             }                    }/* if first */
             else if(agev[m][i] >agemax){                  } /* age mod 5 */
               agemax=agev[m][i];                } /* end loop age */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
             }                first=1;
             /*agev[m][i]=anint[m][i]-annais[i];*/              } /*l12 */
             /*   agev[m][i] = age[i]+2*m;*/            } /* k12 */
           }          } /*l1 */
           else { /* =9 */        }/* k1 */
             agev[m][i]=1;      } /* loop covariates */
             s[m][i]=-1;    }
           }    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
         else /*= 0 Unknown */    free_vector(xp,1,npar);
           agev[m][i]=1;    fclose(ficresprob);
       }    fclose(ficresprobcov);
        fclose(ficresprobcor);
     }    /*  fclose(ficgp);*/
     for (i=1; i<=imx; i++)  {  }
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {  
           printf("Error: Wrong value in nlstate or ndeath\n");    /******************* Printing html file ***********/
           goto end;  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[],\
     }                    int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     free_vector(severity,1,maxwav);    /*char optionfilehtm[FILENAMELENGTH];*/
     free_imatrix(outcome,1,maxwav+1,1,n);  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
     free_vector(moisnais,1,n);  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
     free_vector(annais,1,n);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
     /* free_matrix(mint,1,maxwav,1,n);  /*   } */
        free_matrix(anint,1,maxwav,1,n);*/  
     free_vector(moisdc,1,n);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
     free_vector(andc,1,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 \
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
       - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
     wav=ivector(1,imx);   - Life expectancies by age and initial health status (estepm=%2d months): \
     dh=imatrix(1,lastpass-firstpass+1,1,imx);     <a href=\"%s\">%s</a> <br>\n</li>", \
     mw=imatrix(1,lastpass-firstpass+1,1,imx);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
                 stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
     /* Concatenates waves */             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       Tcode=ivector(1,100);  
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);   m=cptcoveff;
       ncodemax[1]=1;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
         jj1=0;
    codtab=imatrix(1,100,1,10);   for(k1=1; k1<=m;k1++){
    h=0;     for(i1=1; i1<=ncodemax[k1];i1++){
    m=pow(2,cptcoveff);       jj1++;
         if (cptcovn > 0) {
    for(k=1;k<=cptcoveff; k++){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
      for(i=1; i <=(m/pow(2,k));i++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
        for(j=1; j <= ncodemax[k]; j++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
            h++;       }
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;       /* Pij */
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/       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> \
          }  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        }       /* Quasi-incidences */
      }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    }   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
       codtab[1][2]=1;codtab[2][2]=2; */         /* Stable prevalence in each health state */
    /* for(i=1; i <=m ;i++){         for(cpt=1; cpt<nlstate;cpt++){
       for(k=1; k <=cptcovn; k++){           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
       }         }
       printf("\n");       for(cpt=1; cpt<=nlstate;cpt++) {
       }          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
       scanf("%d",i);*/  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
           }
    /* Calculates basic frequencies. Computes observed prevalence at single age       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
        and prints on file fileres'p'. */  health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
         } /* end i1 */
       }/* End k1 */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   fprintf(fichtm,"</ul>");
     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 */   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
         - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
     /* For Powell, parameters are in a vector p[] starting at p[1]   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
     if(mle==1){   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);           rfileres,rfileres,\
     }           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
               subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
     /*--------- results files --------------*/           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
     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);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
             subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
    jk=1;  
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  /*  if(popforecast==1) fprintf(fichtm,"\n */
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
    for(i=1,jk=1; i <=nlstate; i++){  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
      for(k=1; k <=(nlstate+ndeath); k++){  /*      <br>",fileres,fileres,fileres,fileres); */
        if (k != i)  /*  else  */
          {  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
            printf("%d%d ",i,k);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){   m=cptcoveff;
              printf("%f ",p[jk]);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
              fprintf(ficres,"%f ",p[jk]);  
              jk++;   jj1=0;
            }   for(k1=1; k1<=m;k1++){
            printf("\n");     for(i1=1; i1<=ncodemax[k1];i1++){
            fprintf(ficres,"\n");       jj1++;
          }       if (cptcovn > 0) {
      }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
    }         for (cpt=1; cpt<=cptcoveff;cpt++) 
  if(mle==1){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     /* Computing hessian and covariance matrix */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     ftolhess=ftol; /* Usually correct */       }
     hesscov(matcov, p, npar, delti, ftolhess, func);       for(cpt=1; cpt<=nlstate;cpt++) {
  }         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  interval) in state (%d): %s%d%d.png <br>\
     printf("# Scales (for hessian or gradient estimation)\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
      for(i=1,jk=1; i <=nlstate; i++){       }
       for(j=1; j <=nlstate+ndeath; j++){     } /* end i1 */
         if (j!=i) {   }/* End k1 */
           fprintf(ficres,"%1d%1d",i,j);   fprintf(fichtm,"</ul>");
           printf("%1d%1d",i,j);   fflush(fichtm);
           for(k=1; k<=ncovmodel;k++){  }
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);  /******************* Gnuplot file **************/
             jk++;  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
           }  
           printf("\n");    char dirfileres[132],optfileres[132];
           fprintf(ficres,"\n");    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         }    int ng;
       }  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
      }  /*     printf("Problem with file %s",optionfilegnuplot); */
      /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
     k=1;  /*   } */
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");  
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    /*#ifdef windows */
     for(i=1;i<=npar;i++){    fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*  if (k>nlstate) k=1;      /*#endif */
       i1=(i-1)/(ncovmodel*nlstate)+1;    m=pow(2,cptcoveff);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/    strcpy(dirfileres,optionfilefiname);
       fprintf(ficres,"%3d",i);    strcpy(optfileres,"vpl");
       printf("%3d",i);   /* 1eme*/
       for(j=1; j<=i;j++){    for (cpt=1; cpt<= nlstate ; cpt ++) {
         fprintf(ficres," %.5e",matcov[i][j]);     for (k1=1; k1<= m ; k1 ++) {
         printf(" %.5e",matcov[i][j]);       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);
       fprintf(ficres,"\n");       fprintf(ficgp,"set xlabel \"Age\" \n\
       printf("\n");  set ylabel \"Probability\" \n\
       k++;  set ter png small\n\
     }  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);
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);       for (i=1; i<= nlstate ; i ++) {
       fgets(line, MAXLINE, ficpar);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       puts(line);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       fputs(line,ficparo);       }
     }       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);
     ungetc(c,ficpar);       for (i=1; i<= nlstate ; i ++) {
     estepm=0;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     if (estepm==0 || estepm < stepm) estepm=stepm;       } 
     if (fage <= 2) {       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
       bage = ageminpar;       for (i=1; i<= nlstate ; i ++) {
       fage = agemaxpar;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     }         else fprintf(ficgp," \%%*lf (\%%*lf)");
           }  
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     fprintf(ficres,"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);    }
      /*2 eme*/
     while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    for (k1=1; k1<= m ; k1 ++) { 
     fgets(line, MAXLINE, ficpar);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     puts(line);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     fputs(line,ficparo);      
   }      for (i=1; i<= nlstate+1 ; i ++) {
   ungetc(c,ficpar);        k=2*i;
          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        for (j=1; j<= nlstate+1 ; j ++) {
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          else fprintf(ficgp," \%%*lf (\%%*lf)");
              }   
   while((c=getc(ficpar))=='#' && c!= EOF){        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     ungetc(c,ficpar);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     fgets(line, MAXLINE, ficpar);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     puts(line);        for (j=1; j<= nlstate+1 ; j ++) {
     fputs(line,ficparo);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   }          else fprintf(ficgp," \%%*lf (\%%*lf)");
   ungetc(c,ficpar);        }   
          fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        for (j=1; j<= nlstate+1 ; j ++) {
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   fscanf(ficpar,"pop_based=%d\n",&popbased);        }   
   fprintf(ficparo,"pop_based=%d\n",popbased);          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   fprintf(ficres,"pop_based=%d\n",popbased);          else fprintf(ficgp,"\" t\"\" w l 0,");
        }
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    /*3eme*/
     puts(line);    
     fputs(line,ficparo);    for (k1=1; k1<= m ; k1 ++) { 
   }      for (cpt=1; cpt<= nlstate ; cpt ++) {
   ungetc(c,ficpar);        k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);        fprintf(ficgp,"set ter png small\n\
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  set size 0.65,0.65\n\
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     ungetc(c,ficpar);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     fgets(line, MAXLINE, ficpar);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     puts(line);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     fputs(line,ficparo);          
   }        */
   ungetc(c,ficpar);        for (i=1; i< nlstate ; i ++) {
           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);
   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,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
     /* CV preval stable (period) */
 /*------------ gnuplot -------------*/    for (k1=1; k1<= m ; k1 ++) { 
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);      for (cpt=1; cpt<=nlstate ; cpt ++) {
          k=3;
 /*------------ free_vector  -------------*/        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
  chdir(path);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
    set ter png small\nset size 0.65,0.65\n\
  free_ivector(wav,1,imx);  unset log y\n\
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          
  free_ivector(num,1,n);        for (i=1; i< nlstate ; i ++)
  free_vector(agedc,1,n);          fprintf(ficgp,"+$%d",k+i+1);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
  fclose(ficparo);        
  fclose(ficres);        l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
 /*--------- index.htm --------*/        for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);          fprintf(ficgp,"+$%d",l+i+1);
         }
          fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   /*--------------- Prevalence limit --------------*/      } 
      }  
   strcpy(filerespl,"pl");    
   strcat(filerespl,fileres);    /* proba elementaires */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    for(i=1,jk=1; i <=nlstate; i++){
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      for(k=1; k <=(nlstate+ndeath); k++){
   }        if (k != i) {
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          for(j=1; j <=ncovmodel; j++){
   fprintf(ficrespl,"#Prevalence limit\n");            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   fprintf(ficrespl,"#Age ");            jk++; 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            fprintf(ficgp,"\n");
   fprintf(ficrespl,"\n");          }
          }
   prlim=matrix(1,nlstate,1,nlstate);      }
   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 */     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       for(jk=1; jk <=m; jk++) {
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
   k=0;         if (ng==2)
   agebase=ageminpar;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   agelim=agemaxpar;         else
   ftolpl=1.e-10;           fprintf(ficgp,"\nset title \"Probability\"\n");
   i1=cptcoveff;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   if (cptcovn < 1){i1=1;}         i=1;
          for(k2=1; k2<=nlstate; k2++) {
   for(cptcov=1;cptcov<=i1;cptcov++){           k3=i;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           for(k=1; k<=(nlstate+ndeath); k++) {
         k=k+1;             if (k != k2){
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/               if(ng==2)
         fprintf(ficrespl,"\n#******");                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
         for(j=1;j<=cptcoveff;j++)               else
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
         fprintf(ficrespl,"******\n");               ij=1;
                       for(j=3; j <=ncovmodel; j++) {
         for (age=agebase; age<=agelim; age++){                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           fprintf(ficrespl,"%.0f",age );                   ij++;
           for(i=1; i<=nlstate;i++)                 }
           fprintf(ficrespl," %.5f", prlim[i][i]);                 else
           fprintf(ficrespl,"\n");                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         }               }
       }               fprintf(ficgp,")/(1");
     }               
   fclose(ficrespl);               for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   /*------------- h Pij x at various ages ------------*/                 ij=1;
                   for(j=3; j <=ncovmodel; j++){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                     ij++;
   }                   }
   printf("Computing pij: result on file '%s' \n", filerespij);                   else
                       fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   stepsize=(int) (stepm+YEARM-1)/YEARM;                 }
   /*if (stepm<=24) stepsize=2;*/                 fprintf(ficgp,")");
                }
   agelim=AGESUP;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   hstepm=stepsize*YEARM; /* Every year of age */               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */               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(ficrespij,"\n#****** ");     fflush(ficgp); 
         for(j=1;j<=cptcoveff;j++)  }  /* end gnuplot */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");  
          /*************** Moving average **************/
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int i, cpt, cptcod;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int modcovmax =1;
           oldm=oldms;savm=savms;    int mobilavrange, mob;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double age;
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
             for(j=1; j<=nlstate+ndeath;j++)                             a covariate has 2 modalities */
               fprintf(ficrespij," %1d-%1d",i,j);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
           fprintf(ficrespij,"\n");  
            for (h=0; h<=nhstepm; h++){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      if(mobilav==1) mobilavrange=5; /* default */
             for(i=1; i<=nlstate;i++)      else mobilavrange=mobilav;
               for(j=1; j<=nlstate+ndeath;j++)      for (age=bage; age<=fage; age++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        for (i=1; i<=nlstate;i++)
             fprintf(ficrespij,"\n");          for (cptcod=1;cptcod<=modcovmax;cptcod++)
              }            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* We keep the original values on the extreme ages bage, fage and for 
           fprintf(ficrespij,"\n");         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
         }         we use a 5 terms etc. until the borders are no more concerned. 
     }      */ 
   }      for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
   fclose(ficrespij);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   /*---------- Forecasting ------------------*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   if((stepm == 1) && (strcmp(model,".")==0)){                }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);            }
   }          }
   else{        }/* end age */
     erreur=108;      }/* end mob */
     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);    }else return -1;
   }    return 0;
    }/* End movingaverage */
   
   /*---------- Health expectancies and variances ------------*/  
   /************** Forecasting ******************/
   strcpy(filerest,"t");  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){
   strcat(filerest,fileres);    /* proj1, year, month, day of starting projection 
   if((ficrest=fopen(filerest,"w"))==NULL) {       agemin, agemax range of age
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;       dateprev1 dateprev2 range of dates during which prevalence is computed
   }       anproj2 year of en of projection (same day and month as proj1).
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
   strcpy(filerese,"e");    double agec; /* generic age */
   strcat(filerese,fileres);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   if((ficreseij=fopen(filerese,"w"))==NULL) {    double *popeffectif,*popcount;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    double ***p3mat;
   }    double ***mobaverage;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    char fileresf[FILENAMELENGTH];
   
  strcpy(fileresv,"v");    agelim=AGESUP;
   strcat(fileresv,fileres);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {   
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    strcpy(fileresf,"f"); 
   }    strcat(fileresf,fileres);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    if((ficresf=fopen(fileresf,"w"))==NULL) {
   calagedate=-1;      printf("Problem with forecast resultfile: %s\n", fileresf);
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
   k=0;    printf("Computing forecasting: result on file '%s' \n", fileresf);
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    if (mobilav!=0) {
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficrest,"******\n");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       fprintf(ficreseij,"\n#****** ");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       for(j=1;j<=cptcoveff;j++)      }
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
       fprintf(ficreseij,"******\n");  
     stepsize=(int) (stepm+YEARM-1)/YEARM;
       fprintf(ficresvij,"\n#****** ");    if (stepm<=12) stepsize=1;
       for(j=1;j<=cptcoveff;j++)    if(estepm < stepm){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficresvij,"******\n");    }
     else  hstepm=estepm;   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    hstepm=hstepm/stepm; 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                   fractional in yp1 */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    anprojmean=yp;
       oldm=oldms;savm=savms;    yp2=modf((yp1*12),&yp);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    mprojmean=yp;
        yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
      if(jprojmean==0) jprojmean=1;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    if(mprojmean==0) jprojmean=1;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");    i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
       epj=vector(1,nlstate+1);    
       for(age=bage; age <=fage ;age++){    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    
         if (popbased==1) {    fprintf(ficresf,"#****** Routine prevforecast **\n");
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][k];  /*            if (h==(int)(YEARM*yearp)){ */
         }    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
              for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         fprintf(ficrest," %4.0f",age);        k=k+1;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        fprintf(ficresf,"\n#******");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        for(j=1;j<=cptcoveff;j++) {
             epj[j] += prlim[i][i]*eij[i][j][(int)age];          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]]);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/        }
           }        fprintf(ficresf,"******\n");
           epj[nlstate+1] +=epj[j];        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         }        for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
         for(i=1, vepp=0.;i <=nlstate;i++)            fprintf(ficresf," p%d%d",i,j);
           for(j=1;j <=nlstate;j++)          fprintf(ficresf," p.%d",j);
             vepp += vareij[i][j][(int)age];        }
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
         for(j=1;j <=nlstate;j++){          fprintf(ficresf,"\n");
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
         }  
         fprintf(ficrest,"\n");          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);
 free_matrix(mint,1,maxwav,1,n);            oldm=oldms;savm=savms;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
     free_vector(weight,1,n);          
   fclose(ficreseij);            for (h=0; h<=nhstepm; h++){
   fclose(ficresvij);              if (h*hstepm/YEARM*stepm ==yearp) {
   fclose(ficrest);                fprintf(ficresf,"\n");
   fclose(ficpar);                for(j=1;j<=cptcoveff;j++) 
   free_vector(epj,1,nlstate+1);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                  fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
   /*------- Variance limit prevalence------*/                } 
               for(j=1; j<=nlstate+ndeath;j++) {
   strcpy(fileresvpl,"vpl");                ppij=0.;
   strcat(fileresvpl,fileres);                for(i=1; i<=nlstate;i++) {
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                  if (mobilav==1) 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
     exit(0);                  else {
   }                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                  }
                   if (h*hstepm/YEARM*stepm== yearp) {
   k=0;                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
   for(cptcov=1;cptcov<=i1;cptcov++){                  }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                } /* end i */
       k=k+1;                if (h*hstepm/YEARM*stepm==yearp) {
       fprintf(ficresvpl,"\n#****** ");                  fprintf(ficresf," %.3f", ppij);
       for(j=1;j<=cptcoveff;j++)                }
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              }/* end j */
       fprintf(ficresvpl,"******\n");            } /* end h */
                  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          } /* end agec */
       oldm=oldms;savm=savms;        } /* end yearp */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      } /* end cptcod */
     }    } /* end  cptcov */
  }         
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficresvpl);  
     fclose(ficresf);
   /*---------- End : free ----------------*/  }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
    /************** Forecasting *****not tested NB*************/
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  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){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    
      int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
      int *popage;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    double calagedatem, agelim, kk1, kk2;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    double *popeffectif,*popcount;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    double ***p3mat,***tabpop,***tabpopprev;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    double ***mobaverage;
      char filerespop[FILENAMELENGTH];
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_matrix(agev,1,maxwav,1,imx);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   if(erreur >0)    
     printf("End of Imach with error or warning %d\n",erreur);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   else   printf("End of Imach\n");    
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    
      strcpy(filerespop,"pop"); 
   /* 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);*/    strcat(filerespop,fileres);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   /*------ End -----------*/      printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
  end:    printf("Computing forecasting: result on file '%s' \n", filerespop);
 #ifdef windows    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   /* chdir(pathcd);*/  
 #endif    if (cptcoveff==0) ncodemax[cptcoveff]=1;
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/    if (mobilav!=0) {
  /*system("cd ../gp37mgw");*/      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
  strcpy(plotcmd,GNUPLOTPROGRAM);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  strcat(plotcmd," ");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  strcat(plotcmd,optionfilegnuplot);      }
  system(plotcmd);    }
   
 #ifdef windows    stepsize=(int) (stepm+YEARM-1)/YEARM;
   while (z[0] != 'q') {    if (stepm<=12) stepsize=1;
     /* chdir(path); */    
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    agelim=AGESUP;
     scanf("%s",z);    
     if (z[0] == 'c') system("./imach");    hstepm=1;
     else if (z[0] == 'e') system(optionfilehtm);    hstepm=hstepm/stepm; 
     else if (z[0] == 'g') system(plotcmd);    
     else if (z[0] == 'q') exit(0);    if (popforecast==1) {
   }      if((ficpop=fopen(popfile,"r"))==NULL) {
 #endif        printf("Problem with population file : %s\n",popfile);exit(0);
 }        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     }
   
   } /* end of prwizard */
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
     struct timeval start_time, end_time, curr_time;
     struct timezone tzp;
     extern int gettimeofday();
     struct tm tmg, tm, *gmtime(), *localtime();
     long time_value;
     extern long time();
    
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Localtime (at start):%s",strstart);
     fprintf(ficlog,"Localtime (at start): %s",strstart);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
             model,fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     /*fclose(fichtm);*/
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     strcpy(lfileres,fileres);
     strcat(lfileres,"/");
     strcat(lfileres,optionfilefiname);
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Localtime at start %s\nLocal time at end   %s",strstart, strtend); 
     /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
   
     printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(ficgp);
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
     chdir(path);
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
   

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  Added in v.1.90


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