Diff for /imach/src/imach.c between versions 1.18 and 1.87

version 1.18, 2002/02/20 17:17:09 version 1.87, 2003/06/18 12:26:01
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.87  2003/06/18 12:26:01  brouard
   individuals from different ages are interviewed on their health status    Version 0.96
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.86  2003/06/17 20:04:08  brouard
   Health expectancies are computed from the transistions observed between    (Module): Change position of html and gnuplot routines and added
   waves and are computed for each degree of severity of disability (number    routine fileappend.
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.85  2003/06/17 13:12:43  brouard
   The simplest model is the multinomial logistic model where pij is    * imach.c (Repository): Check when date of death was earlier that
   the probabibility to be observed in state j at the second wave conditional    current date of interview. It may happen when the death was just
   to be observed in state i at the first wave. Therefore the model is:    prior to the death. In this case, dh was negative and likelihood
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    was wrong (infinity). We still send an "Error" but patch by
   is a covariate. If you want to have a more complex model than "constant and    assuming that the date of death was just one stepm after the
   age", you should modify the program where the markup    interview.
     *Covariates have to be included here again* invites you to do it.    (Repository): Because some people have very long ID (first column)
   More covariates you add, less is the speed of the convergence.    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
   The advantage that this computer programme claims, comes from that if the    truncation)
   delay between waves is not identical for each individual, or if some    (Repository): No more line truncation errors.
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.84  2003/06/13 21:44:43  brouard
   hPijx is the probability to be    * imach.c (Repository): Replace "freqsummary" at a correct
   observed in state i at age x+h conditional to the observed state i at age    place. It differs from routine "prevalence" which may be called
   x. The delay 'h' can be split into an exact number (nh*stepm) of    many times. Probs is memory consuming and must be used with
   unobserved intermediate  states. This elementary transition (by month or    parcimony.
   quarter trimester, semester or year) is model as a multinomial logistic.    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply hPijx.    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.82  2003/06/05 15:57:20  brouard
      Add log in  imach.c and  fullversion number is now printed.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.  */
   This software have been partly granted by Euro-REVES, a concerted action  /*
   from the European Union.     Interpolated Markov Chain
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Short summary of the programme:
   can be accessed at http://euroreves.ined.fr/imach .    
   **********************************************************************/    This program computes Healthy Life Expectancies from
      cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #include <math.h>    first survey ("cross") where individuals from different ages are
 #include <stdio.h>    interviewed on their health status or degree of disability (in the
 #include <stdlib.h>    case of a health survey which is our main interest) -2- at least a
 #include <unistd.h>    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 #define MAXLINE 256    computed from the time spent in each health state according to a
 #define FILENAMELENGTH 80    model. More health states you consider, more time is necessary to reach the
 /*#define DEBUG*/    Maximum Likelihood of the parameters involved in the model.  The
 #define windows    simplest model is the multinomial logistic model where pij is the
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    probability to be observed in state j at the second wave
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    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 MAXPARM 30 /* Maximum number of parameters for the optimization */    'age' is age and 'sex' is a covariate. If you want to have a more
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 #define NINTERVMAX 8    you to do it.  More covariates you add, slower the
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    convergence.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    The advantage of this computer programme, compared to a simple
 #define MAXN 20000    multinomial logistic model, is clear when the delay between waves is not
 #define YEARM 12. /* Number of months per year */    identical for each individual. Also, if a individual missed an
 #define AGESUP 130    intermediate interview, the information is lost, but taken into
 #define AGEBASE 40    account using an interpolation or extrapolation.  
   
     hPijx is the probability to be observed in state i at age x+h
 int nvar;    conditional to the observed state i at age x. The delay 'h' can be
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    split into an exact number (nh*stepm) of unobserved intermediate
 int npar=NPARMAX;    states. This elementary transition (by month, quarter,
 int nlstate=2; /* Number of live states */    semester or year) is modelled as a multinomial logistic.  The hPx
 int ndeath=1; /* Number of dead states */    matrix is simply the matrix product of nh*stepm elementary matrices
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    and the contribution of each individual to the likelihood is simply
 int popbased=0;    hPijx.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Also this programme outputs the covariance matrix of the parameters but also
 int maxwav; /* Maxim number of waves */    of the life expectancies. It also computes the stable prevalence. 
 int jmin, jmax; /* min, max spacing between 2 waves */    
 int mle, weightopt;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */             Institut national d'études démographiques, Paris.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    This software have been partly granted by Euro-REVES, a concerted action
 double jmean; /* Mean space between 2 waves */    from the European Union.
 double **oldm, **newm, **savm; /* Working pointers to matrices */    It is copyrighted identically to a GNU software product, ie programme and
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    software can be distributed freely for non commercial use. Latest version
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    can be accessed at http://euroreves.ined.fr/imach .
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;  
 FILE *ficreseij;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   char filerese[FILENAMELENGTH];    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
  FILE  *ficresvij;    
   char fileresv[FILENAMELENGTH];    **********************************************************************/
  FILE  *ficresvpl;  /*
   char fileresvpl[FILENAMELENGTH];    main
     read parameterfile
 #define NR_END 1    read datafile
 #define FREE_ARG char*    concatwav
 #define FTOL 1.0e-10    freqsummary
     if (mle >= 1)
 #define NRANSI      mlikeli
 #define ITMAX 200    print results files
     if mle==1 
 #define TOL 2.0e-4       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 #define CGOLD 0.3819660        begin-prev-date,...
 #define ZEPS 1.0e-10    open gnuplot file
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    open html file
     stable prevalence
 #define GOLD 1.618034     for age prevalim()
 #define GLIMIT 100.0    h Pij x
 #define TINY 1.0e-20    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 static double maxarg1,maxarg2;    health expectancies
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Variance-covariance of DFLE
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    prevalence()
       movingaverage()
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    varevsij() 
 #define rint(a) floor(a+0.5)    if popbased==1 varevsij(,popbased)
     total life expectancies
 static double sqrarg;    Variance of stable prevalence
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)   end
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  */
   
 int imx;  
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/   
   #include <math.h>
 int m,nb;  #include <stdio.h>
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #include <stdlib.h>
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #include <unistd.h>
 double **pmmij, ***probs, ***mobaverage;  
   #include <sys/time.h>
 double *weight;  #include <time.h>
 int **s; /* Status */  #include "timeval.h"
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double ftolhess; /* Tolerance for computing hessian */  #define FILENAMELENGTH 132
   /*#define DEBUG*/
 /**************** split *************************/  /*#define windows*/
 static  int split( char *path, char *dirc, char *name )  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define NINTERVMAX 8
    s = strrchr( path, '\\' );           /* find last / */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    if ( s == NULL ) {                   /* no directory, so use current */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #if     defined(__bsd__)                /* get current working directory */  #define NCOVMAX 8 /* Maximum number of covariates */
       extern char       *getwd( );  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
       if ( getwd( dirc ) == NULL ) {  #define AGESUP 130
 #else  #define AGEBASE 40
       extern char       *getcwd( );  #ifdef unix
   #define DIRSEPARATOR '/'
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define ODIRSEPARATOR '\\'
 #endif  #else
          return( GLOCK_ERROR_GETCWD );  #define DIRSEPARATOR '\\'
       }  #define ODIRSEPARATOR '/'
       strcpy( name, path );             /* we've got it */  #endif
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  /* $Id$ */
       l2 = strlen( s );                 /* length of filename */  /* $State$ */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */  char version[]="Imach version 0.96, June 2003, INED-EUROREVES ";
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  char fullversion[]="$Revision$ $Date$"; 
       dirc[l1-l2] = 0;                  /* add zero */  int erreur; /* Error number */
    }  int nvar;
    l1 = strlen( dirc );                 /* length of directory */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int npar=NPARMAX;
    return( 0 );                         /* we're done */  int nlstate=2; /* Number of live states */
 }  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 /******************************************/  
   int *wav; /* Number of waves for this individuual 0 is possible */
 void replace(char *s, char*t)  int maxwav; /* Maxim number of waves */
 {  int jmin, jmax; /* min, max spacing between 2 waves */
   int i;  int gipmx, gsw; /* Global variables on the number of contributions 
   int lg=20;                     to the likelihood and the sum of weights (done by funcone)*/
   i=0;  int mle, weightopt;
   lg=strlen(t);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   for(i=0; i<= lg; i++) {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     (s[i] = t[i]);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     if (t[i]== '\\') s[i]='/';             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   }  double jmean; /* Mean space between 2 waves */
 }  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 int nbocc(char *s, char occ)  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 {  FILE *ficlog, *ficrespow;
   int i,j=0;  int globpr; /* Global variable for printing or not */
   int lg=20;  double fretone; /* Only one call to likelihood */
   i=0;  long ipmx; /* Number of contributions */
   lg=strlen(s);  double sw; /* Sum of weights */
   for(i=0; i<= lg; i++) {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   if  (s[i] == occ ) j++;  FILE *ficresilk;
   }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   return j;  FILE *ficresprobmorprev;
 }  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 void cutv(char *u,char *v, char*t, char occ)  char filerese[FILENAMELENGTH];
 {  FILE  *ficresvij;
   int i,lg,j,p=0;  char fileresv[FILENAMELENGTH];
   i=0;  FILE  *ficresvpl;
   for(j=0; j<=strlen(t)-1; j++) {  char fileresvpl[FILENAMELENGTH];
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  char title[MAXLINE];
   }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   lg=strlen(t);  
   for(j=0; j<p; j++) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     (u[j] = t[j]);  char filelog[FILENAMELENGTH]; /* Log file */
   }  char filerest[FILENAMELENGTH];
      u[p]='\0';  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   }  
 }  #define NR_END 1
   #define FREE_ARG char*
 /********************** nrerror ********************/  #define FTOL 1.0e-10
   
 void nrerror(char error_text[])  #define NRANSI 
 {  #define ITMAX 200 
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  #define TOL 2.0e-4 
   exit(1);  
 }  #define CGOLD 0.3819660 
 /*********************** vector *******************/  #define ZEPS 1.0e-10 
 double *vector(int nl, int nh)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 {  
   double *v;  #define GOLD 1.618034 
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define GLIMIT 100.0 
   if (!v) nrerror("allocation failure in vector");  #define TINY 1.0e-20 
   return v-nl+NR_END;  
 }  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 /************************ free vector ******************/  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 void free_vector(double*v, int nl, int nh)    
 {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   free((FREE_ARG)(v+nl-NR_END));  #define rint(a) floor(a+0.5)
 }  
   static double sqrarg;
 /************************ivector *******************************/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 int *ivector(long nl,long nh)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 {  
   int *v;  int imx; 
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  int stepm;
   if (!v) nrerror("allocation failure in ivector");  /* Stepm, step in month: minimum step interpolation*/
   return v-nl+NR_END;  
 }  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  int m,nb;
 {  long *num;
   free((FREE_ARG)(v+nl-NR_END));  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 /******************* imatrix *******************************/  double dateintmean=0;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  double *weight;
 {  int **s; /* Status */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  double *agedc, **covar, idx;
   int **m;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
    
   /* allocate pointers to rows */  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  double ftolhess; /* Tolerance for computing hessian */
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /**************** split *************************/
   m -= nrl;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    {
      char  *ss;                            /* pointer */
   /* allocate rows and set pointers to them */    int   l1, l2;                         /* length counters */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    l1 = strlen(path );                   /* length of path */
   m[nrl] += NR_END;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   m[nrl] -= ncl;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      if ( ss == NULL ) {                   /* no directory, so use current */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
          printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   /* return pointer to array of pointers to rows */      /* get current working directory */
   return m;      /*    extern  char* getcwd ( char *buf , int len);*/
 }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
 /****************** free_imatrix *************************/      }
 void free_imatrix(m,nrl,nrh,ncl,nch)      strcpy( name, path );               /* we've got it */
       int **m;    } else {                              /* strip direcotry from path */
       long nch,ncl,nrh,nrl;      ss++;                               /* after this, the filename */
      /* free an int matrix allocated by imatrix() */      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   free((FREE_ARG) (m[nrl]+ncl-NR_END));      strcpy( name, ss );         /* save file name */
   free((FREE_ARG) (m+nrl-NR_END));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 }      dirc[l1-l2] = 0;                    /* add zero */
     }
 /******************* matrix *******************************/    l1 = strlen( dirc );                  /* length of directory */
 double **matrix(long nrl, long nrh, long ncl, long nch)    /*#ifdef windows
 {    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #else
   double **m;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    */
   if (!m) nrerror("allocation failure 1 in matrix()");    ss = strrchr( name, '.' );            /* find last / */
   m += NR_END;    ss++;
   m -= nrl;    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    l2= strlen(ss)+1;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    strncpy( finame, name, l1-l2);
   m[nrl] += NR_END;    finame[l1-l2]= 0;
   m[nrl] -= ncl;    return( 0 );                          /* we're done */
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  
 }  /******************************************/
   
 /*************************free matrix ************************/  void replace(char *s, char*t)
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  {
 {    int i;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int lg=20;
   free((FREE_ARG)(m+nrl-NR_END));    i=0;
 }    lg=strlen(t);
     for(i=0; i<= lg; i++) {
 /******************* ma3x *******************************/      (s[i] = t[i]);
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)      if (t[i]== '\\') s[i]='/';
 {    }
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  }
   double ***m;  
   int nbocc(char *s, char occ)
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    int i,j=0;
   m += NR_END;    int lg=20;
   m -= nrl;    i=0;
     lg=strlen(s);
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    for(i=0; i<= lg; i++) {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if  (s[i] == occ ) j++;
   m[nrl] += NR_END;    }
   m[nrl] -= ncl;    return j;
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   void cutv(char *u,char *v, char*t, char occ)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  {
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    /* cuts string t into u and v where u is ended by char occ excluding it
   m[nrl][ncl] += NR_END;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   m[nrl][ncl] -= nll;       gives u="abcedf" and v="ghi2j" */
   for (j=ncl+1; j<=nch; j++)    int i,lg,j,p=0;
     m[nrl][j]=m[nrl][j-1]+nlay;    i=0;
      for(j=0; j<=strlen(t)-1; j++) {
   for (i=nrl+1; i<=nrh; i++) {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    }
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;    lg=strlen(t);
   }    for(j=0; j<p; j++) {
   return m;      (u[j] = t[j]);
 }    }
        u[p]='\0';
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)     for(j=0; j<= lg; j++) {
 {      if (j>=(p+1))(v[j-p-1] = t[j]);
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  }
   free((FREE_ARG)(m+nrl-NR_END));  
 }  /********************** nrerror ********************/
   
 /***************** f1dim *************************/  void nrerror(char error_text[])
 extern int ncom;  {
 extern double *pcom,*xicom;    fprintf(stderr,"ERREUR ...\n");
 extern double (*nrfunc)(double []);    fprintf(stderr,"%s\n",error_text);
      exit(EXIT_FAILURE);
 double f1dim(double x)  }
 {  /*********************** vector *******************/
   int j;  double *vector(int nl, int nh)
   double f;  {
   double *xt;    double *v;
      v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   xt=vector(1,ncom);    if (!v) nrerror("allocation failure in vector");
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    return v-nl+NR_END;
   f=(*nrfunc)(xt);  }
   free_vector(xt,1,ncom);  
   return f;  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /*****************brent *************************/    free((FREE_ARG)(v+nl-NR_END));
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  }
 {  
   int iter;  /************************ivector *******************************/
   double a,b,d,etemp;  int *ivector(long nl,long nh)
   double fu,fv,fw,fx;  {
   double ftemp;    int *v;
   double p,q,r,tol1,tol2,u,v,w,x,xm;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   double e=0.0;    if (!v) nrerror("allocation failure in ivector");
      return v-nl+NR_END;
   a=(ax < cx ? ax : cx);  }
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  /******************free ivector **************************/
   fw=fv=fx=(*f)(x);  void free_ivector(int *v, long nl, long nh)
   for (iter=1;iter<=ITMAX;iter++) {  {
     xm=0.5*(a+b);    free((FREE_ARG)(v+nl-NR_END));
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  }
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  /************************lvector *******************************/
 #ifdef DEBUG  long *lvector(long nl,long nh)
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    long *v;
 #endif    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if (!v) nrerror("allocation failure in ivector");
       *xmin=x;    return v-nl+NR_END;
       return fx;  }
     }  
     ftemp=fu;  /******************free lvector **************************/
     if (fabs(e) > tol1) {  void free_lvector(long *v, long nl, long nh)
       r=(x-w)*(fx-fv);  {
       q=(x-v)*(fx-fw);    free((FREE_ARG)(v+nl-NR_END));
       p=(x-v)*q-(x-w)*r;  }
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /******************* imatrix *******************************/
       q=fabs(q);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       etemp=e;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       e=d;  { 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    int **m; 
       else {    
         d=p/q;    /* allocate pointers to rows */ 
         u=x+d;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         if (u-a < tol2 || b-u < tol2)    if (!m) nrerror("allocation failure 1 in matrix()"); 
           d=SIGN(tol1,xm-x);    m += NR_END; 
       }    m -= nrl; 
     } else {    
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    
     }    /* allocate rows and set pointers to them */ 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     fu=(*f)(u);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     if (fu <= fx) {    m[nrl] += NR_END; 
       if (u >= x) a=x; else b=x;    m[nrl] -= ncl; 
       SHFT(v,w,x,u)    
         SHFT(fv,fw,fx,fu)    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         } else {    
           if (u < x) a=u; else b=u;    /* return pointer to array of pointers to rows */ 
           if (fu <= fw || w == x) {    return m; 
             v=w;  } 
             w=u;  
             fv=fw;  /****************** free_imatrix *************************/
             fw=fu;  void free_imatrix(m,nrl,nrh,ncl,nch)
           } else if (fu <= fv || v == x || v == w) {        int **m;
             v=u;        long nch,ncl,nrh,nrl; 
             fv=fu;       /* free an int matrix allocated by imatrix() */ 
           }  { 
         }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   }    free((FREE_ARG) (m+nrl-NR_END)); 
   nrerror("Too many iterations in brent");  } 
   *xmin=x;  
   return fx;  /******************* matrix *******************************/
 }  double **matrix(long nrl, long nrh, long ncl, long nch)
   {
 /****************** mnbrak ***********************/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   double ulim,u,r,q, dum;    m += NR_END;
   double fu;    m -= nrl;
    
   *fa=(*func)(*ax);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   *fb=(*func)(*bx);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   if (*fb > *fa) {    m[nrl] += NR_END;
     SHFT(dum,*ax,*bx,dum)    m[nrl] -= ncl;
       SHFT(dum,*fb,*fa,dum)  
       }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   *cx=(*bx)+GOLD*(*bx-*ax);    return m;
   *fc=(*func)(*cx);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   while (*fb > *fc) {     */
     r=(*bx-*ax)*(*fb-*fc);  }
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  /*************************free matrix ************************/
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     ulim=(*bx)+GLIMIT*(*cx-*bx);  {
     if ((*bx-u)*(u-*cx) > 0.0) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       fu=(*func)(u);    free((FREE_ARG)(m+nrl-NR_END));
     } else if ((*cx-u)*(u-ulim) > 0.0) {  }
       fu=(*func)(u);  
       if (fu < *fc) {  /******************* ma3x *******************************/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
           SHFT(*fb,*fc,fu,(*func)(u))  {
           }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    double ***m;
       u=ulim;  
       fu=(*func)(u);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     } else {    if (!m) nrerror("allocation failure 1 in matrix()");
       u=(*cx)+GOLD*(*cx-*bx);    m += NR_END;
       fu=(*func)(u);    m -= nrl;
     }  
     SHFT(*ax,*bx,*cx,u)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       SHFT(*fa,*fb,*fc,fu)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       }    m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /*************** linmin ************************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
 int ncom;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 double *pcom,*xicom;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 double (*nrfunc)(double []);    m[nrl][ncl] += NR_END;
      m[nrl][ncl] -= nll;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    for (j=ncl+1; j<=nch; j++) 
 {      m[nrl][j]=m[nrl][j-1]+nlay;
   double brent(double ax, double bx, double cx,    
                double (*f)(double), double tol, double *xmin);    for (i=nrl+1; i<=nrh; i++) {
   double f1dim(double x);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      for (j=ncl+1; j<=nch; j++) 
               double *fc, double (*func)(double));        m[i][j]=m[i][j-1]+nlay;
   int j;    }
   double xx,xmin,bx,ax;    return m; 
   double fx,fb,fa;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
               &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   ncom=n;    */
   pcom=vector(1,n);  }
   xicom=vector(1,n);  
   nrfunc=func;  /*************************free ma3x ************************/
   for (j=1;j<=n;j++) {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     pcom[j]=p[j];  {
     xicom[j]=xi[j];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   ax=0.0;    free((FREE_ARG)(m+nrl-NR_END));
   xx=1.0;  }
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  /***************** f1dim *************************/
 #ifdef DEBUG  extern int ncom; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  extern double *pcom,*xicom;
 #endif  extern double (*nrfunc)(double []); 
   for (j=1;j<=n;j++) {   
     xi[j] *= xmin;  double f1dim(double x) 
     p[j] += xi[j];  { 
   }    int j; 
   free_vector(xicom,1,n);    double f;
   free_vector(pcom,1,n);    double *xt; 
 }   
     xt=vector(1,ncom); 
 /*************** powell ************************/    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    f=(*nrfunc)(xt); 
             double (*func)(double []))    free_vector(xt,1,ncom); 
 {    return f; 
   void linmin(double p[], double xi[], int n, double *fret,  } 
               double (*func)(double []));  
   int i,ibig,j;  /*****************brent *************************/
   double del,t,*pt,*ptt,*xit;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   double fp,fptt;  { 
   double *xits;    int iter; 
   pt=vector(1,n);    double a,b,d,etemp;
   ptt=vector(1,n);    double fu,fv,fw,fx;
   xit=vector(1,n);    double ftemp;
   xits=vector(1,n);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   *fret=(*func)(p);    double e=0.0; 
   for (j=1;j<=n;j++) pt[j]=p[j];   
   for (*iter=1;;++(*iter)) {    a=(ax < cx ? ax : cx); 
     fp=(*fret);    b=(ax > cx ? ax : cx); 
     ibig=0;    x=w=v=bx; 
     del=0.0;    fw=fv=fx=(*f)(x); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    for (iter=1;iter<=ITMAX;iter++) { 
     for (i=1;i<=n;i++)      xm=0.5*(a+b); 
       printf(" %d %.12f",i, p[i]);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     printf("\n");      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for (i=1;i<=n;i++) {      printf(".");fflush(stdout);
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      fprintf(ficlog,".");fflush(ficlog);
       fptt=(*fret);  #ifdef DEBUG
 #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);
       printf("fret=%lf \n",*fret);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 #endif      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       printf("%d",i);fflush(stdout);  #endif
       linmin(p,xit,n,fret,func);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       if (fabs(fptt-(*fret)) > del) {        *xmin=x; 
         del=fabs(fptt-(*fret));        return fx; 
         ibig=i;      } 
       }      ftemp=fu;
 #ifdef DEBUG      if (fabs(e) > tol1) { 
       printf("%d %.12e",i,(*fret));        r=(x-w)*(fx-fv); 
       for (j=1;j<=n;j++) {        q=(x-v)*(fx-fw); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);        p=(x-v)*q-(x-w)*r; 
         printf(" x(%d)=%.12e",j,xit[j]);        q=2.0*(q-r); 
       }        if (q > 0.0) p = -p; 
       for(j=1;j<=n;j++)        q=fabs(q); 
         printf(" p=%.12e",p[j]);        etemp=e; 
       printf("\n");        e=d; 
 #endif        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        else { 
 #ifdef DEBUG          d=p/q; 
       int k[2],l;          u=x+d; 
       k[0]=1;          if (u-a < tol2 || b-u < tol2) 
       k[1]=-1;            d=SIGN(tol1,xm-x); 
       printf("Max: %.12e",(*func)(p));        } 
       for (j=1;j<=n;j++)      } else { 
         printf(" %.12e",p[j]);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       printf("\n");      } 
       for(l=0;l<=1;l++) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         for (j=1;j<=n;j++) {      fu=(*f)(u); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      if (fu <= fx) { 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        if (u >= x) a=x; else b=x; 
         }        SHFT(v,w,x,u) 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));          SHFT(fv,fw,fx,fu) 
       }          } else { 
 #endif            if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
               v=w; 
       free_vector(xit,1,n);              w=u; 
       free_vector(xits,1,n);              fv=fw; 
       free_vector(ptt,1,n);              fw=fu; 
       free_vector(pt,1,n);            } else if (fu <= fv || v == x || v == w) { 
       return;              v=u; 
     }              fv=fu; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");            } 
     for (j=1;j<=n;j++) {          } 
       ptt[j]=2.0*p[j]-pt[j];    } 
       xit[j]=p[j]-pt[j];    nrerror("Too many iterations in brent"); 
       pt[j]=p[j];    *xmin=x; 
     }    return fx; 
     fptt=(*func)(ptt);  } 
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  /****************** mnbrak ***********************/
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         for (j=1;j<=n;j++) {              double (*func)(double)) 
           xi[j][ibig]=xi[j][n];  { 
           xi[j][n]=xit[j];    double ulim,u,r,q, dum;
         }    double fu; 
 #ifdef DEBUG   
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    *fa=(*func)(*ax); 
         for(j=1;j<=n;j++)    *fb=(*func)(*bx); 
           printf(" %.12e",xit[j]);    if (*fb > *fa) { 
         printf("\n");      SHFT(dum,*ax,*bx,dum) 
 #endif        SHFT(dum,*fb,*fa,dum) 
       }        } 
     }    *cx=(*bx)+GOLD*(*bx-*ax); 
   }    *fc=(*func)(*cx); 
 }    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
 /**** Prevalence limit ****************/      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 {      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      if ((*bx-u)*(u-*cx) > 0.0) { 
      matrix by transitions matrix until convergence is reached */        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
   int i, ii,j,k;        fu=(*func)(u); 
   double min, max, maxmin, maxmax,sumnew=0.;        if (fu < *fc) { 
   double **matprod2();          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double **out, cov[NCOVMAX], **pmij();            SHFT(*fb,*fc,fu,(*func)(u)) 
   double **newm;            } 
   double agefin, delaymax=50 ; /* Max number of years to converge */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
   for (ii=1;ii<=nlstate+ndeath;ii++)        fu=(*func)(u); 
     for (j=1;j<=nlstate+ndeath;j++){      } else { 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        u=(*cx)+GOLD*(*cx-*bx); 
     }        fu=(*func)(u); 
       } 
    cov[1]=1.;      SHFT(*ax,*bx,*cx,u) 
          SHFT(*fa,*fb,*fc,fu) 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        } 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  } 
     newm=savm;  
     /* Covariates have to be included here again */  /*************** linmin ************************/
      cov[2]=agefin;  
    int ncom; 
       for (k=1; k<=cptcovn;k++) {  double *pcom,*xicom;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  double (*nrfunc)(double []); 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/   
       }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       for (k=1; k<=cptcovage;k++)  { 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    double brent(double ax, double bx, double cx, 
       for (k=1; k<=cptcovprod;k++)                 double (*f)(double), double tol, double *xmin); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/                double *fc, double (*func)(double)); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    int j; 
     double xx,xmin,bx,ax; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    double fx,fb,fa;
    
     savm=oldm;    ncom=n; 
     oldm=newm;    pcom=vector(1,n); 
     maxmax=0.;    xicom=vector(1,n); 
     for(j=1;j<=nlstate;j++){    nrfunc=func; 
       min=1.;    for (j=1;j<=n;j++) { 
       max=0.;      pcom[j]=p[j]; 
       for(i=1; i<=nlstate; i++) {      xicom[j]=xi[j]; 
         sumnew=0;    } 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    ax=0.0; 
         prlim[i][j]= newm[i][j]/(1-sumnew);    xx=1.0; 
         max=FMAX(max,prlim[i][j]);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         min=FMIN(min,prlim[i][j]);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       }  #ifdef DEBUG
       maxmin=max-min;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       maxmax=FMAX(maxmax,maxmin);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }  #endif
     if(maxmax < ftolpl){    for (j=1;j<=n;j++) { 
       return prlim;      xi[j] *= xmin; 
     }      p[j] += xi[j]; 
   }    } 
 }    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
 /*************** transition probabilities ***************/  } 
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /*************** powell ************************/
 {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   double s1, s2;              double (*func)(double [])) 
   /*double t34;*/  { 
   int i,j,j1, nc, ii, jj;    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
     for(i=1; i<= nlstate; i++){    int i,ibig,j; 
     for(j=1; j<i;j++){    double del,t,*pt,*ptt,*xit;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double fp,fptt;
         /*s2 += param[i][j][nc]*cov[nc];*/    double *xits;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    pt=vector(1,n); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    ptt=vector(1,n); 
       }    xit=vector(1,n); 
       ps[i][j]=s2;    xits=vector(1,n); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    *fret=(*func)(p); 
     }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for(j=i+1; j<=nlstate+ndeath;j++){    for (*iter=1;;++(*iter)) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      fp=(*fret); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      ibig=0; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      del=0.0; 
       }      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       ps[i][j]=(s2);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     }      fprintf(ficrespow,"%d %.12f",*iter,*fret);
   }      for (i=1;i<=n;i++) {
     /*ps[3][2]=1;*/        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
   for(i=1; i<= nlstate; i++){        fprintf(ficrespow," %.12lf", p[i]);
      s1=0;      }
     for(j=1; j<i; j++)      printf("\n");
       s1+=exp(ps[i][j]);      fprintf(ficlog,"\n");
     for(j=i+1; j<=nlstate+ndeath; j++)      fprintf(ficrespow,"\n");
       s1+=exp(ps[i][j]);      for (i=1;i<=n;i++) { 
     ps[i][i]=1./(s1+1.);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     for(j=1; j<i; j++)        fptt=(*fret); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #ifdef DEBUG
     for(j=i+1; j<=nlstate+ndeath; j++)        printf("fret=%lf \n",*fret);
       ps[i][j]= exp(ps[i][j])*ps[i][i];        fprintf(ficlog,"fret=%lf \n",*fret);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #endif
   } /* end i */        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        linmin(p,xit,n,fret,func); 
     for(jj=1; jj<= nlstate+ndeath; jj++){        if (fabs(fptt-(*fret)) > del) { 
       ps[ii][jj]=0;          del=fabs(fptt-(*fret)); 
       ps[ii][ii]=1;          ibig=i; 
     }        } 
   }  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        for (j=1;j<=n;j++) {
     for(jj=1; jj<= nlstate+ndeath; jj++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
      printf("%lf ",ps[ii][jj]);          printf(" x(%d)=%.12e",j,xit[j]);
    }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     printf("\n ");        }
     }        for(j=1;j<=n;j++) {
     printf("\n ");printf("%lf ",cov[2]);*/          printf(" p=%.12e",p[j]);
 /*          fprintf(ficlog," p=%.12e",p[j]);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        }
   goto end;*/        printf("\n");
     return ps;        fprintf(ficlog,"\n");
 }  #endif
       } 
 /**************** Product of 2 matrices ******************/      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        int k[2],l;
 {        k[0]=1;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        k[1]=-1;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        printf("Max: %.12e",(*func)(p));
   /* in, b, out are matrice of pointers which should have been initialized        fprintf(ficlog,"Max: %.12e",(*func)(p));
      before: only the contents of out is modified. The function returns        for (j=1;j<=n;j++) {
      a pointer to pointers identical to out */          printf(" %.12e",p[j]);
   long i, j, k;          fprintf(ficlog," %.12e",p[j]);
   for(i=nrl; i<= nrh; i++)        }
     for(k=ncolol; k<=ncoloh; k++)        printf("\n");
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        fprintf(ficlog,"\n");
         out[i][k] +=in[i][j]*b[j][k];        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
   return out;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
 /************* Higher Matrix Product ***************/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        }
 {  #endif
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        free_vector(xit,1,n); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        free_vector(xits,1,n); 
      (typically every 2 years instead of every month which is too big).        free_vector(ptt,1,n); 
      Model is determined by parameters x and covariates have to be        free_vector(pt,1,n); 
      included manually here.        return; 
       } 
      */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
   int i, j, d, h, k;        ptt[j]=2.0*p[j]-pt[j]; 
   double **out, cov[NCOVMAX];        xit[j]=p[j]-pt[j]; 
   double **newm;        pt[j]=p[j]; 
       } 
   /* Hstepm could be zero and should return the unit matrix */      fptt=(*func)(ptt); 
   for (i=1;i<=nlstate+ndeath;i++)      if (fptt < fp) { 
     for (j=1;j<=nlstate+ndeath;j++){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        if (t < 0.0) { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);          linmin(p,xit,n,fret,func); 
     }          for (j=1;j<=n;j++) { 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */            xi[j][ibig]=xi[j][n]; 
   for(h=1; h <=nhstepm; h++){            xi[j][n]=xit[j]; 
     for(d=1; d <=hstepm; d++){          }
       newm=savm;  #ifdef DEBUG
       /* Covariates have to be included here again */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       cov[1]=1.;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          for(j=1;j<=n;j++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            printf(" %.12e",xit[j]);
       for (k=1; k<=cptcovage;k++)            fprintf(ficlog," %.12e",xit[j]);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          }
       for (k=1; k<=cptcovprod;k++)          printf("\n");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          fprintf(ficlog,"\n");
   #endif
         }
       /*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));  
       savm=oldm;  /**** Prevalence limit (stable prevalence)  ****************/
       oldm=newm;  
     }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for(i=1; i<=nlstate+ndeath; i++)  {
       for(j=1;j<=nlstate+ndeath;j++) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         po[i][j][h]=newm[i][j];       matrix by transitions matrix until convergence is reached */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */    int i, ii,j,k;
       }    double min, max, maxmin, maxmax,sumnew=0.;
   } /* end h */    double **matprod2();
   return po;    double **out, cov[NCOVMAX], **pmij();
 }    double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
   
 /*************** log-likelihood *************/    for (ii=1;ii<=nlstate+ndeath;ii++)
 double func( double *x)      for (j=1;j<=nlstate+ndeath;j++){
 {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, ii, j, k, mi, d, kk;      }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;     cov[1]=1.;
   double sw; /* Sum of weights */   
   double lli; /* Individual log likelihood */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   long ipmx;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   /*extern weight */      newm=savm;
   /* We are differentiating ll according to initial status */      /* Covariates have to be included here again */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/       cov[2]=agefin;
   /*for(i=1;i<imx;i++)    
     printf(" %d\n",s[4][i]);        for (k=1; k<=cptcovn;k++) {
   */          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   cov[1]=1.;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         }
   for(k=1; k<=nlstate; k++) ll[k]=0.;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        for (k=1; k<=cptcovprod;k++)
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       for(d=0; d<dh[mi][i]; d++){        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         newm=savm;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {      savm=oldm;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      oldm=newm;
         }      maxmax=0.;
              for(j=1;j<=nlstate;j++){
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        min=1.;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        max=0.;
         savm=oldm;        for(i=1; i<=nlstate; i++) {
         oldm=newm;          sumnew=0;
                  for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
                  prlim[i][j]= newm[i][j]/(1-sumnew);
       } /* end mult */          max=FMAX(max,prlim[i][j]);
                min=FMIN(min,prlim[i][j]);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        maxmin=max-min;
       ipmx +=1;        maxmax=FMAX(maxmax,maxmin);
       sw += weight[i];      }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      if(maxmax < ftolpl){
     } /* end of wave */        return prlim;
   } /* 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 */  /*************** transition probabilities ***************/ 
   return -l;  
 }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
     double s1, s2;
 /*********** Maximum Likelihood Estimation ***************/    /*double t34;*/
     int i,j,j1, nc, ii, jj;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {      for(i=1; i<= nlstate; i++){
   int i,j, iter;      for(j=1; j<i;j++){
   double **xi,*delti;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double fret;          /*s2 += param[i][j][nc]*cov[nc];*/
   xi=matrix(1,npar,1,npar);          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   for (i=1;i<=npar;i++)          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
     for (j=1;j<=npar;j++)        }
       xi[i][j]=(i==j ? 1.0 : 0.0);        ps[i][j]=s2;
   printf("Powell\n");        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   powell(p,xi,npar,ftol,&iter,&fret,func);      }
       for(j=i+1; j<=nlstate+ndeath;j++){
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
 }        }
         ps[i][j]=s2;
 /**** Computes Hessian and covariance matrix ***/      }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    }
 {      /*ps[3][2]=1;*/
   double  **a,**y,*x,pd;  
   double **hess;    for(i=1; i<= nlstate; i++){
   int i, j,jk;       s1=0;
   int *indx;      for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
   double hessii(double p[], double delta, int theta, double delti[]);      for(j=i+1; j<=nlstate+ndeath; j++)
   double hessij(double p[], double delti[], int i, int j);        s1+=exp(ps[i][j]);
   void lubksb(double **a, int npar, int *indx, double b[]) ;      ps[i][i]=1./(s1+1.);
   void ludcmp(double **a, int npar, int *indx, double *d) ;      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
   hess=matrix(1,npar,1,npar);      for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
   printf("\nCalculation of the hessian matrix. Wait...\n");      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   for (i=1;i<=npar;i++){    } /* end i */
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     /*printf(" %f ",p[i]);*/      for(jj=1; jj<= nlstate+ndeath; jj++){
     /*printf(" %lf ",hess[i][i]);*/        ps[ii][jj]=0;
   }        ps[ii][ii]=1;
        }
   for (i=1;i<=npar;i++) {    }
     for (j=1;j<=npar;j++)  {  
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
         hess[i][j]=hessij(p,delti,i,j);      for(jj=1; jj<= nlstate+ndeath; jj++){
         hess[j][i]=hess[i][j];           printf("%lf ",ps[ii][jj]);
         /*printf(" %lf ",hess[i][j]);*/     }
       }      printf("\n ");
     }      }
   }      printf("\n ");printf("%lf ",cov[2]);*/
   printf("\n");  /*
     for(i=1; i<= npar; i++) printf("%f ",x[i]);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    goto end;*/
        return ps;
   a=matrix(1,npar,1,npar);  }
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);  /**************** Product of 2 matrices ******************/
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  {
   ludcmp(a,npar,indx,&pd);    /* 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(...) */
   for (j=1;j<=npar;j++) {    /* in, b, out are matrice of pointers which should have been initialized 
     for (i=1;i<=npar;i++) x[i]=0;       before: only the contents of out is modified. The function returns
     x[j]=1;       a pointer to pointers identical to out */
     lubksb(a,npar,indx,x);    long i, j, k;
     for (i=1;i<=npar;i++){    for(i=nrl; i<= nrh; i++)
       matcov[i][j]=x[i];      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];
   
   printf("\n#Hessian matrix#\n");    return out;
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  
     }  /************* Higher Matrix Product ***************/
     printf("\n");  
   }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
   /* Recompute Inverse */    /* Computes the transition matrix starting at age 'age' over 
   for (i=1;i<=npar;i++)       'nhstepm*hstepm*stepm' months (i.e. until
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   ludcmp(a,npar,indx,&pd);       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   /*  printf("\n#Hessian matrix recomputed#\n");       (typically every 2 years instead of every month which is too big 
        for the memory).
   for (j=1;j<=npar;j++) {       Model is determined by parameters x and covariates have to be 
     for (i=1;i<=npar;i++) x[i]=0;       included manually here. 
     x[j]=1;  
     lubksb(a,npar,indx,x);       */
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];    int i, j, d, h, k;
       printf("%.3e ",y[i][j]);    double **out, cov[NCOVMAX];
     }    double **newm;
     printf("\n");  
   }    /* Hstepm could be zero and should return the unit matrix */
   */    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   free_matrix(a,1,npar,1,npar);        oldm[i][j]=(i==j ? 1.0 : 0.0);
   free_matrix(y,1,npar,1,npar);        po[i][j][0]=(i==j ? 1.0 : 0.0);
   free_vector(x,1,npar);      }
   free_ivector(indx,1,npar);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   free_matrix(hess,1,npar,1,npar);    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
         newm=savm;
 }        /* Covariates have to be included here again */
         cov[1]=1.;
 /*************** hessian matrix ****************/        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 double hessii( double x[], double delta, int theta, double delti[])        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 {        for (k=1; k<=cptcovage;k++)
   int i;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   int l=1, lmax=20;        for (k=1; k<=cptcovprod;k++)
   double k1,k2;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double p2[NPARMAX+1];  
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   double fx;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   int k=0,kmax=10;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double l1;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
   fx=func(x);        oldm=newm;
   for (i=1;i<=npar;i++) p2[i]=x[i];      }
   for(l=0 ; l <=lmax; l++){      for(i=1; i<=nlstate+ndeath; i++)
     l1=pow(10,l);        for(j=1;j<=nlstate+ndeath;j++) {
     delts=delt;          po[i][j][h]=newm[i][j];
     for(k=1 ; k <kmax; k=k+1){          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       delt = delta*(l1*k);           */
       p2[theta]=x[theta] +delt;        }
       k1=func(p2)-fx;    } /* end h */
       p2[theta]=x[theta]-delt;    return po;
       k2=func(p2)-fx;  }
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
        /*************** log-likelihood *************/
 #ifdef DEBUG  double func( double *x)
       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);  {
 #endif    int i, ii, j, k, mi, d, kk;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    double **out;
         k=kmax;    double sw; /* Sum of weights */
       }    double lli; /* Individual log likelihood */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    int s1, s2;
         k=kmax; l=lmax*10.;    double bbh, survp;
       }    long ipmx;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    /*extern weight */
         delts=delt;    /* We are differentiating ll according to initial status */
       }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     }    /*for(i=1;i<imx;i++) 
   }      printf(" %d\n",s[4][i]);
   delti[theta]=delts;    */
   return res;    cov[1]=1.;
    
 }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 double hessij( double x[], double delti[], int thetai,int thetaj)    if(mle==1){
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int l=1, l1, lmax=20;        for(mi=1; mi<= wav[i]-1; mi++){
   double k1,k2,k3,k4,res,fx;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double p2[NPARMAX+1];            for (j=1;j<=nlstate+ndeath;j++){
   int k;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fx=func(x);            }
   for (k=1; k<=2; k++) {          for(d=0; d<dh[mi][i]; d++){
     for (i=1;i<=npar;i++) p2[i]=x[i];            newm=savm;
     p2[thetai]=x[thetai]+delti[thetai]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            for (kk=1; kk<=cptcovage;kk++) {
     k1=func(p2)-fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
     p2[thetai]=x[thetai]+delti[thetai]/k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     k2=func(p2)-fx;            savm=oldm;
              oldm=newm;
     p2[thetai]=x[thetai]-delti[thetai]/k;          } /* end mult */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        
     k3=func(p2)-fx;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
            /* But now since version 0.9 we anticipate for bias and large stepm.
     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 
     k4=func(p2)-fx;           * the nearest (and in case of equal distance, to the lowest) interval but now
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 #ifdef DEBUG           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     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);           * probability in order to take into account the bias as a fraction of the way
 #endif           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   }           * -stepm/2 to stepm/2 .
   return res;           * For stepm=1 the results are the same as for previous versions of Imach.
 }           * For stepm > 1 the results are less biased than in previous versions. 
            */
 /************** Inverse of matrix **************/          s1=s[mw[mi][i]][i];
 void ludcmp(double **a, int n, int *indx, double *d)          s2=s[mw[mi+1][i]][i];
 {          bbh=(double)bh[mi][i]/(double)stepm; 
   int i,imax,j,k;          /* bias is positive if real duration
   double big,dum,sum,temp;           * is higher than the multiple of stepm and negative otherwise.
   double *vv;           */
            /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   vv=vector(1,n);          if( s2 > nlstate){ 
   *d=1.0;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   for (i=1;i<=n;i++) {               to the likelihood is the probability to die between last step unit time and current 
     big=0.0;               step unit time, which is also the differences between probability to die before dh 
     for (j=1;j<=n;j++)               and probability to die before dh-stepm . 
       if ((temp=fabs(a[i][j])) > big) big=temp;               In version up to 0.92 likelihood was computed
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          as if date of death was unknown. Death was treated as any other
     vv[i]=1.0/big;          health state: the date of the interview describes the actual state
   }          and not the date of a change in health state. The former idea was
   for (j=1;j<=n;j++) {          to consider that at each interview the state was recorded
     for (i=1;i<j;i++) {          (healthy, disable or death) and IMaCh was corrected; but when we
       sum=a[i][j];          introduced the exact date of death then we should have modified
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          the contribution of an exact death to the likelihood. This new
       a[i][j]=sum;          contribution is smaller and very dependent of the step unit
     }          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 (i=j;i<=n;i++) {          interview up to one month before death multiplied by the
       sum=a[i][j];          probability to die within a month. Thanks to Chris
       for (k=1;k<j;k++)          Jackson for correcting this bug.  Former versions increased
         sum -= a[i][k]*a[k][j];          mortality artificially. The bad side is that we add another loop
       a[i][j]=sum;          which slows down the processing. The difference can be up to 10%
       if ( (dum=vv[i]*fabs(sum)) >= big) {          lower mortality.
         big=dum;            */
         imax=i;            lli=log(out[s1][s2] - savm[s1][s2]);
       }          }else{
     }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     if (j != imax) {            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       for (k=1;k<=n;k++) {          } 
         dum=a[imax][k];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         a[imax][k]=a[j][k];          /*if(lli ==000.0)*/
         a[j][k]=dum;          /*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;
       *d = -(*d);          sw += weight[i];
       vv[imax]=vv[j];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     indx[j]=imax;      } /* end of individual */
     if (a[j][j] == 0.0) a[j][j]=TINY;    }  else if(mle==2){
     if (j != n) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       dum=1.0/(a[j][j]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   free_vector(vv,1,n);  /* Doesn't work */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 ;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<=dh[mi][i]; d++){
 void lubksb(double **a, int n, int *indx, double b[])            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i,ii=0,ip,j;            for (kk=1; kk<=cptcovage;kk++) {
   double sum;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   for (i=1;i<=n;i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     ip=indx[i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     sum=b[ip];            savm=oldm;
     b[ip]=b[i];            oldm=newm;
     if (ii)          } /* end mult */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        
     else if (sum) ii=i;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     b[i]=sum;          /* But now since version 0.9 we anticipate for bias and large stepm.
   }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   for (i=n;i>=1;i--) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
     sum=b[i];           * the nearest (and in case of equal distance, to the lowest) interval but now
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     b[i]=sum/a[i][i];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   }           * probability in order to take into account the bias as a fraction of the way
 }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
 /************ Frequencies ********************/           * For stepm=1 the results are the same as for previous versions of Imach.
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1,double **mint,double **anint, int boolprev, double dateprev1,double dateprev2)           * For stepm > 1 the results are less biased than in previous versions. 
 {  /* Some frequencies */           */
            s1=s[mw[mi][i]][i];
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          s2=s[mw[mi+1][i]][i];
   double ***freq; /* Frequencies */          bbh=(double)bh[mi][i]/(double)stepm; 
   double *pp;          /* bias is positive if real duration
   double pos, k2;           * is higher than the multiple of stepm and negative otherwise.
   FILE *ficresp;           */
   char fileresp[FILENAMELENGTH];          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]));*/
   pp=vector(1,nlstate);          /*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 */
   probs= ma3x(1,130 ,1,8, 1,8);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   strcpy(fileresp,"p");          /*if(lli ==000.0)*/
   strcat(fileresp,fileres);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   if((ficresp=fopen(fileresp,"w"))==NULL) {          ipmx +=1;
     printf("Problem with prevalence resultfile: %s\n", fileresp);          sw += weight[i];
     exit(0);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      } /* end of individual */
   j1=0;    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   j=cptcoveff;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   for(k1=1; k1<=j;k1++){            for (j=1;j<=nlstate+ndeath;j++){
    for(i1=1; i1<=ncodemax[k1];i1++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        j1++;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            }
          scanf("%d", i);*/          for(d=0; d<dh[mi][i]; d++){
         for (i=-1; i<=nlstate+ndeath; i++)              newm=savm;
          for (jk=-1; jk<=nlstate+ndeath; jk++)              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
            for(m=agemin; m <= agemax+3; m++)            for (kk=1; kk<=cptcovage;kk++) {
              freq[i][jk][m]=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                    }
        for (i=1; i<=imx; i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
          bool=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          if  (cptcovn>0) {            savm=oldm;
            for (z1=1; z1<=cptcoveff; z1++)            oldm=newm;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          } /* end mult */
                bool=0;        
          }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
          if (bool==1) {          /* But now since version 0.9 we anticipate for bias and large stepm.
            if (boolprev==1){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
              for(m=fprev1; m<=lprev1; m++){           * (in months) between two waves is not a multiple of stepm, we rounded to 
                if(agev[m][i]==0) agev[m][i]=agemax+1;           * the nearest (and in case of equal distance, to the lowest) interval but now
                if(agev[m][i]==1) agev[m][i]=agemax+2;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];           * probability in order to take into account the bias as a fraction of the way
              }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            }           * -stepm/2 to stepm/2 .
            else {           * For stepm=1 the results are the same as for previous versions of Imach.
             for(m=firstpass; m<=lastpass; m++){           * For stepm > 1 the results are less biased than in previous versions. 
              k2=anint[m][i]+(mint[m][i]/12.);           */
              if ((k2>=dateprev1) && (k2<=dateprev2)) {          s1=s[mw[mi][i]][i];
              if(agev[m][i]==0) agev[m][i]=agemax+1;          s2=s[mw[mi+1][i]][i];
              if(agev[m][i]==1) agev[m][i]=agemax+2;          bbh=(double)bh[mi][i]/(double)stepm; 
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          /* bias is positive if real duration
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];           * is higher than the multiple of stepm and negative otherwise.
              }           */
             }          /* 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])); /* exponential inter-extrapolation */
           }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
        }          /*if(lli ==000.0)*/
         if  (cptcovn>0) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          fprintf(ficresp, "\n#********** Variable ");          ipmx +=1;
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          sw += weight[i];
        fprintf(ficresp, "**********\n#");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
        for(i=1; i<=nlstate;i++)      } /* end of individual */
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
        fprintf(ficresp, "\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for(i=(int)agemin; i <= (int)agemax+3; i++){        for(mi=1; mi<= wav[i]-1; mi++){
     if(i==(int)agemax+3)          for (ii=1;ii<=nlstate+ndeath;ii++)
       printf("Total");            for (j=1;j<=nlstate+ndeath;j++){
     else              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("Age %d", i);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(jk=1; jk <=nlstate ; jk++){            }
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          for(d=0; d<dh[mi][i]; d++){
         pp[jk] += freq[jk][m][i];            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(jk=1; jk <=nlstate ; jk++){            for (kk=1; kk<=cptcovage;kk++) {
       for(m=-1, pos=0; m <=0 ; m++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         pos += freq[jk][m][i];            }
       if(pp[jk]>=1.e-10)          
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            savm=oldm;
     }            oldm=newm;
           } /* end mult */
      for(jk=1; jk <=nlstate ; jk++){        
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          s1=s[mw[mi][i]][i];
         pp[jk] += freq[jk][m][i];          s2=s[mw[mi+1][i]][i];
      }          if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
     for(jk=1,pos=0; jk <=nlstate ; jk++)          }else{
       pos += pp[jk];            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(jk=1; jk <=nlstate ; jk++){          }
       if(pos>=1.e-5)          ipmx +=1;
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          sw += weight[i];
       else          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         printf(" %d.=%.0f prev[%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]); */
       if( i <= (int) agemax){        } /* end of wave */
         if(pos>=1.e-5){      } /* end of individual */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           probs[i][jk][j1]= pp[jk]/pos;      for (i=1,ipmx=0, sw=0.; i<=imx; 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 (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
       else          for (ii=1;ii<=nlstate+ndeath;ii++)
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(jk=-1; jk <=nlstate+ndeath; jk++)            }
       for(m=-1; m <=nlstate+ndeath; m++)          for(d=0; d<dh[mi][i]; d++){
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            newm=savm;
     if(i <= (int) agemax)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       fprintf(ficresp,"\n");            for (kk=1; kk<=cptcovage;kk++) {
     printf("\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
     }          
  }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fclose(ficresp);            savm=oldm;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            oldm=newm;
   free_vector(pp,1,nlstate);          } /* end mult */
         
 }  /* End of Freq */          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 /************ Prevalence ********************/          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1, double **mint,double **anint,int boolprev, double dateprev1, double dateprev2)          ipmx +=1;
 {  /* Some frequencies */          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          /*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]);*/
   double ***freq; /* Frequencies */        } /* end of wave */
   double *pp;      } /* end of individual */
   double pos, k2;    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   pp=vector(1,nlstate);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   probs= ma3x(1,130 ,1,8, 1,8);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      return -l;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  }
   j1=0;  
    /*************** log-likelihood *************/
   j=cptcoveff;  double funcone( double *x)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  {
      /* Same as likeli but slower because of a lot of printf and if */
  for(k1=1; k1<=j;k1++){    int i, ii, j, k, mi, d, kk;
     for(i1=1; i1<=ncodemax[k1];i1++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       j1++;    double **out;
      double lli; /* Individual log likelihood */
       for (i=-1; i<=nlstate+ndeath; i++)      double llt;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      int s1, s2;
           for(m=agemin; m <= agemax+3; m++)    double bbh, survp;
           freq[i][jk][m]=0;    /*extern weight */
          /* We are differentiating ll according to initial status */
       for (i=1; i<=imx; i++) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         bool=1;    /*for(i=1;i<imx;i++) 
         if  (cptcovn>0) {      printf(" %d\n",s[4][i]);
           for (z1=1; z1<=cptcoveff; z1++)    */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    cov[1]=1.;
               bool=0;  
               }    for(k=1; k<=nlstate; k++) ll[k]=0.;
         if (bool==1) {  
           if (boolprev==1){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             for(m=fprev1; m<=lprev1; m++){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               if(agev[m][i]==0) agev[m][i]=agemax+1;      for(mi=1; mi<= wav[i]-1; mi++){
               if(agev[m][i]==1) agev[m][i]=agemax+2;        for (ii=1;ii<=nlstate+ndeath;ii++)
               freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          for (j=1;j<=nlstate+ndeath;j++){
               freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }          }
           else {        for(d=0; d<dh[mi][i]; d++){
             for(m=firstpass; m<=lastpass; m++){          newm=savm;
               k2=anint[m][i]+(mint[m][i]/12.);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               if ((k2>=dateprev1) && (k2<=dateprev2)) {          for (kk=1; kk<=cptcovage;kk++) {
                 if(agev[m][i]==0) agev[m][i]=agemax+1;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                 if(agev[m][i]==1) agev[m][i]=agemax+2;          }
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               }          savm=oldm;
             }          oldm=newm;
           }        } /* end mult */
         }        
       }        s1=s[mw[mi][i]][i];
         for(i=(int)agemin; i <= (int)agemax+3; i++){        s2=s[mw[mi+1][i]][i];
           for(jk=1; jk <=nlstate ; jk++){        bbh=(double)bh[mi][i]/(double)stepm; 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        /* bias is positive if real duration
               pp[jk] += freq[jk][m][i];         * is higher than the multiple of stepm and negative otherwise.
           }         */
           for(jk=1; jk <=nlstate ; jk++){        if( s2 > nlstate && (mle <5) ){  /* Jackson */
             for(m=-1, pos=0; m <=0 ; m++)          lli=log(out[s1][s2] - savm[s1][s2]);
             pos += freq[jk][m][i];        } else if (mle==1){
         }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                } else if(mle==2){
          for(jk=1; jk <=nlstate ; jk++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        } else if(mle==3){  /* exponential inter-extrapolation */
              pp[jk] += freq[jk][m][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 */
          }        } else if (mle==4){  /* mle=4 no inter-extrapolation */
                    lli=log(out[s1][s2]); /* Original formula */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        } 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 */
            if( i <= (int) agemax){        ipmx +=1;
              if(pos>=1.e-5){        sw += weight[i];
                probs[i][jk][j1]= pp[jk]/pos;        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]); */
            }        if(globpr){
          }          fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
             %10.6f %10.6f %10.6f ", \
         }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
              llt +=ll[k]*gipmx/gsw;
              fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          }
   free_vector(pp,1,nlstate);          fprintf(ficresilk," %10.6f\n", -llt);
          }
 }  /* End of Freq */      } /* end of wave */
 /************* Waves Concatenation ***************/    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    /* 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 */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    if(globpr==0){ /* First time we count the contributions and weights */
      Death is a valid wave (if date is known).      gipmx=ipmx;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      gsw=sw;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    }
      and mw[mi+1][i]. dh depends on stepm.    return -l;
      */  }
   
   int i, mi, m;  
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
      double sum=0., jmean=0.;*/  {
     /* This routine should help understanding what is done with 
   int j, k=0,jk, ju, jl;       the selection of individuals/waves and
   double sum=0.;       to check the exact contribution to the likelihood.
   jmin=1e+5;       Plotting could be done.
   jmax=-1;     */
   jmean=0.;    int k;
   for(i=1; i<=imx; i++){  
     mi=0;    if(*globpri !=0){ /* Just counts and sums no printings */
     m=firstpass;      strcpy(fileresilk,"ilk"); 
     while(s[m][i] <= nlstate){      strcat(fileresilk,fileres);
       if(s[m][i]>=1)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         mw[++mi][i]=m;        printf("Problem with resultfile: %s\n", fileresilk);
       if(m >=lastpass)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         break;      }
       else      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");
         m++;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight out sav ");
     }/* end while */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     if (s[m][i] > nlstate){      for(k=1; k<=nlstate; k++) 
       mi++;     /* Death is another wave */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       /* if(mi==0)  never been interviewed correctly before death */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
          /* Only death is a correct wave */    }
       mw[mi][i]=m;  
     }    *fretone=(*funcone)(p);
     if(*globpri !=0){
     wav[i]=mi;      fclose(ficresilk);
     if(mi==0)      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",fileresilk,fileresilk);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      fflush(fichtm); 
   }    } 
     return;
   for(i=1; i<=imx; i++){  }
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)  /*********** Maximum Likelihood Estimation ***************/
         dh[mi][i]=1;  
       else{  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         if (s[mw[mi+1][i]][i] > nlstate) {  {
           if (agedc[i] < 2*AGESUP) {    int i,j, iter;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    double **xi;
           if(j==0) j=1;  /* Survives at least one month after exam */    double fret;
           k=k+1;    double fretone; /* Only one call to likelihood */
           if (j >= jmax) jmax=j;    char filerespow[FILENAMELENGTH];
           if (j <= jmin) jmin=j;    xi=matrix(1,npar,1,npar);
           sum=sum+j;    for (i=1;i<=npar;i++)
           /* if (j<10) printf("j=%d num=%d ",j,i); */      for (j=1;j<=npar;j++)
           }        xi[i][j]=(i==j ? 1.0 : 0.0);
         }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         else{    strcpy(filerespow,"pow"); 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    strcat(filerespow,fileres);
           k=k+1;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           if (j >= jmax) jmax=j;      printf("Problem with resultfile: %s\n", filerespow);
           else if (j <= jmin)jmin=j;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    }
           sum=sum+j;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         }    for (i=1;i<=nlstate;i++)
         jk= j/stepm;      for(j=1;j<=nlstate+ndeath;j++)
         jl= j -jk*stepm;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         ju= j -(jk+1)*stepm;    fprintf(ficrespow,"\n");
         if(jl <= -ju)  
           dh[mi][i]=jk;    powell(p,xi,npar,ftol,&iter,&fret,func);
         else  
           dh[mi][i]=jk+1;    fclose(ficrespow);
         if(dh[mi][i]==0)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           dh[mi][i]=1; /* At least one step */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     }  
   }  }
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  /**** Computes Hessian and covariance matrix ***/
  }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 /*********** Tricode ****************************/  {
 void tricode(int *Tvar, int **nbcode, int imx)    double  **a,**y,*x,pd;
 {    double **hess;
   int Ndum[20],ij=1, k, j, i;    int i, j,jk;
   int cptcode=0;    int *indx;
   cptcoveff=0;  
      double hessii(double p[], double delta, int theta, double delti[]);
   for (k=0; k<19; k++) Ndum[k]=0;    double hessij(double p[], double delti[], int i, int j);
   for (k=1; k<=7; k++) ncodemax[k]=0;    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {    hess=matrix(1,npar,1,npar);
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;    printf("\nCalculation of the hessian matrix. Wait...\n");
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       if (ij > cptcode) cptcode=ij;    for (i=1;i<=npar;i++){
     }      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
     for (i=0; i<=cptcode; i++) {      hess[i][i]=hessii(p,ftolhess,i,delti);
       if(Ndum[i]!=0) ncodemax[j]++;      /*printf(" %f ",p[i]);*/
     }      /*printf(" %lf ",hess[i][i]);*/
     ij=1;    }
     
     for (i=1;i<=npar;i++) {
     for (i=1; i<=ncodemax[j]; i++) {      for (j=1;j<=npar;j++)  {
       for (k=0; k<=19; k++) {        if (j>i) { 
         if (Ndum[k] != 0) {          printf(".%d%d",i,j);fflush(stdout);
           nbcode[Tvar[j]][ij]=k;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           ij++;          hess[i][j]=hessij(p,delti,i,j);
         }          hess[j][i]=hess[i][j];    
         if (ij > ncodemax[j]) break;          /*printf(" %lf ",hess[i][j]);*/
       }          }
     }      }
   }      }
     printf("\n");
  for (k=0; k<19; k++) Ndum[k]=0;    fprintf(ficlog,"\n");
   
  for (i=1; i<=ncovmodel-2; i++) {    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       ij=Tvar[i];    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       Ndum[ij]++;    
     }    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
  ij=1;    x=vector(1,npar);
  for (i=1; i<=10; i++) {    indx=ivector(1,npar);
    if((Ndum[i]!=0) && (i<=ncov)){    for (i=1;i<=npar;i++)
      Tvaraff[ij]=i;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
      ij++;    ludcmp(a,npar,indx,&pd);
    }  
  }    for (j=1;j<=npar;j++) {
        for (i=1;i<=npar;i++) x[i]=0;
     cptcoveff=ij-1;      x[j]=1;
 }      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
 /*********** Health Expectancies ****************/        matcov[i][j]=x[i];
       }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    }
 {  
   /* Health expectancies */    printf("\n#Hessian matrix#\n");
   int i, j, nhstepm, hstepm, h;    fprintf(ficlog,"\n#Hessian matrix#\n");
   double age, agelim,hf;    for (i=1;i<=npar;i++) { 
   double ***p3mat;      for (j=1;j<=npar;j++) { 
          printf("%.3e ",hess[i][j]);
   fprintf(ficreseij,"# Health expectancies\n");        fprintf(ficlog,"%.3e ",hess[i][j]);
   fprintf(ficreseij,"# Age");      }
   for(i=1; i<=nlstate;i++)      printf("\n");
     for(j=1; j<=nlstate;j++)      fprintf(ficlog,"\n");
       fprintf(ficreseij," %1d-%1d",i,j);    }
   fprintf(ficreseij,"\n");  
     /* Recompute Inverse */
   hstepm=1*YEARM; /*  Every j years of age (in month) */    for (i=1;i<=npar;i++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /*  printf("\n#Hessian matrix recomputed#\n");
     /* nhstepm age range expressed in number of stepm */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    for (j=1;j<=npar;j++) {
     /* Typically if 20 years = 20*12/6=40 stepm */      for (i=1;i<=npar;i++) x[i]=0;
     if (stepm >= YEARM) hstepm=1;      x[j]=1;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      lubksb(a,npar,indx,x);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1;i<=npar;i++){ 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        y[i][j]=x[i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        printf("%.3e ",y[i][j]);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          fprintf(ficlog,"%.3e ",y[i][j]);
       }
       printf("\n");
     for(i=1; i<=nlstate;i++)      fprintf(ficlog,"\n");
       for(j=1; j<=nlstate;j++)    }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    */
           eij[i][j][(int)age] +=p3mat[i][j][h];  
         }    free_matrix(a,1,npar,1,npar);
        free_matrix(y,1,npar,1,npar);
     hf=1;    free_vector(x,1,npar);
     if (stepm >= YEARM) hf=stepm/YEARM;    free_ivector(indx,1,npar);
     fprintf(ficreseij,"%.0f",age );    free_matrix(hess,1,npar,1,npar);
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);  }
       }  
     fprintf(ficreseij,"\n");  /*************** hessian matrix ****************/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  double hessii( double x[], double delta, int theta, double delti[])
   }  {
 }    int i;
     int l=1, lmax=20;
 /************ Variance ******************/    double k1,k2;
 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)    double p2[NPARMAX+1];
 {    double res;
   /* Variance of health expectancies */    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double fx;
   double **newm;    int k=0,kmax=10;
   double **dnewm,**doldm;    double l1;
   int i, j, nhstepm, hstepm, h;  
   int k, cptcode;    fx=func(x);
   double *xp;    for (i=1;i<=npar;i++) p2[i]=x[i];
   double **gp, **gm;    for(l=0 ; l <=lmax; l++){
   double ***gradg, ***trgradg;      l1=pow(10,l);
   double ***p3mat;      delts=delt;
   double age,agelim;      for(k=1 ; k <kmax; k=k+1){
   int theta;        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
    fprintf(ficresvij,"# Covariances of life expectancies\n");        k1=func(p2)-fx;
   fprintf(ficresvij,"# Age");        p2[theta]=x[theta]-delt;
   for(i=1; i<=nlstate;i++)        k2=func(p2)-fx;
     for(j=1; j<=nlstate;j++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   fprintf(ficresvij,"\n");        
   #ifdef DEBUG
   xp=vector(1,npar);        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);
   dnewm=matrix(1,nlstate,1,npar);        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);
   doldm=matrix(1,nlstate,1,nlstate);  #endif
          /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   hstepm=1*YEARM; /* Every year of age */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          k=kmax;
   agelim = AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          k=kmax; l=lmax*10.;
     if (stepm >= YEARM) hstepm=1;        }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          delts=delt;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        }
     gp=matrix(0,nhstepm,1,nlstate);      }
     gm=matrix(0,nhstepm,1,nlstate);    }
     delti[theta]=delts;
     for(theta=1; theta <=npar; theta++){    return res; 
       for(i=1; i<=npar; i++){ /* Computes gradient */    
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  }
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    double hessij( double x[], double delti[], int thetai,int thetaj)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
     int i;
       if (popbased==1) {    int l=1, l1, lmax=20;
         for(i=1; i<=nlstate;i++)    double k1,k2,k3,k4,res,fx;
           prlim[i][i]=probs[(int)age][i][ij];    double p2[NPARMAX+1];
       }    int k;
        
       for(j=1; j<= nlstate; j++){    fx=func(x);
         for(h=0; h<=nhstepm; h++){    for (k=1; k<=2; k++) {
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      for (i=1;i<=npar;i++) p2[i]=x[i];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      p2[thetai]=x[thetai]+delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k1=func(p2)-fx;
        
       for(i=1; i<=npar; i++) /* Computes gradient */      p2[thetai]=x[thetai]+delti[thetai]/k;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        k2=func(p2)-fx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    
       p2[thetai]=x[thetai]-delti[thetai]/k;
       if (popbased==1) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         for(i=1; i<=nlstate;i++)      k3=func(p2)-fx;
           prlim[i][i]=probs[(int)age][i][ij];    
       }      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(j=1; j<= nlstate; j++){      k4=func(p2)-fx;
         for(h=0; h<=nhstepm; h++){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  #ifdef DEBUG
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       }  #endif
     }
       for(j=1; j<= nlstate; j++)    return res;
         for(h=0; h<=nhstepm; h++){  }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }  /************** Inverse of matrix **************/
     } /* End theta */  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    int i,imax,j,k; 
     double big,dum,sum,temp; 
     for(h=0; h<=nhstepm; h++)    double *vv; 
       for(j=1; j<=nlstate;j++)   
         for(theta=1; theta <=npar; theta++)    vv=vector(1,n); 
           trgradg[h][j][theta]=gradg[h][theta][j];    *d=1.0; 
     for (i=1;i<=n;i++) { 
     for(i=1;i<=nlstate;i++)      big=0.0; 
       for(j=1;j<=nlstate;j++)      for (j=1;j<=n;j++) 
         vareij[i][j][(int)age] =0.;        if ((temp=fabs(a[i][j])) > big) big=temp; 
     for(h=0;h<=nhstepm;h++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       for(k=0;k<=nhstepm;k++){      vv[i]=1.0/big; 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    } 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    for (j=1;j<=n;j++) { 
         for(i=1;i<=nlstate;i++)      for (i=1;i<j;i++) { 
           for(j=1;j<=nlstate;j++)        sum=a[i][j]; 
             vareij[i][j][(int)age] += doldm[i][j];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       }        a[i][j]=sum; 
     }      } 
     h=1;      big=0.0; 
     if (stepm >= YEARM) h=stepm/YEARM;      for (i=j;i<=n;i++) { 
     fprintf(ficresvij,"%.0f ",age );        sum=a[i][j]; 
     for(i=1; i<=nlstate;i++)        for (k=1;k<j;k++) 
       for(j=1; j<=nlstate;j++){          sum -= a[i][k]*a[k][j]; 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        a[i][j]=sum; 
       }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     fprintf(ficresvij,"\n");          big=dum; 
     free_matrix(gp,0,nhstepm,1,nlstate);          imax=i; 
     free_matrix(gm,0,nhstepm,1,nlstate);        } 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      } 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      if (j != imax) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1;k<=n;k++) { 
   } /* End age */          dum=a[imax][k]; 
            a[imax][k]=a[j][k]; 
   free_vector(xp,1,npar);          a[j][k]=dum; 
   free_matrix(doldm,1,nlstate,1,npar);        } 
   free_matrix(dnewm,1,nlstate,1,nlstate);        *d = -(*d); 
         vv[imax]=vv[j]; 
 }      } 
       indx[j]=imax; 
 /************ Variance of prevlim ******************/      if (a[j][j] == 0.0) a[j][j]=TINY; 
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      if (j != n) { 
 {        dum=1.0/(a[j][j]); 
   /* Variance of prevalence limit */        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      } 
   double **newm;    } 
   double **dnewm,**doldm;    free_vector(vv,1,n);  /* Doesn't work */
   int i, j, nhstepm, hstepm;  ;
   int k, cptcode;  } 
   double *xp;  
   double *gp, *gm;  void lubksb(double **a, int n, int *indx, double b[]) 
   double **gradg, **trgradg;  { 
   double age,agelim;    int i,ii=0,ip,j; 
   int theta;    double sum; 
       
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    for (i=1;i<=n;i++) { 
   fprintf(ficresvpl,"# Age");      ip=indx[i]; 
   for(i=1; i<=nlstate;i++)      sum=b[ip]; 
       fprintf(ficresvpl," %1d-%1d",i,i);      b[ip]=b[i]; 
   fprintf(ficresvpl,"\n");      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   xp=vector(1,npar);      else if (sum) ii=i; 
   dnewm=matrix(1,nlstate,1,npar);      b[i]=sum; 
   doldm=matrix(1,nlstate,1,nlstate);    } 
      for (i=n;i>=1;i--) { 
   hstepm=1*YEARM; /* Every year of age */      sum=b[i]; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   agelim = AGESUP;      b[i]=sum/a[i][i]; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    } 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  } 
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  /************ Frequencies ********************/
     gradg=matrix(1,npar,1,nlstate);  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
     gp=vector(1,nlstate);  {  /* Some frequencies */
     gm=vector(1,nlstate);    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     for(theta=1; theta <=npar; theta++){    int first;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double ***freq; /* Frequencies */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double *pp, **prop;
       }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    FILE *ficresp;
       for(i=1;i<=nlstate;i++)    char fileresp[FILENAMELENGTH];
         gp[i] = prlim[i][i];    
        pp=vector(1,nlstate);
       for(i=1; i<=npar; i++) /* Computes gradient */    prop=matrix(1,nlstate,iagemin,iagemax+3);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    strcpy(fileresp,"p");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    strcat(fileresp,fileres);
       for(i=1;i<=nlstate;i++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
         gm[i] = prlim[i][i];      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       for(i=1;i<=nlstate;i++)      exit(0);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    }
     } /* End theta */    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
     trgradg =matrix(1,nlstate,1,npar);    
     j=cptcoveff;
     for(j=1; j<=nlstate;j++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];    first=1;
   
     for(i=1;i<=nlstate;i++)    for(k1=1; k1<=j;k1++){
       varpl[i][(int)age] =0.;      for(i1=1; i1<=ncodemax[k1];i1++){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        j1++;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     for(i=1;i<=nlstate;i++)          scanf("%d", i);*/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
     fprintf(ficresvpl,"%.0f ",age );            for(m=iagemin; m <= iagemax+3; m++)
     for(i=1; i<=nlstate;i++)              freq[i][jk][m]=0;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");      for (i=1; i<=nlstate; i++)  
     free_vector(gp,1,nlstate);        for(m=iagemin; m <= iagemax+3; m++)
     free_vector(gm,1,nlstate);          prop[i][m]=0;
     free_matrix(gradg,1,npar,1,nlstate);        
     free_matrix(trgradg,1,nlstate,1,npar);        dateintsum=0;
   } /* End age */        k2cpt=0;
         for (i=1; i<=imx; i++) {
   free_vector(xp,1,npar);          bool=1;
   free_matrix(doldm,1,nlstate,1,npar);          if  (cptcovn>0) {
   free_matrix(dnewm,1,nlstate,1,nlstate);            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 }                bool=0;
           }
 /************ Variance of one-step probabilities  ******************/          if (bool==1){
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)            for(m=firstpass; m<=lastpass; m++){
 {              k2=anint[m][i]+(mint[m][i]/12.);
   int i, j;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   int k=0, cptcode;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   double **dnewm,**doldm;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   double *xp;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   double *gp, *gm;                if (m<lastpass) {
   double **gradg, **trgradg;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   double age,agelim, cov[NCOVMAX];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   int theta;                }
   char fileresprob[FILENAMELENGTH];                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   strcpy(fileresprob,"prob");                  dateintsum=dateintsum+k2;
   strcat(fileresprob,fileres);                  k2cpt++;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {                }
     printf("Problem with resultfile: %s\n", fileresprob);                /*}*/
   }            }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          }
          }
          
   xp=vector(1,npar);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        if  (cptcovn>0) {
            fprintf(ficresp, "\n#********** Variable "); 
   cov[1]=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for (age=bage; age<=fage; age ++){          fprintf(ficresp, "**********\n#");
     cov[2]=age;        }
     gradg=matrix(1,npar,1,9);        for(i=1; i<=nlstate;i++) 
     trgradg=matrix(1,9,1,npar);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        fprintf(ficresp, "\n");
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        
            for(i=iagemin; i <= iagemax+3; i++){
     for(theta=1; theta <=npar; theta++){          if(i==iagemax+3){
       for(i=1; i<=npar; i++)            fprintf(ficlog,"Total");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }else{
                  if(first==1){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              first=0;
                  printf("See log file for details...\n");
       k=0;            }
       for(i=1; i<= (nlstate+ndeath); i++){            fprintf(ficlog,"Age %d", i);
         for(j=1; j<=(nlstate+ndeath);j++){          }
            k=k+1;          for(jk=1; jk <=nlstate ; jk++){
           gp[k]=pmmij[i][j];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         }              pp[jk] += freq[jk][m][i]; 
       }          }
           for(jk=1; jk <=nlstate ; jk++){
       for(i=1; i<=npar; i++)            for(m=-1, pos=0; m <=0 ; m++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              pos += freq[jk][m][i];
                if(pp[jk]>=1.e-10){
               if(first==1){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       k=0;              }
       for(i=1; i<=(nlstate+ndeath); i++){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for(j=1; j<=(nlstate+ndeath);j++){            }else{
           k=k+1;              if(first==1)
           gm[k]=pmmij[i][j];                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       }            }
                }
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            for(jk=1; jk <=nlstate ; jk++){
     }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          }       
       for(theta=1; theta <=npar; theta++)          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       trgradg[j][theta]=gradg[theta][j];            pos += pp[jk];
              posprop += prop[jk][i];
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
      pmij(pmmij,cov,ncovmodel,x,nlstate);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      k=0;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      for(i=1; i<=(nlstate+ndeath); i++){            }else{
        for(j=1; j<=(nlstate+ndeath);j++){              if(first==1)
          k=k+1;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
          gm[k]=pmmij[i][j];              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         }            }
      }            if( i <= iagemax){
                    if(pos>=1.e-5){
      /*printf("\n%d ",(int)age);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){                /*probs[i][jk][j1]= pp[jk]/pos;*/
                        /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              else
      }*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
   fprintf(ficresprob,"\n%d ",(int)age);          }
           
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            for(m=-1; m <=nlstate+ndeath; m++)
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);              if(freq[jk][m][i] !=0 ) {
   }              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));              }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          if(i <= iagemax)
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            fprintf(ficresp,"\n");
 }          if(first==1)
  free_vector(xp,1,npar);            printf("Others in log...\n");
 fclose(ficresprob);          fprintf(ficlog,"\n");
  exit(0);        }
 }      }
     }
 /***********************************************/    dateintmean=dateintsum/k2cpt; 
 /**************** Main Program *****************/   
 /***********************************************/    fclose(ficresp);
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
 /*int main(int argc, char *argv[])*/    free_vector(pp,1,nlstate);
 int main()    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 {    /* End of Freq */
   }
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  
   double agedeb, agefin,hf;  /************ Prevalence ********************/
   double agemin=1.e20, agemax=-1.e20;  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)
   {  
   double fret;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   double **xi,tmp,delta;       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
   double dum; /* Dummy variable */    */
   double ***p3mat;   
   int *indx;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   char line[MAXLINE], linepar[MAXLINE];    double ***freq; /* Frequencies */
   char title[MAXLINE];    double *pp, **prop;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    double pos,posprop; 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];    double  y2; /* in fractional years */
   char filerest[FILENAMELENGTH];    int iagemin, iagemax;
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];    iagemin= (int) agemin;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    iagemax= (int) agemax;
   int firstobs=1, lastobs=10;    /*pp=vector(1,nlstate);*/
   int sdeb, sfin; /* Status at beginning and end */    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   int c,  h , cpt,l;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   int ju,jl, mi;    j1=0;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    j=cptcoveff;
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   int hstepm, nhstepm;    
   int *popage,boolprev=0;/*boolprev=0 if date and zero if wave*/    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   double bage, fage, age, agelim, agebase;        j1++;
   double ftolpl=FTOL;        
   double **prlim;        for (i=1; i<=nlstate; i++)  
   double *severity;          for(m=iagemin; m <= iagemax+3; m++)
   double ***param; /* Matrix of parameters */            prop[i][m]=0.0;
   double  *p;       
   double **matcov; /* Matrix of covariance */        for (i=1; i<=imx; i++) { /* Each individual */
   double ***delti3; /* Scale */          bool=1;
   double *delti; /* Scale */          if  (cptcovn>0) {
   double ***eij, ***vareij;            for (z1=1; z1<=cptcoveff; z1++) 
   double **varpl; /* Variances of prevalence limits by age */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double *epj, vepp;                bool=0;
   double kk1, kk2;          } 
   double *popeffectif,*popcount;          if (bool==1) { 
   double dateprev1, dateprev2;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   char *alph[]={"a","a","b","c","d","e"}, str[4];                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   char z[1]="c", occ;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
 #include <sys/time.h>                  /*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]]);*/
 #include <time.h>                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                  prop[s[m][i]][iagemax+3] += weight[i]; 
   char strfprev[10], strlprev[10];                } 
   char strfprevfore[10], strlprevfore[10];              }
   /* long total_usecs;            } /* end selection of waves */
   struct timeval start_time, end_time;          }
          }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        for(i=iagemin; i <= iagemax+3; i++){  
           
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   printf("\nIMACH, Version 0.7");            posprop += prop[jk][i]; 
   printf("\nEnter the parameter file name: ");          } 
   
 #ifdef windows          for(jk=1; jk <=nlstate ; jk++){     
   scanf("%s",pathtot);            if( i <=  iagemax){ 
   getcwd(pathcd, size);              if(posprop>=1.e-5){ 
   /*cygwin_split_path(pathtot,path,optionfile);                probs[i][jk][j1]= prop[jk][i]/posprop;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/              } 
   /* cutv(path,optionfile,pathtot,'\\');*/            } 
           }/* end jk */ 
 split(pathtot, path,optionfile);        }/* end i */ 
   chdir(path);      } /* end i1 */
   replace(pathc,path);    } /* end k1 */
 #endif    
 #ifdef unix    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   scanf("%s",optionfile);    /*free_vector(pp,1,nlstate);*/
 #endif    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
 /*-------- arguments in the command line --------*/  
   /************* Waves Concatenation ***************/
   strcpy(fileres,"r");  
   strcat(fileres, optionfile);  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)
   {
   /*---------arguments file --------*/    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
   if((ficpar=fopen(optionfile,"r"))==NULL)    {       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     printf("Problem with optionfile %s\n",optionfile);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     goto end;       and mw[mi+1][i]. dh depends on stepm.
   }       */
   
   strcpy(filereso,"o");    int i, mi, m;
   strcat(filereso,fileres);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   if((ficparo=fopen(filereso,"w"))==NULL) {       double sum=0., jmean=0.;*/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    int first;
   }    int j, k=0,jk, ju, jl;
     double sum=0.;
   /* Reads comments: lines beginning with '#' */    first=0;
   while((c=getc(ficpar))=='#' && c!= EOF){    jmin=1e+5;
     ungetc(c,ficpar);    jmax=-1;
     fgets(line, MAXLINE, ficpar);    jmean=0.;
     puts(line);    for(i=1; i<=imx; i++){
     fputs(line,ficparo);      mi=0;
   }      m=firstpass;
   ungetc(c,ficpar);      while(s[m][i] <= nlstate){
         if(s[m][i]>=1)
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          mw[++mi][i]=m;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        if(m >=lastpass)
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);          break;
 while((c=getc(ficpar))=='#' && c!= EOF){        else
     ungetc(c,ficpar);          m++;
     fgets(line, MAXLINE, ficpar);      }/* end while */
     puts(line);      if (s[m][i] > nlstate){
     fputs(line,ficparo);        mi++;     /* Death is another wave */
   }        /* if(mi==0)  never been interviewed correctly before death */
   ungetc(c,ficpar);           /* Only death is a correct wave */
          mw[mi][i]=m;
   fscanf(ficpar,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,&popbased);      }
   fprintf(ficparo,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);  
        wav[i]=mi;
   /* printf("%s %s",strfprev,strlprev);      if(mi==0){
      exit(0);*/        if(first==0){
  while((c=getc(ficpar))=='#' && c!= EOF){          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     ungetc(c,ficpar);          first=1;
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        if(first==1){
     fputs(line,ficparo);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   }        }
   ungetc(c,ficpar);      } /* end mi==0 */
      } /* End individuals */
   fscanf(ficpar,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,&nforecast,&mobilav);  
   fprintf(ficparo,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);    for(i=1; i<=imx; i++){
            for(mi=1; mi<wav[i];mi++){
          if (stepm <=0)
 while((c=getc(ficpar))=='#' && c!= EOF){          dh[mi][i]=1;
     ungetc(c,ficpar);        else{
     fgets(line, MAXLINE, ficpar);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     puts(line);            if (agedc[i] < 2*AGESUP) {
     fputs(line,ficparo);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   }              if(j==0) j=1;  /* Survives at least one month after exam */
   ungetc(c,ficpar);              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]);
   fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);                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);
   covar=matrix(0,NCOVMAX,1,n);                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]);
   cptcovn=0;                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;              }
               k=k+1;
   ncovmodel=2+cptcovn;              if (j >= jmax) jmax=j;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */              if (j <= jmin) jmin=j;
                sum=sum+j;
   /* Read guess parameters */              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   /* Reads comments: lines beginning with '#' */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          else{
     puts(line);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     fputs(line,ficparo);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   }            k=k+1;
   ungetc(c,ficpar);            if (j >= jmax) jmax=j;
              else if (j <= jmin)jmin=j;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     for(i=1; i <=nlstate; i++)            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
     for(j=1; j <=nlstate+ndeath-1; j++){            if(j<0){
       fscanf(ficpar,"%1d%1d",&i1,&j1);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficparo,"%1d%1d",i1,j1);              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       printf("%1d%1d",i,j);            }
       for(k=1; k<=ncovmodel;k++){            sum=sum+j;
         fscanf(ficpar," %lf",&param[i][j][k]);          }
         printf(" %lf",param[i][j][k]);          jk= j/stepm;
         fprintf(ficparo," %lf",param[i][j][k]);          jl= j -jk*stepm;
       }          ju= j -(jk+1)*stepm;
       fscanf(ficpar,"\n");          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       printf("\n");            if(jl==0){
       fprintf(ficparo,"\n");              dh[mi][i]=jk;
     }              bh[mi][i]=0;
              }else{ /* We want a negative bias in order to only have interpolation ie
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
   p=param[1][1];              bh[mi][i]=ju;
              }
   /* Reads comments: lines beginning with '#' */          }else{
   while((c=getc(ficpar))=='#' && c!= EOF){            if(jl <= -ju){
     ungetc(c,ficpar);              dh[mi][i]=jk;
     fgets(line, MAXLINE, ficpar);              bh[mi][i]=jl;       /* bias is positive if real duration
     puts(line);                                   * is higher than the multiple of stepm and negative otherwise.
     fputs(line,ficparo);                                   */
   }            }
   ungetc(c,ficpar);            else{
               dh[mi][i]=jk+1;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              bh[mi][i]=ju;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            }
   for(i=1; i <=nlstate; i++){            if(dh[mi][i]==0){
     for(j=1; j <=nlstate+ndeath-1; j++){              dh[mi][i]=1; /* At least one step */
       fscanf(ficpar,"%1d%1d",&i1,&j1);              bh[mi][i]=ju; /* At least one step */
       printf("%1d%1d",i,j);              /*  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);*/
       fprintf(ficparo,"%1d%1d",i1,j1);            }
       for(k=1; k<=ncovmodel;k++){          } /* end if mle */
         fscanf(ficpar,"%le",&delti3[i][j][k]);        }
         printf(" %le",delti3[i][j][k]);      } /* end wave */
         fprintf(ficparo," %le",delti3[i][j][k]);    }
       }    jmean=sum/k;
       fscanf(ficpar,"\n");    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       printf("\n");    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       fprintf(ficparo,"\n");   }
     }  
   }  /*********** Tricode ****************************/
   delti=delti3[1][1];  void tricode(int *Tvar, int **nbcode, int imx)
    {
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){    int Ndum[20],ij=1, k, j, i, maxncov=19;
     ungetc(c,ficpar);    int cptcode=0;
     fgets(line, MAXLINE, ficpar);    cptcoveff=0; 
     puts(line);   
     fputs(line,ficparo);    for (k=0; k<maxncov; k++) Ndum[k]=0;
   }    for (k=1; k<=7; k++) ncodemax[k]=0;
   ungetc(c,ficpar);  
      for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   matcov=matrix(1,npar,1,npar);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   for(i=1; i <=npar; i++){                                 modality*/ 
     fscanf(ficpar,"%s",&str);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     printf("%s",str);        Ndum[ij]++; /*store the modality */
     fprintf(ficparo,"%s",str);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     for(j=1; j <=i; j++){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       fscanf(ficpar," %le",&matcov[i][j]);                                         Tvar[j]. If V=sex and male is 0 and 
       printf(" %.5le",matcov[i][j]);                                         female is 1, then  cptcode=1.*/
       fprintf(ficparo," %.5le",matcov[i][j]);      }
     }  
     fscanf(ficpar,"\n");      for (i=0; i<=cptcode; i++) {
     printf("\n");        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
     fprintf(ficparo,"\n");      }
   }  
   for(i=1; i <=npar; i++)      ij=1; 
     for(j=i+1;j<=npar;j++)      for (i=1; i<=ncodemax[j]; i++) {
       matcov[i][j]=matcov[j][i];        for (k=0; k<= maxncov; k++) {
              if (Ndum[k] != 0) {
   printf("\n");            nbcode[Tvar[j]][ij]=k; 
             /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             
     /*-------- data file ----------*/            ij++;
     if((ficres =fopen(fileres,"w"))==NULL) {          }
       printf("Problem with resultfile: %s\n", fileres);goto end;          if (ij > ncodemax[j]) break; 
     }        }  
     fprintf(ficres,"#%s\n",version);      } 
        }  
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;   for (k=0; k< maxncov; k++) Ndum[k]=0;
     }  
    for (i=1; i<=ncovmodel-2; i++) { 
     n= lastobs;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     severity = vector(1,maxwav);     ij=Tvar[i];
     outcome=imatrix(1,maxwav+1,1,n);     Ndum[ij]++;
     num=ivector(1,n);   }
     moisnais=vector(1,n);  
     annais=vector(1,n);   ij=1;
     moisdc=vector(1,n);   for (i=1; i<= maxncov; i++) {
     andc=vector(1,n);     if((Ndum[i]!=0) && (i<=ncovcol)){
     agedc=vector(1,n);       Tvaraff[ij]=i; /*For printing */
     cod=ivector(1,n);       ij++;
     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);   cptcoveff=ij-1; /*Number of simple covariates*/
     s=imatrix(1,maxwav+1,1,n);  }
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);  /*********** Health Expectancies ****************/
     ncodemax=ivector(1,8);  
   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 )
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {  {
       if ((i >= firstobs) && (i <=lastobs)) {    /* Health expectancies */
            int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         for (j=maxwav;j>=1;j--){    double age, agelim, hf;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    double ***p3mat,***varhe;
           strcpy(line,stra);    double **dnewm,**doldm;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double *xp;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double **gp, **gm;
         }    double ***gradg, ***trgradg;
            int theta;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    dnewm=matrix(1,nlstate*nlstate,1,npar);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficreseij,"# Health expectancies\n");
         for (j=ncov;j>=1;j--){    fprintf(ficreseij,"# Age");
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for(i=1; i<=nlstate;i++)
         }      for(j=1; j<=nlstate;j++)
         num[i]=atol(stra);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
            fprintf(ficreseij,"\n");
         /*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;}*/    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
         i=i+1;    }
       }    else  hstepm=estepm;   
     }    /* We compute the life expectancy from trapezoids spaced every estepm months
     /* printf("ii=%d", ij);     * This is mainly to measure the difference between two models: for example
        scanf("%d",i);*/     * if stepm=24 months pijx are given only every 2 years and by summing them
   imx=i-1; /* Number of individuals */     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   /* for (i=1; i<=imx; i++){     * to the curvature of the survival function. If, for the same date, we 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;     * to compare the new estimate of Life expectancy with the same linear 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;     * hypothesis. A more precise result, taking into account a more precise
     }     * curvature will be obtained if estepm is as small as stepm. */
     for (i=1; i<=imx; i++) 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]));*/  
     /* For example we decided to compute the life expectancy with the smallest unit */
   /* Calculation of the number of parameter from char model*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   Tvar=ivector(1,15);       nhstepm is the number of hstepm from age to agelim 
   Tprod=ivector(1,15);       nstepm is the number of stepm from age to agelin. 
   Tvaraff=ivector(1,15);       Look at hpijx to understand the reason of that which relies in memory size
   Tvard=imatrix(1,15,1,2);       and note for a fixed period like estepm months */
   Tage=ivector(1,15);          /* 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
   if (strlen(model) >1){       means that if the survival funtion is printed only each two years of age and if
     j=0, j1=0, k1=1, k2=1;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     j=nbocc(model,'+');       results. So we changed our mind and took the option of the best precision.
     j1=nbocc(model,'*');    */
     cptcovn=j+1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     cptcovprod=j1;  
        agelim=AGESUP;
        for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     strcpy(modelsav,model);      /* nhstepm age range expressed in number of stepm */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       printf("Error. Non available option model=%s ",model);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       goto end;      /* if (stepm >= YEARM) hstepm=1;*/
     }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(i=(j+1); i>=1;i--){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       cutv(stra,strb,modelsav,'+');      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       if (strchr(strb,'*')) {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         cutv(strd,strc,strb,'*');      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
         if (strcmp(strc,"age")==0) {   
           cptcovprod--;  
           cutv(strb,stre,strd,'V');      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           Tvar[i]=atoi(stre);  
           cptcovage++;      /* Computing Variances of health expectancies */
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/       for(theta=1; theta <=npar; theta++){
         }        for(i=1; i<=npar; i++){ 
         else if (strcmp(strd,"age")==0) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           cptcovprod--;        }
           cutv(strb,stre,strc,'V');        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           Tvar[i]=atoi(stre);    
           cptcovage++;        cptj=0;
           Tage[cptcovage]=i;        for(j=1; j<= nlstate; j++){
         }          for(i=1; i<=nlstate; i++){
         else {            cptj=cptj+1;
           cutv(strb,stre,strc,'V');            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           Tvar[i]=ncov+k1;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           cutv(strb,strc,strd,'V');            }
           Tprod[k1]=i;          }
           Tvard[k1][1]=atoi(strc);        }
           Tvard[k1][2]=atoi(stre);       
           Tvar[cptcovn+k2]=Tvard[k1][1];       
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        for(i=1; i<=npar; i++) 
           for (k=1; k<=lastobs;k++)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           k1++;        
           k2=k2+2;        cptj=0;
         }        for(j=1; j<= nlstate; j++){
       }          for(i=1;i<=nlstate;i++){
       else {            cptj=cptj+1;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       Tvar[i]=atoi(strc);            }
       }          }
       strcpy(modelsav,stra);          }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        for(j=1; j<= nlstate*nlstate; j++)
         scanf("%d",i);*/          for(h=0; h<=nhstepm-1; h++){
     }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 }          }
         } 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);     
   printf("cptcovprod=%d ", cptcovprod);  /* End theta */
   scanf("%d ",i);*/  
     fclose(fic);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   
     /*  if(mle==1){*/       for(h=0; h<=nhstepm-1; h++)
     if (weightopt != 1) { /* Maximisation without weights*/        for(j=1; j<=nlstate*nlstate;j++)
       for(i=1;i<=n;i++) weight[i]=1.0;          for(theta=1; theta <=npar; theta++)
     }            trgradg[h][j][theta]=gradg[h][theta][j];
     /*-calculation of age at interview from date of interview and age at death -*/       
     agev=matrix(1,maxwav,1,imx);  
        for(i=1;i<=nlstate*nlstate;i++)
    for (i=1; i<=imx; i++)        for(j=1;j<=nlstate*nlstate;j++)
      for(m=2; (m<= maxwav); m++)          varhe[i][j][(int)age] =0.;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;       printf("%d|",(int)age);fflush(stdout);
          s[m][i]=-1;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        }       for(h=0;h<=nhstepm-1;h++){
            for(k=0;k<=nhstepm-1;k++){
     for (i=1; i<=imx; i++)  {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       for(m=1; (m<= maxwav); m++){          for(i=1;i<=nlstate*nlstate;i++)
         if(s[m][i] >0){            for(j=1;j<=nlstate*nlstate;j++)
           if (s[m][i] == nlstate+1) {              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
             if(agedc[i]>0)        }
               if(moisdc[i]!=99 && andc[i]!=9999)      }
               agev[m][i]=agedc[i];      /* Computing expectancies */
             else {      for(i=1; i<=nlstate;i++)
               if (andc[i]!=9999){        for(j=1; j<=nlstate;j++)
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
               agev[m][i]=-1;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
               }            
             }  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
           }  
           else if(s[m][i] !=9){ /* Should no more exist */          }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)      fprintf(ficreseij,"%3.0f",age );
               agev[m][i]=1;      cptj=0;
             else if(agev[m][i] <agemin){      for(i=1; i<=nlstate;i++)
               agemin=agev[m][i];        for(j=1; j<=nlstate;j++){
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          cptj++;
             }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
             else if(agev[m][i] >agemax){        }
               agemax=agev[m][i];      fprintf(ficreseij,"\n");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/     
             }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
             /*agev[m][i]=anint[m][i]-annais[i];*/      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
             /*   agev[m][i] = age[i]+2*m;*/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
           else { /* =9 */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             agev[m][i]=1;    }
             s[m][i]=-1;    printf("\n");
           }    fprintf(ficlog,"\n");
         }  
         else /*= 0 Unknown */    free_vector(xp,1,npar);
           agev[m][i]=1;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
        free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     }  }
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){  /************ Variance ******************/
         if (s[m][i] > (nlstate+ndeath)) {  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)
           printf("Error: Wrong value in nlstate or ndeath\n");    {
           goto end;    /* Variance of health expectancies */
         }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       }    /* double **newm;*/
     }    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     free_vector(severity,1,maxwav);    double *xp;
     free_imatrix(outcome,1,maxwav+1,1,n);    double **gp, **gm;  /* for var eij */
     free_vector(moisnais,1,n);    double ***gradg, ***trgradg; /*for var eij */
     free_vector(annais,1,n);    double **gradgp, **trgradgp; /* for var p point j */
     /* free_matrix(mint,1,maxwav,1,n);    double *gpp, *gmp; /* for var p point j */
        free_matrix(anint,1,maxwav,1,n);*/    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     free_vector(moisdc,1,n);    double ***p3mat;
     free_vector(andc,1,n);    double age,agelim, hf;
     double ***mobaverage;
        int theta;
     wav=ivector(1,imx);    char digit[4];
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    char digitp[25];
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
        char fileresprobmorprev[FILENAMELENGTH];
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       Tcode=ivector(1,100);      else strcpy(digitp,"-populbased-nomobil-");
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    }
       ncodemax[1]=1;    else 
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      strcpy(digitp,"-stablbased-");
        
    codtab=imatrix(1,100,1,10);    if (mobilav!=0) {
    h=0;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    m=pow(2,cptcoveff);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
    for(k=1;k<=cptcoveff; k++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
      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++;    strcpy(fileresprobmorprev,"prmorprev"); 
            if (h>m) h=1;codtab[h][k]=j;    sprintf(digit,"%-d",ij);
          }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
        }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
      }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
    }    strcat(fileresprobmorprev,fileres);
        if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
    /* Calculates basic frequencies. Computes observed prevalence at single age      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        and prints on file fileres'p'. */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     if ((nbocc(strfprev,'/')==1) && (nbocc(strlprev,'/')==1)){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      boolprev=0;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      cutv(stra,strb,strfprev,'/');    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);
      dateprev1=(double)(atoi(strb)+atoi(stra)/12.);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      cutv(stra,strb,strlprev,'/');    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
      dateprev2=(double)(atoi(strb)+atoi(stra)/12.);      fprintf(ficresprobmorprev," p.%-d SE",j);
    }      for(i=1; i<=nlstate;i++)
            fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
    else if ((nbocc(strfprev,'/')==0) &&(nbocc(strlprev,'/')==0)){    }  
      boolprev=1;    fprintf(ficresprobmorprev,"\n");
      fprev=atoi(strfprev); lprev=atoi(strlprev);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
    }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     else {      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       printf("Error in statement lprevalence or fprevalence\n");      exit(0);
       goto end;    }
     }    else{
          fprintf(ficgp,"\n# Routine varevsij");
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev,mint,anint,boolprev,dateprev1,dateprev2);    }
    /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*     printf("Problem with html file: %s\n", optionfilehtm); */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*     exit(0); */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*   } */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  /*   else{ */
          fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
        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) */    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     if(mle==1){    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");
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    fprintf(ficresvij,"# Age");
     }    for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
     /*--------- results files --------------*/        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);    fprintf(ficresvij,"\n");
    fprintf(ficres,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);  
    fprintf(ficres,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
    jk=1;    doldm=matrix(1,nlstate,1,nlstate);
    fprintf(ficres,"# Parameters\n");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
    printf("# Parameters\n");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
        if (k != i)    gpp=vector(nlstate+1,nlstate+ndeath);
          {    gmp=vector(nlstate+1,nlstate+ndeath);
            printf("%d%d ",i,k);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
            fprintf(ficres,"%1d%1d ",i,k);    
            for(j=1; j <=ncovmodel; j++){    if(estepm < stepm){
              printf("%f ",p[jk]);      printf ("Problem %d lower than %d\n",estepm, stepm);
              fprintf(ficres,"%f ",p[jk]);    }
              jk++;    else  hstepm=estepm;   
            }    /* For example we decided to compute the life expectancy with the smallest unit */
            printf("\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
            fprintf(ficres,"\n");       nhstepm is the number of hstepm from age to agelim 
          }       nstepm is the number of stepm from age to agelin. 
      }       Look at hpijx to understand the reason of that which relies in memory size
    }       and note for a fixed period like k years */
  if(mle==1){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     /* Computing hessian and covariance matrix */       survival function given by stepm (the optimization length). Unfortunately it
     ftolhess=ftol; /* Usually correct */       means that if the survival funtion is printed every two years of age and if
     hesscov(matcov, p, npar, delti, ftolhess, func);       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.
     fprintf(ficres,"# Scales\n");    */
     printf("# Scales\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      for(i=1,jk=1; i <=nlstate; i++){    agelim = AGESUP;
       for(j=1; j <=nlstate+ndeath; j++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         if (j!=i) {      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           fprintf(ficres,"%1d%1d",i,j);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           printf("%1d%1d",i,j);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           for(k=1; k<=ncovmodel;k++){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
             printf(" %.5e",delti[jk]);      gp=matrix(0,nhstepm,1,nlstate);
             fprintf(ficres," %.5e",delti[jk]);      gm=matrix(0,nhstepm,1,nlstate);
             jk++;  
           }  
           printf("\n");      for(theta=1; theta <=npar; theta++){
           fprintf(ficres,"\n");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
         }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
      }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     k=1;  
     fprintf(ficres,"# Covariance\n");        if (popbased==1) {
     printf("# Covariance\n");          if(mobilav ==0){
     for(i=1;i<=npar;i++){            for(i=1; i<=nlstate;i++)
       /*  if (k>nlstate) k=1;              prlim[i][i]=probs[(int)age][i][ij];
       i1=(i-1)/(ncovmodel*nlstate)+1;          }else{ /* mobilav */ 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            for(i=1; i<=nlstate;i++)
       printf("%s%d%d",alph[k],i1,tab[i]);*/              prlim[i][i]=mobaverage[(int)age][i][ij];
       fprintf(ficres,"%3d",i);          }
       printf("%3d",i);        }
       for(j=1; j<=i;j++){    
         fprintf(ficres," %.5e",matcov[i][j]);        for(j=1; j<= nlstate; j++){
         printf(" %.5e",matcov[i][j]);          for(h=0; h<=nhstepm; h++){
       }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       fprintf(ficres,"\n");              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       printf("\n");          }
       k++;        }
     }        /* This for computing probability of death (h=1 means
               computed over hstepm matrices product = hstepm*stepm months) 
     while((c=getc(ficpar))=='#' && c!= EOF){           as a weighted average of prlim.
       ungetc(c,ficpar);        */
       fgets(line, MAXLINE, ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       puts(line);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       fputs(line,ficparo);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     }        }    
     ungetc(c,ficpar);        /* end probability of death */
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     if (fage <= 2) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       bage = agemin;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fage = agemax;   
     }        if (popbased==1) {
           if(mobilav ==0){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");            for(i=1; i<=nlstate;i++)
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
                for(i=1; i<=nlstate;i++)
 /*------------ gnuplot -------------*/              prlim[i][i]=mobaverage[(int)age][i][ij];
 chdir(pathcd);          }
   if((ficgp=fopen("graph.plt","w"))==NULL) {        }
     printf("Problem with file graph.gp");goto end;  
   }        for(j=1; j<= nlstate; j++){
 #ifdef windows          for(h=0; h<=nhstepm; h++){
   fprintf(ficgp,"cd \"%s\" \n",pathc);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 #endif              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 m=pow(2,cptcoveff);          }
          }
  /* 1eme*/        /* This for computing probability of death (h=1 means
   for (cpt=1; cpt<= nlstate ; cpt ++) {           computed over hstepm matrices product = hstepm*stepm months) 
    for (k1=1; k1<= m ; k1 ++) {           as a weighted average of prlim.
         */
 #ifdef windows        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
 #endif           gmp[j] += prlim[i][i]*p3mat[i][j][1];
 #ifdef unix        }    
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        /* end probability of death */
 #endif  
         for(j=1; j<= nlstate; j++) /* vareij */
 for (i=1; i<= nlstate ; i ++) {          for(h=0; h<=nhstepm; h++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }  
     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(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     for (i=1; i<= nlstate ; i ++) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      } /* End theta */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(h=0; h<=nhstepm; h++) /* veij */
 }          for(j=1; j<=nlstate;j++)
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          for(theta=1; theta <=npar; theta++)
 #ifdef unix            trgradg[h][j][theta]=gradg[h][theta][j];
 fprintf(ficgp,"\nset ter gif small size 400,300");  
 #endif      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for(theta=1; theta <=npar; theta++)
    }          trgradgp[j][theta]=gradgp[theta][j];
   }    
   /*2 eme*/  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   for (k1=1; k1<= m ; k1 ++) {      for(i=1;i<=nlstate;i++)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        for(j=1;j<=nlstate;j++)
              vareij[i][j][(int)age] =0.;
     for (i=1; i<= nlstate+1 ; i ++) {  
       k=2*i;      for(h=0;h<=nhstepm;h++){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        for(k=0;k<=nhstepm;k++){
       for (j=1; j<= nlstate+1 ; j ++) {          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(i=1;i<=nlstate;i++)
 }              for(j=1;j<=nlstate;j++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      }
       for (j=1; j<= nlstate+1 ; j ++) {    
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      /* pptj */
         else fprintf(ficgp," \%%*lf (\%%*lf)");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
 }        matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       fprintf(ficgp,"\" t\"\" w l 0,");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       for (j=1; j<= nlstate+1 ; j ++) {          varppt[j][i]=doldmp[j][i];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      /* end ppptj */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /*  x centered again */
 }        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       else fprintf(ficgp,"\" t\"\" w l 0,");   
     }      if (popbased==1) {
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        if(mobilav ==0){
   }          for(i=1; i<=nlstate;i++)
              prlim[i][i]=probs[(int)age][i][ij];
   /*3eme*/        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
   for (k1=1; k1<= m ; k1 ++) {            prlim[i][i]=mobaverage[(int)age][i][ij];
     for (cpt=1; cpt<= nlstate ; cpt ++) {        }
       k=2+nlstate*(cpt-1);      }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);               
       for (i=1; i< nlstate ; i ++) {      /* This for computing probability of death (h=1 means
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       }         as a weighted average of prlim.
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      */
     }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   /* CV preval stat */      }    
   for (k1=1; k1<= m ; k1 ++) {      /* end probability of death */
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       for (i=1; i< nlstate ; i ++)        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         fprintf(ficgp,"+$%d",k+i+1);        for(i=1; i<=nlstate;i++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
              }
       l=3+(nlstate+ndeath)*cpt;      } 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      fprintf(ficresprobmorprev,"\n");
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;      fprintf(ficresvij,"%.0f ",age );
         fprintf(ficgp,"+$%d",l+i+1);      for(i=1; i<=nlstate;i++)
       }        for(j=1; j<=nlstate;j++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        }
     }      fprintf(ficresvij,"\n");
   }        free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
   /* proba elementaires */      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
    for(i=1,jk=1; i <=nlstate; i++){      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     for(k=1; k <=(nlstate+ndeath); k++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if (k != i) {    } /* End age */
         for(j=1; j <=ncovmodel; j++){    free_vector(gpp,nlstate+1,nlstate+ndeath);
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    free_vector(gmp,nlstate+1,nlstate+ndeath);
           /*fprintf(ficgp,"%s",alph[1]);*/    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           jk++;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           fprintf(ficgp,"\n");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
         }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
   for(jk=1; jk <=m; jk++) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
    i=1;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
    for(k2=1; k2<=nlstate; k2++) {    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
      k3=i;    /*  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);
      for(k=1; k<=(nlstate+ndeath); k++) {  */
        if (k != k2){    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;    free_vector(xp,1,npar);
         for(j=3; j <=ncovmodel; j++) {    free_matrix(doldm,1,nlstate,1,nlstate);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    free_matrix(dnewm,1,nlstate,1,npar);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             ij++;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           else    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    fclose(ficresprobmorprev);
         }    fclose(ficgp);
           fprintf(ficgp,")/(1");  /*   fclose(fichtm); */
          }  /* end varevsij */
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  /************ Variance of prevlim ******************/
 ij=1;  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(j=3; j <=ncovmodel; j++){  {
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* Variance of prevalence limit */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
             ij++;    double **newm;
           }    double **dnewm,**doldm;
           else    int i, j, nhstepm, hstepm;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int k, cptcode;
           }    double *xp;
           fprintf(ficgp,")");    double *gp, *gm;
         }    double **gradg, **trgradg;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    double age,agelim;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    int theta;
         i=i+ncovmodel;     
        }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
      }    fprintf(ficresvpl,"# Age");
    }    for(i=1; i<=nlstate;i++)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        fprintf(ficresvpl," %1d-%1d",i,i);
   }    fprintf(ficresvpl,"\n");
      
   fclose(ficgp);    xp=vector(1,npar);
        dnewm=matrix(1,nlstate,1,npar);
 chdir(path);    doldm=matrix(1,nlstate,1,nlstate);
        
     free_ivector(wav,1,imx);    hstepm=1*YEARM; /* Every year of age */
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      agelim = AGESUP;
     free_ivector(num,1,n);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     free_vector(agedc,1,n);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      if (stepm >= YEARM) hstepm=1;
     fclose(ficparo);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     fclose(ficres);      gradg=matrix(1,npar,1,nlstate);
     /*  }*/      gp=vector(1,nlstate);
          gm=vector(1,nlstate);
    /*________fin mle=1_________*/  
          for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
     /* No more information from the sample is required now */        }
   /* Reads comments: lines beginning with '#' */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   while((c=getc(ficpar))=='#' && c!= EOF){        for(i=1;i<=nlstate;i++)
     ungetc(c,ficpar);          gp[i] = prlim[i][i];
     fgets(line, MAXLINE, ficpar);      
     puts(line);        for(i=1; i<=npar; i++) /* Computes gradient */
     fputs(line,ficparo);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   ungetc(c,ficpar);        for(i=1;i<=nlstate;i++)
            gm[i] = prlim[i][i];
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        for(i=1;i<=nlstate;i++)
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 /*--------- index.htm --------*/      } /* End theta */
   
   strcpy(optionfilehtm,optionfile);      trgradg =matrix(1,nlstate,1,npar);
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      for(j=1; j<=nlstate;j++)
     printf("Problem with %s \n",optionfilehtm);goto end;        for(theta=1; theta <=npar; theta++)
   }          trgradg[j][theta]=gradg[theta][j];
   
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">      for(i=1;i<=nlstate;i++)
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>        varpl[i][(int)age] =0.;
 Total number of observations=%d <br>      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 <hr  size=\"2\" color=\"#EC5E5E\">      for(i=1;i<=nlstate;i++)
 <li>Outputs files<br><br>\n        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>      fprintf(ficresvpl,"%.0f ",age );
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      for(i=1; i<=nlstate;i++)
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>      fprintf(ficresvpl,"\n");
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      free_vector(gp,1,nlstate);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>      free_vector(gm,1,nlstate);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      free_matrix(gradg,1,npar,1,nlstate);
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>      free_matrix(trgradg,1,nlstate,1,npar);
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    } /* End age */
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  
     free_vector(xp,1,npar);
  fprintf(fichtm," <li>Graphs</li><p>");    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  }
   
  j1=0;  /************ Variance of one-step probabilities  ******************/
  for(k1=1; k1<=m;k1++){  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
    for(i1=1; i1<=ncodemax[k1];i1++){  {
        j1++;    int i, j=0,  i1, k1, l1, t, tj;
        if (cptcovn > 0) {    int k2, l2, j1,  z1;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    int k=0,l, cptcode;
          for (cpt=1; cpt<=cptcoveff;cpt++)    int first=1, first1;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double **dnewm,**doldm;
        }    double *xp;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    double *gp, *gm;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        double **gradg, **trgradg;
        for(cpt=1; cpt<nlstate;cpt++){    double **mu;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    double age,agelim, cov[NCOVMAX];
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
        }    int theta;
     for(cpt=1; cpt<=nlstate;cpt++) {    char fileresprob[FILENAMELENGTH];
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    char fileresprobcov[FILENAMELENGTH];
 interval) in state (%d): v%s%d%d.gif <br>    char fileresprobcor[FILENAMELENGTH];
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    
      }    double ***varpij;
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    strcpy(fileresprob,"prob"); 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    strcat(fileresprob,fileres);
      }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      printf("Problem with resultfile: %s\n", fileresprob);
 health expectancies in states (1) and (2): e%s%d.gif<br>      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    }
 fprintf(fichtm,"\n</body>");    strcpy(fileresprobcov,"probcov"); 
    }    strcat(fileresprobcov,fileres);
  }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 fclose(fichtm);      printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   /*--------------- Prevalence limit --------------*/    }
      strcpy(fileresprobcor,"probcor"); 
   strcpy(filerespl,"pl");    strcat(fileresprobcor,fileres);
   strcat(filerespl,fileres);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      printf("Problem with resultfile: %s\n", fileresprobcor);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }    }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   fprintf(ficrespl,"#Prevalence limit\n");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   fprintf(ficrespl,"#Age ");    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   fprintf(ficrespl,"\n");    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   prlim=matrix(1,nlstate,1,nlstate);    
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprob,"# Age");
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcov,"# Age");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   k=0;    fprintf(ficresprobcov,"# Age");
   agebase=agemin;  
   agelim=agemax;  
   ftolpl=1.e-10;    for(i=1; i<=nlstate;i++)
   i1=cptcoveff;      for(j=1; j<=(nlstate+ndeath);j++){
   if (cptcovn < 1){i1=1;}        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }  
         k=k+1;   /* fprintf(ficresprob,"\n");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    fprintf(ficresprobcov,"\n");
         fprintf(ficrespl,"\n#******");    fprintf(ficresprobcor,"\n");
         for(j=1;j<=cptcoveff;j++)   */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   xp=vector(1,npar);
         fprintf(ficrespl,"******\n");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
            doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         for (age=agebase; age<=agelim; age++){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           fprintf(ficrespl,"%.0f",age );    first=1;
           for(i=1; i<=nlstate;i++)    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           fprintf(ficrespl," %.5f", prlim[i][i]);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
           fprintf(ficrespl,"\n");      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
         }      exit(0);
       }    }
     }    else{
   fclose(ficrespl);      fprintf(ficgp,"\n# Routine varprob");
     }
   /*------------- h Pij x at various ages ------------*/  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
    /*     printf("Problem with html file: %s\n", optionfilehtm); */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  /*     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  /*     exit(0); */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  /*   } */
   }  /*   else{ */
   printf("Computing pij: result on file '%s' \n", filerespij);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
        fprintf(fichtm,"\n");
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       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");
   agelim=AGESUP;      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");
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  /*   } */
    
   k=0;    cov[1]=1;
   for(cptcov=1;cptcov<=i1;cptcov++){    tj=cptcoveff;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       k=k+1;    j1=0;
         fprintf(ficrespij,"\n#****** ");    for(t=1; t<=tj;t++){
         for(j=1;j<=cptcoveff;j++)      for(i1=1; i1<=ncodemax[t];i1++){ 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        j1++;
         fprintf(ficrespij,"******\n");        if  (cptcovn>0) {
                  fprintf(ficresprob, "\n#********** Variable "); 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          fprintf(ficresprob, "**********\n#\n");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          fprintf(ficresprobcov, "\n#********** Variable "); 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           oldm=oldms;savm=savms;          fprintf(ficresprobcov, "**********\n#\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            
           fprintf(ficrespij,"# Age");          fprintf(ficgp, "\n#********** Variable "); 
           for(i=1; i<=nlstate;i++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficgp, "**********\n#\n");
               fprintf(ficrespij," %1d-%1d",i,j);          
           fprintf(ficrespij,"\n");          
           for (h=0; h<=nhstepm; h++){          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             for(i=1; i<=nlstate;i++)          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
               for(j=1; j<=nlstate+ndeath;j++)          
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          fprintf(ficresprobcor, "\n#********** Variable ");    
             fprintf(ficrespij,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(ficresprobcor, "**********\n#");    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
           fprintf(ficrespij,"\n");        
         }        for (age=bage; age<=fage; age ++){ 
     }          cov[2]=age;
   }          for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   fclose(ficrespij);          for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   /*---------- Forecasting ------------------*/          
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   strcpy(fileresf,"f");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   strcat(fileresf,fileres);          gp=vector(1,(nlstate)*(nlstate+ndeath));
   if((ficresf=fopen(fileresf,"w"))==NULL) {          gm=vector(1,(nlstate)*(nlstate+ndeath));
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;      
   }          for(theta=1; theta <=npar; theta++){
   printf("Computing forecasting: result on file '%s' \n", fileresf);            for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
  if ((nbocc(strfprevfore,'/')==1) && (nbocc(strlprevfore,'/')==1)){            
      boolprev=0;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
      cutv(stra,strb,strfprevfore,'/');            
      dateprev1=(double)(atoi(strb)+atoi(stra)/12.);            k=0;
      cutv(stra,strb,strlprevfore,'/');            for(i=1; i<= (nlstate); i++){
      dateprev2=(double)(atoi(strb)+atoi(stra)/12.);              for(j=1; j<=(nlstate+ndeath);j++){
    }                k=k+1;
                    gp[k]=pmmij[i][j];
    else if ((nbocc(strfprevfore,'/')==0) &&(nbocc(strlprevfore,'/')==0)){              }
      boolprev=1;            }
      fprev=atoi(strfprevfore); lprev=atoi(strlprevfore);            
    }            for(i=1; i<=npar; i++)
     else {              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       printf("Error in statement lprevalence or fprevalence\n");      
       goto end;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     }            k=0;
             for(i=1; i<=(nlstate); i++){
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore,mint,anint,boolprev,dateprev1,dateprev2);              for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
   free_matrix(mint,1,maxwav,1,n);                gm[k]=pmmij[i][j];
   free_matrix(anint,1,maxwav,1,n);              }
   free_matrix(agev,1,maxwav,1,imx);            }
   /* Mobile average */       
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)            for(theta=1; theta <=npar; theta++)
       for (i=1; i<=nlstate;i++)              trgradg[j][theta]=gradg[theta][j];
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          
           mobaverage[(int)agedeb][i][cptcod]=0.;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
              matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     for (agedeb=bage+4; agedeb<=fage; agedeb++){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
       for (i=1; i<=nlstate;i++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           for (cpt=0;cpt<=4;cpt++){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }          pmij(pmmij,cov,ncovmodel,x,nlstate);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          
         }          k=0;
       }          for(i=1; i<=(nlstate); i++){
     }              for(j=1; j<=(nlstate+ndeath);j++){
   }              k=k+1;
               mu[k][(int) age]=pmmij[i][j];
   stepsize=(int) (stepm+YEARM-1)/YEARM;            }
   if (stepm<=12) stepsize=1;          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   agelim=AGESUP;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   hstepm=stepsize*YEARM; /* Every year of age */              varpij[i][j][(int)age] = doldm[i][j];
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */  
            /*printf("\n%d ",(int)age);
   if (popforecast==1) {            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     if((ficpop=fopen(popfile,"r"))==NULL)    {            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       printf("Problem with population file : %s\n",popfile);goto end;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     }            }*/
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);          fprintf(ficresprob,"\n%d ",(int)age);
     popcount=vector(0,AGESUP);          fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       {            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
         i=i+1;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     imx=i;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
            }
   for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          i=0;
   }          for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
   for(cptcov=1;cptcov<=i1;cptcov++){              i=i++;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
       k=k+1;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       fprintf(ficresf,"\n#****** ");              for (j=1; j<=i;j++){
       for(j=1;j<=cptcoveff;j++) {                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       }              }
       fprintf(ficresf,"******\n");            }
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");          }/* end of loop for state */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        } /* end of loop for age */
       if (popforecast==1)  fprintf(ficresf," [Population]");  
         /* Confidence intervalle of pij  */
       for (agedeb=fage; agedeb>=bage; agedeb--){        /*
         fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);          fprintf(ficgp,"\nset noparametric;unset label");
        if (mobilav==1) {          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
         for(j=1; j<=nlstate;j++)          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
         }          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         else {          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           for(j=1; j<=nlstate;j++)          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);        */
         }    
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
        for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");        first1=1;
        if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);        for (k2=1; k2<=(nlstate);k2++){
       }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                  if(l2==k2) continue;
       for (cpt=1; cpt<=nforecast;cpt++) {            j=(k2-1)*(nlstate+ndeath)+l2;
         fprintf(ficresf,"\n");            for (k1=1; k1<=(nlstate);k1++){
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                if(l1==k1) continue;
         nhstepm = nhstepm/hstepm;                i=(k1-1)*(nlstate+ndeath)+l1;
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  if ((int)age %5==0){
         oldm=oldms;savm=savms;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                      v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         for (h=0; h<=nhstepm; h++){                    mu1=mu[i][(int) age]/stepm*YEARM ;
                            mu2=mu[j][(int) age]/stepm*YEARM;
          if (h*hstepm/YEARM*stepm==cpt)                    c12=cv12/sqrt(v1*v2);
             fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);                    /* Computing eigen value of matrix of covariance */
                              lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                              lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
          for(j=1; j<=nlstate+ndeath;j++) {                    /* Eigen vectors */
            kk1=0.;kk2=0;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
            for(i=1; i<=nlstate;i++) {                            /*v21=sqrt(1.-v11*v11); *//* error */
              if (mobilav==1)                    v21=(lc1-v1)/cv12*v11;
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];                    v12=-v21;
              else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];                    v22=v11;
              if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];                    tnalp=v21/v11;
             }                    if(first1==1){
            if (h*hstepm/YEARM*stepm==cpt) {                      first1=0;
              fprintf(ficresf," %.3f", kk1);                      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 (popforecast==1) fprintf(ficresf," [%.f]", kk2);                    }
            }                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
           }                    /*printf(fignu*/
         }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                            if(first==1){
       }                      first=0;
       }                      fprintf(ficgp,"\nset parametric;unset label");
     }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   }                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
   if (popforecast==1) {                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
     free_ivector(popage,0,AGESUP);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     free_vector(popeffectif,0,AGESUP);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
     free_vector(popcount,0,AGESUP);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   free_imatrix(s,1,maxwav+1,1,n);                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   free_vector(weight,1,n);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   fclose(ficresf);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   /*---------- Health expectancies and variances ------------*/                    }else{
                       first=0;
   strcpy(filerest,"t");                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   strcat(filerest,fileres);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   if((ficrest=fopen(filerest,"w"))==NULL) {                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
   strcpy(filerese,"e");                } /* end loop age */
   strcat(filerese,fileres);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   if((ficreseij=fopen(filerese,"w"))==NULL) {                first=1;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);              } /*l12 */
   }            } /* k12 */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          } /*l1 */
         }/* k1 */
  strcpy(fileresv,"v");      } /* loop covariates */
   strcat(fileresv,fileres);    }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   }    free_vector(xp,1,npar);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    fclose(ficresprob);
     fclose(ficresprobcov);
   k=0;    fclose(ficresprobcor);
   for(cptcov=1;cptcov<=i1;cptcov++){    fclose(ficgp);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  }
       k=k+1;  
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)  /******************* Printing html file ***********/
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       fprintf(ficrest,"******\n");                    int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
       fprintf(ficreseij,"\n#****** ");                    int popforecast, int estepm ,\
       for(j=1;j<=cptcoveff;j++)                    double jprev1, double mprev1,double anprev1, \
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                    double jprev2, double mprev2,double anprev2){
       fprintf(ficreseij,"******\n");    int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
       fprintf(ficresvij,"\n#****** ");  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
       for(j=1;j<=cptcoveff;j++)  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
       fprintf(ficresvij,"******\n");  /*   } */
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
       oldm=oldms;savm=savms;   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n \
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);     - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
       oldm=oldms;savm=savms;   - Life expectancies by age and initial health status (estepm=%2d months): \
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
          jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       fprintf(ficrest,"\n");  
           m=cptcoveff;
       hf=1;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       if (stepm >= YEARM) hf=stepm/YEARM;  
       epj=vector(1,nlstate+1);   jj1=0;
       for(age=bage; age <=fage ;age++){   for(k1=1; k1<=m;k1++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     for(i1=1; i1<=ncodemax[k1];i1++){
         if (popbased==1) {       jj1++;
           for(i=1; i<=nlstate;i++)       if (cptcovn > 0) {
             prlim[i][i]=probs[(int)age][i][k];         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         }         for (cpt=1; cpt<=cptcoveff;cpt++) 
                   fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         fprintf(ficrest," %.0f",age);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {       /* Pij */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br> \
           }  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
           epj[nlstate+1] +=epj[j];       /* Quasi-incidences */
         }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
         for(i=1, vepp=0.;i <=nlstate;i++)   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> \
           for(j=1;j <=nlstate;j++)  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
             vepp += vareij[i][j][(int)age];         /* Stable prevalence in each health state */
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));         for(cpt=1; cpt<nlstate;cpt++){
         for(j=1;j <=nlstate;j++){           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
         }         }
         fprintf(ficrest,"\n");       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> \
     }  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   }       }
               fprintf(fichtm,"\n<br>- Total life expectancy by age and \
          health expectancies in states (1) and (2): e%s%d.png<br>\
   <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
      } /* end i1 */
  fclose(ficreseij);   }/* End k1 */
  fclose(ficresvij);   fprintf(fichtm,"</ul>");
   fclose(ficrest);  
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
   /*  scanf("%d ",i); */   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
    - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
   /*------- Variance limit prevalence------*/     - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
    - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
 strcpy(fileresvpl,"vpl");   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
   strcat(fileresvpl,fileres);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);  /*  if(popforecast==1) fprintf(fichtm,"\n */
   }  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
  k=0;  /*  else  */
  for(cptcov=1;cptcov<=i1;cptcov++){  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
      k=k+1;  
      fprintf(ficresvpl,"\n#****** ");   m=cptcoveff;
      for(j=1;j<=cptcoveff;j++)   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
      fprintf(ficresvpl,"******\n");   jj1=0;
         for(k1=1; k1<=m;k1++){
      varpl=matrix(1,nlstate,(int) bage, (int) fage);     for(i1=1; i1<=ncodemax[k1];i1++){
      oldm=oldms;savm=savms;       jj1++;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       if (cptcovn > 0) {
    }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
  }         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   fclose(ficresvpl);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   /*---------- End : free ----------------*/       for(cpt=1; cpt<=nlstate;cpt++) {
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
    interval) in state (%d): v%s%d%d.png <br>\
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       }
       } /* end i1 */
     }/* End k1 */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);   fprintf(fichtm,"</ul>");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);   fflush(fichtm);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
    /******************* Gnuplot file **************/
   free_matrix(matcov,1,npar,1,npar);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   free_vector(delti,1,npar);  
      int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    int ng;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   printf("End of Imach\n");      printf("Problem with file %s",optionfilegnuplot);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
      }
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/    /*#ifdef windows */
   /*------ End -----------*/      fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   m=pow(2,cptcoveff);
  end:    
 #ifdef windows   /* 1eme*/
  chdir(pathcd);    for (cpt=1; cpt<= nlstate ; cpt ++) {
 #endif     for (k1=1; k1<= m ; k1 ++) {
         fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
  system("..\\gp37mgw\\wgnuplot graph.plt");       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);
   
 #ifdef windows       for (i=1; i<= nlstate ; i ++) {
   while (z[0] != 'q') {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     chdir(pathcd);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("\nType e to edit output files, c to start again, and q for exiting: ");       }
     scanf("%s",z);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
     if (z[0] == 'c') system("./imach");       for (i=1; i<= nlstate ; i ++) {
     else if (z[0] == 'e') {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       chdir(path);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       system(optionfilehtm);       } 
     }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
     else if (z[0] == 'q') exit(0);       for (i=1; i<= nlstate ; i ++) {
   }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 #endif         else fprintf(ficgp," \%%*lf (\%%*lf)");
 }       }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \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);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    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++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fclose(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               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];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[132],pathc[132],pathcd[132],pathtot[132],model[132];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char *strt, *strtend;
     char *stratrunc;
     int lstra;
   
     long total_usecs;
     struct timeval start_time, end_time, curr_time;
     struct timezone tzp;
     extern int gettimeofday();
     struct tm tmg, tm, *gmtime(), *localtime();
     long time_value;
     extern long time();
    
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strt=asctime(&tm);
   
   /*  printf("Localtime (at start)=%s",strt); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strt);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strt=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strt); 
   */
   
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 132)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Localtime (at start)=%s",strt);
     fprintf(ficlog,"Localtime (at start)=%s",strt);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
             model,fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strt);
     /*fclose(fichtm);*/
     fflush(fichtm);
   
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
   /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
   /*     printf("Problem with file: %s\n", optionfilehtm); */
   /*     fprintf(ficlog,"Problem with file: %s\n", optionfilehtm); */
   /*   } */
   
   
   /*   if(fileappend(fichtm, optionfilehtm)){ */
       fprintf(fichtm,"\n");
       fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
           imx,agemin,agemax,jmin,jmax,jmean);
   /*     fclose(fichtm); */
   /*   } */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strtend=asctime(&tm);
     printf("Localtime at start %s and at end=%s",strt, strtend); 
     fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend); 
     /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
   
     printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Localtime at start %s and at end=%s<br>",strt, strtend);
     fclose(fichtm);
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.18  
changed lines
  Added in v.1.87


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