Diff for /imach/src/imach.c between versions 1.6 and 1.86

version 1.6, 2001/05/02 17:47:10 version 1.86, 2003/06/17 20:04:08
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 1.86  2003/06/17 20:04:08  brouard
   individuals from different ages are interviewed on their health status    (Module): Change position of html and gnuplot routines and added
   or degree of  disability. At least a second wave of interviews    routine fileappend.
   ("longitudinal") should  measure each new individual health status.  
   Health expectancies are computed from the transistions observed between    Revision 1.85  2003/06/17 13:12:43  brouard
   waves and are computed for each degree of severity of disability (number    * imach.c (Repository): Check when date of death was earlier that
   of life states). More degrees you consider, more time is necessary to    current date of interview. It may happen when the death was just
   reach the Maximum Likelihood of the parameters involved in the model.    prior to the death. In this case, dh was negative and likelihood
   The simplest model is the multinomial logistic model where pij is    was wrong (infinity). We still send an "Error" but patch by
   the probabibility to be observed in state j at the second wave conditional    assuming that the date of death was just one stepm after the
   to be observed in state i at the first wave. Therefore the model is:    interview.
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    (Repository): Because some people have very long ID (first column)
   is a covariate. If you want to have a more complex model than "constant and    we changed int to long in num[] and we added a new lvector for
   age", you should modify the program where the markup    memory allocation. But we also truncated to 8 characters (left
     *Covariates have to be included here again* invites you to do it.    truncation)
   More covariates you add, less is the speed of the convergence.    (Repository): No more line truncation errors.
   
   The advantage that this computer programme claims, comes from that if the    Revision 1.84  2003/06/13 21:44:43  brouard
   delay between waves is not identical for each individual, or if some    * imach.c (Repository): Replace "freqsummary" at a correct
   individual missed an interview, the information is not rounded or lost, but    place. It differs from routine "prevalence" which may be called
   taken into account using an interpolation or extrapolation.    many times. Probs is memory consuming and must be used with
   hPijx is the probability to be    parcimony.
   observed in state i at age x+h conditional to the observed state i at age    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.83  2003/06/10 13:39:11  lievre
   quarter trimester, semester or year) is model as a multinomial logistic.    *** empty log message ***
   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 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.  */
    /*
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).     Interpolated Markov Chain
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Short summary of the programme:
   from the European Union.    
   It is copyrighted identically to a GNU software product, ie programme and    This program computes Healthy Life Expectancies from
   software can be distributed freely for non commercial use. Latest version    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   can be accessed at http://euroreves.ined.fr/imach .    first survey ("cross") where individuals from different ages are
   **********************************************************************/    interviewed on their health status or degree of disability (in the
      case of a health survey which is our main interest) -2- at least a
 #include <math.h>    second wave of interviews ("longitudinal") which measure each change
 #include <stdio.h>    (if any) in individual health status.  Health expectancies are
 #include <stdlib.h>    computed from the time spent in each health state according to a
 #include <unistd.h>    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 #define MAXLINE 256    simplest model is the multinomial logistic model where pij is the
 #define FILENAMELENGTH 80    probability to be observed in state j at the second wave
 /*#define DEBUG*/    conditional to be observed in state i at the first wave. Therefore
 #define windows    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    'age' is age and 'sex' is a covariate. If you want to have a more
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    you to do it.  More covariates you add, slower the
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    convergence.
   
 #define NINTERVMAX 8    The advantage of this computer programme, compared to a simple
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    multinomial logistic model, is clear when the delay between waves is not
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    identical for each individual. Also, if a individual missed an
 #define NCOVMAX 8 /* Maximum number of covariates */    intermediate interview, the information is lost, but taken into
 #define MAXN 20000    account using an interpolation or extrapolation.  
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    hPijx is the probability to be observed in state i at age x+h
 #define AGEBASE 40    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 int nvar;    semester or year) is modelled as a multinomial logistic.  The hPx
 static int cptcov;    matrix is simply the matrix product of nh*stepm elementary matrices
 int cptcovn, cptcovage=0;    and the contribution of each individual to the likelihood is simply
 int npar=NPARMAX;    hPijx.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Also this programme outputs the covariance matrix of the parameters but also
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    of the life expectancies. It also computes the stable prevalence. 
     
 int *wav; /* Number of waves for this individuual 0 is possible */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int maxwav; /* Maxim number of waves */             Institut national d'études démographiques, Paris.
 int mle, weightopt;    This software have been partly granted by Euro-REVES, a concerted action
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    from the European Union.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    It is copyrighted identically to a GNU software product, ie programme and
 double **oldm, **newm, **savm; /* Working pointers to matrices */    software can be distributed freely for non commercial use. Latest version
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    can be accessed at http://euroreves.ined.fr/imach .
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  
 FILE *ficgp, *fichtm;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 FILE *ficreseij;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   char filerese[FILENAMELENGTH];    
  FILE  *ficresvij;    **********************************************************************/
   char fileresv[FILENAMELENGTH];  /*
  FILE  *ficresvpl;    main
   char fileresvpl[FILENAMELENGTH];    read parameterfile
     read datafile
 #define NR_END 1    concatwav
 #define FREE_ARG char*    freqsummary
 #define FTOL 1.0e-10    if (mle >= 1)
       mlikeli
 #define NRANSI    print results files
 #define ITMAX 200    if mle==1 
        computes hessian
 #define TOL 2.0e-4    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 #define CGOLD 0.3819660    open gnuplot file
 #define ZEPS 1.0e-10    open html file
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    stable prevalence
      for age prevalim()
 #define GOLD 1.618034    h Pij x
 #define GLIMIT 100.0    variance of p varprob
 #define TINY 1.0e-20    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 static double maxarg1,maxarg2;    Variance-covariance of DFLE
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    prevalence()
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))     movingaverage()
      varevsij() 
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    if popbased==1 varevsij(,popbased)
 #define rint(a) floor(a+0.5)    total life expectancies
     Variance of stable prevalence
 static double sqrarg;   end
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   
 int imx;  
 int stepm;   
 /* Stepm, step in month: minimum step interpolation*/  #include <math.h>
   #include <stdio.h>
 int m,nb;  #include <stdlib.h>
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #include <unistd.h>
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij;  #include <sys/time.h>
   #include <time.h>
 double *weight;  #include "timeval.h"
 int **s; /* Status */  
 double *agedc, **covar, idx;  #define MAXLINE 256
 int **nbcode, *Tcode, *Tvar, **codtab;  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define FILENAMELENGTH 132
 double ftolhess; /* Tolerance for computing hessian */  /*#define DEBUG*/
   /*#define windows*/
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 static  int split( char *path, char *dirc, char *name )  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 {  
    char *s;                             /* pointer */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    int  l1, l2;                         /* length counters */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
    l1 = strlen( path );                 /* length of path */  #define NINTERVMAX 8
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    s = strrchr( path, '\\' );           /* find last / */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    if ( s == NULL ) {                   /* no directory, so use current */  #define NCOVMAX 8 /* Maximum number of covariates */
 #if     defined(__bsd__)                /* get current working directory */  #define MAXN 20000
       extern char       *getwd( );  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
       if ( getwd( dirc ) == NULL ) {  #define AGEBASE 40
 #else  #ifdef unix
       extern char       *getcwd( );  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #else
 #endif  #define DIRSEPARATOR '\\'
          return( GLOCK_ERROR_GETCWD );  #define ODIRSEPARATOR '/'
       }  #endif
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  /* $Id$ */
       s++;                              /* after this, the filename */  /* $State$ */
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
       strcpy( name, s );                /* save file name */  char fullversion[]="$Revision$ $Date$"; 
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  int erreur; /* Error number */
       dirc[l1-l2] = 0;                  /* add zero */  int nvar;
    }  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    l1 = strlen( dirc );                 /* length of directory */  int npar=NPARMAX;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int nlstate=2; /* Number of live states */
    return( 0 );                         /* we're done */  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 */
   int maxwav; /* Maxim number of waves */
 void replace(char *s, char*t)  int jmin, jmax; /* min, max spacing between 2 waves */
 {  int mle, weightopt;
   int i;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int lg=20;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   i=0;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   lg=strlen(t);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   for(i=0; i<= lg; i++) {  double jmean; /* Mean space between 2 waves */
     (s[i] = t[i]);  double **oldm, **newm, **savm; /* Working pointers to matrices */
     if (t[i]== '\\') s[i]='/';  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   }  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 }  FILE *ficlog, *ficrespow;
   int globpr; /* Global variable for printing or not */
 int nbocc(char *s, char occ)  double fretone; /* Only one call to likelihood */
 {  long ipmx; /* Number of contributions */
   int i,j=0;  double sw; /* Sum of weights */
   int lg=20;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   i=0;  FILE *ficresilk;
   lg=strlen(s);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   for(i=0; i<= lg; i++) {  FILE *ficresprobmorprev;
   if  (s[i] == occ ) j++;  FILE *fichtm; /* Html File */
   }  FILE *ficreseij;
   return j;  char filerese[FILENAMELENGTH];
 }  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 void cutv(char *u,char *v, char*t, char occ)  FILE  *ficresvpl;
 {  char fileresvpl[FILENAMELENGTH];
   int i,lg,j,p=0;  char title[MAXLINE];
   i=0;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   for(j=0; j<=strlen(t)-1; j++) {  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
   lg=strlen(t);  char filerest[FILENAMELENGTH];
   for(j=0; j<p; j++) {  char fileregp[FILENAMELENGTH];
     (u[j] = t[j]);  char popfile[FILENAMELENGTH];
   }  
      u[p]='\0';  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   
    for(j=0; j<= lg; j++) {  #define NR_END 1
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define FREE_ARG char*
   }  #define FTOL 1.0e-10
 }  
   #define NRANSI 
 /********************** nrerror ********************/  #define ITMAX 200 
   
 void nrerror(char error_text[])  #define TOL 2.0e-4 
 {  
   fprintf(stderr,"ERREUR ...\n");  #define CGOLD 0.3819660 
   fprintf(stderr,"%s\n",error_text);  #define ZEPS 1.0e-10 
   exit(1);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
 /*********************** vector *******************/  #define GOLD 1.618034 
 double *vector(int nl, int nh)  #define GLIMIT 100.0 
 {  #define TINY 1.0e-20 
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  static double maxarg1,maxarg2;
   if (!v) nrerror("allocation failure in vector");  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   return v-nl+NR_END;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 }    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 /************************ free vector ******************/  #define rint(a) floor(a+0.5)
 void free_vector(double*v, int nl, int nh)  
 {  static double sqrarg;
   free((FREE_ARG)(v+nl-NR_END));  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
 /************************ivector *******************************/  int imx; 
 int *ivector(long nl,long nh)  int stepm;
 {  /* Stepm, step in month: minimum step interpolation*/
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  int estepm;
   if (!v) nrerror("allocation failure in ivector");  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   return v-nl+NR_END;  
 }  int m,nb;
   long *num;
 /******************free ivector **************************/  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 void free_ivector(int *v, long nl, long nh)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 {  double **pmmij, ***probs;
   free((FREE_ARG)(v+nl-NR_END));  double dateintmean=0;
 }  
   double *weight;
 /******************* imatrix *******************************/  int **s; /* Status */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  double *agedc, **covar, idx;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   int **m;  double ftolhess; /* Tolerance for computing hessian */
    
   /* allocate pointers to rows */  /**************** split *************************/
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    char  *ss;                            /* pointer */
   m -= nrl;    int   l1, l2;                         /* length counters */
    
      l1 = strlen(path );                   /* length of path */
   /* allocate rows and set pointers to them */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if ( ss == NULL ) {                   /* no directory, so use current */
   m[nrl] += NR_END;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   m[nrl] -= ncl;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
        /* get current working directory */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;      /*    extern  char* getcwd ( char *buf , int len);*/
        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   /* return pointer to array of pointers to rows */        return( GLOCK_ERROR_GETCWD );
   return m;      }
 }      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 /****************** free_imatrix *************************/      ss++;                               /* after this, the filename */
 void free_imatrix(m,nrl,nrh,ncl,nch)      l2 = strlen( ss );                  /* length of filename */
       int **m;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       long nch,ncl,nrh,nrl;      strcpy( name, ss );         /* save file name */
      /* free an int matrix allocated by imatrix() */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 {      dirc[l1-l2] = 0;                    /* add zero */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    }
   free((FREE_ARG) (m+nrl-NR_END));    l1 = strlen( dirc );                  /* length of directory */
 }    /*#ifdef windows
     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 /******************* matrix *******************************/  #else
 double **matrix(long nrl, long nrh, long ncl, long nch)    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 {  #endif
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    */
   double **m;    ss = strrchr( name, '.' );            /* find last / */
     ss++;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    strcpy(ext,ss);                       /* save extension */
   if (!m) nrerror("allocation failure 1 in matrix()");    l1= strlen( name);
   m += NR_END;    l2= strlen(ss)+1;
   m -= nrl;    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    return( 0 );                          /* we're done */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  }
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  
   /******************************************/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  void replace(char *s, char*t)
 }  {
     int i;
 /*************************free matrix ************************/    int lg=20;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    i=0;
 {    lg=strlen(t);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    for(i=0; i<= lg; i++) {
   free((FREE_ARG)(m+nrl-NR_END));      (s[i] = t[i]);
 }      if (t[i]== '\\') s[i]='/';
     }
 /******************* ma3x *******************************/  }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  int nbocc(char *s, char occ)
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  {
   double ***m;    int i,j=0;
     int lg=20;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    i=0;
   if (!m) nrerror("allocation failure 1 in matrix()");    lg=strlen(s);
   m += NR_END;    for(i=0; i<= lg; i++) {
   m -= nrl;    if  (s[i] == occ ) j++;
     }
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    return j;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  }
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  void cutv(char *u,char *v, char*t, char occ)
   {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    /* cuts string t into u and v where u is ended by char occ excluding it
        and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));       gives u="abcedf" and v="ghi2j" */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    int i,lg,j,p=0;
   m[nrl][ncl] += NR_END;    i=0;
   m[nrl][ncl] -= nll;    for(j=0; j<=strlen(t)-1; j++) {
   for (j=ncl+1; j<=nch; j++)      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     m[nrl][j]=m[nrl][j-1]+nlay;    }
    
   for (i=nrl+1; i<=nrh; i++) {    lg=strlen(t);
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    for(j=0; j<p; j++) {
     for (j=ncl+1; j<=nch; j++)      (u[j] = t[j]);
       m[i][j]=m[i][j-1]+nlay;    }
   }       u[p]='\0';
   return m;  
 }     for(j=0; j<= lg; j++) {
       if (j>=(p+1))(v[j-p-1] = t[j]);
 /*************************free ma3x ************************/    }
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  }
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  /********************** nrerror ********************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  void nrerror(char error_text[])
 }  {
     fprintf(stderr,"ERREUR ...\n");
 /***************** f1dim *************************/    fprintf(stderr,"%s\n",error_text);
 extern int ncom;    exit(EXIT_FAILURE);
 extern double *pcom,*xicom;  }
 extern double (*nrfunc)(double []);  /*********************** vector *******************/
    double *vector(int nl, int nh)
 double f1dim(double x)  {
 {    double *v;
   int j;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double f;    if (!v) nrerror("allocation failure in vector");
   double *xt;    return v-nl+NR_END;
    }
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /************************ free vector ******************/
   f=(*nrfunc)(xt);  void free_vector(double*v, int nl, int nh)
   free_vector(xt,1,ncom);  {
   return f;    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
 /*****************brent *************************/  /************************ivector *******************************/
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int *ivector(long nl,long nh)
 {  {
   int iter;    int *v;
   double a,b,d,etemp;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   double fu,fv,fw,fx;    if (!v) nrerror("allocation failure in ivector");
   double ftemp;    return v-nl+NR_END;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    /******************free ivector **************************/
   a=(ax < cx ? ax : cx);  void free_ivector(int *v, long nl, long nh)
   b=(ax > cx ? ax : cx);  {
   x=w=v=bx;    free((FREE_ARG)(v+nl-NR_END));
   fw=fv=fx=(*f)(x);  }
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  /************************lvector *******************************/
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  long *lvector(long nl,long nh)
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  {
     printf(".");fflush(stdout);    long *v;
 #ifdef DEBUG    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     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 (!v) nrerror("allocation failure in ivector");
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    return v-nl+NR_END;
 #endif  }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /******************free lvector **************************/
       return fx;  void free_lvector(long *v, long nl, long nh)
     }  {
     ftemp=fu;    free((FREE_ARG)(v+nl-NR_END));
     if (fabs(e) > tol1) {  }
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  /******************* imatrix *******************************/
       p=(x-v)*q-(x-w)*r;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       q=2.0*(q-r);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       if (q > 0.0) p = -p;  { 
       q=fabs(q);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       etemp=e;    int **m; 
       e=d;    
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    /* allocate pointers to rows */ 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       else {    if (!m) nrerror("allocation failure 1 in matrix()"); 
         d=p/q;    m += NR_END; 
         u=x+d;    m -= nrl; 
         if (u-a < tol2 || b-u < tol2)    
           d=SIGN(tol1,xm-x);    
       }    /* allocate rows and set pointers to them */ 
     } else {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     }    m[nrl] += NR_END; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    m[nrl] -= ncl; 
     fu=(*f)(u);    
     if (fu <= fx) {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       if (u >= x) a=x; else b=x;    
       SHFT(v,w,x,u)    /* return pointer to array of pointers to rows */ 
         SHFT(fv,fw,fx,fu)    return m; 
         } else {  } 
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /****************** free_imatrix *************************/
             v=w;  void free_imatrix(m,nrl,nrh,ncl,nch)
             w=u;        int **m;
             fv=fw;        long nch,ncl,nrh,nrl; 
             fw=fu;       /* free an int matrix allocated by imatrix() */ 
           } else if (fu <= fv || v == x || v == w) {  { 
             v=u;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
             fv=fu;    free((FREE_ARG) (m+nrl-NR_END)); 
           }  } 
         }  
   }  /******************* matrix *******************************/
   nrerror("Too many iterations in brent");  double **matrix(long nrl, long nrh, long ncl, long nch)
   *xmin=x;  {
   return fx;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /****************** mnbrak ***********************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    m += NR_END;
             double (*func)(double))    m -= nrl;
 {  
   double ulim,u,r,q, dum;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double fu;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      m[nrl] += NR_END;
   *fa=(*func)(*ax);    m[nrl] -= ncl;
   *fb=(*func)(*bx);  
   if (*fb > *fa) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     SHFT(dum,*ax,*bx,dum)    return m;
       SHFT(dum,*fb,*fa,dum)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       }     */
   *cx=(*bx)+GOLD*(*bx-*ax);  }
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  /*************************free matrix ************************/
     r=(*bx-*ax)*(*fb-*fc);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     q=(*bx-*cx)*(*fb-*fa);  {
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    free((FREE_ARG)(m+nrl-NR_END));
     ulim=(*bx)+GLIMIT*(*cx-*bx);  }
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  /******************* ma3x *******************************/
     } else if ((*cx-u)*(u-ulim) > 0.0) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       fu=(*func)(u);  {
       if (fu < *fc) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    double ***m;
           SHFT(*fb,*fc,fu,(*func)(u))  
           }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    if (!m) nrerror("allocation failure 1 in matrix()");
       u=ulim;    m += NR_END;
       fu=(*func)(u);    m -= nrl;
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       fu=(*func)(u);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
     SHFT(*ax,*bx,*cx,u)    m[nrl] -= ncl;
       SHFT(*fa,*fb,*fc,fu)  
       }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 }  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 /*************** linmin ************************/    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
 int ncom;    m[nrl][ncl] -= nll;
 double *pcom,*xicom;    for (j=ncl+1; j<=nch; j++) 
 double (*nrfunc)(double []);      m[nrl][j]=m[nrl][j-1]+nlay;
      
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    for (i=nrl+1; i<=nrh; i++) {
 {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   double brent(double ax, double bx, double cx,      for (j=ncl+1; j<=nch; j++) 
                double (*f)(double), double tol, double *xmin);        m[i][j]=m[i][j-1]+nlay;
   double f1dim(double x);    }
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    return m; 
               double *fc, double (*func)(double));    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   int j;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   double xx,xmin,bx,ax;    */
   double fx,fb,fa;  }
    
   ncom=n;  /*************************free ma3x ************************/
   pcom=vector(1,n);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   xicom=vector(1,n);  {
   nrfunc=func;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   for (j=1;j<=n;j++) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     pcom[j]=p[j];    free((FREE_ARG)(m+nrl-NR_END));
     xicom[j]=xi[j];  }
   }  
   ax=0.0;  /***************** f1dim *************************/
   xx=1.0;  extern int ncom; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  extern double *pcom,*xicom;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  extern double (*nrfunc)(double []); 
 #ifdef DEBUG   
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double f1dim(double x) 
 #endif  { 
   for (j=1;j<=n;j++) {    int j; 
     xi[j] *= xmin;    double f;
     p[j] += xi[j];    double *xt; 
   }   
   free_vector(xicom,1,n);    xt=vector(1,ncom); 
   free_vector(pcom,1,n);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 }    f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
 /*************** powell ************************/    return f; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  } 
             double (*func)(double []))  
 {  /*****************brent *************************/
   void linmin(double p[], double xi[], int n, double *fret,  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
               double (*func)(double []));  { 
   int i,ibig,j;    int iter; 
   double del,t,*pt,*ptt,*xit;    double a,b,d,etemp;
   double fp,fptt;    double fu,fv,fw,fx;
   double *xits;    double ftemp;
   pt=vector(1,n);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   ptt=vector(1,n);    double e=0.0; 
   xit=vector(1,n);   
   xits=vector(1,n);    a=(ax < cx ? ax : cx); 
   *fret=(*func)(p);    b=(ax > cx ? ax : cx); 
   for (j=1;j<=n;j++) pt[j]=p[j];    x=w=v=bx; 
   for (*iter=1;;++(*iter)) {    fw=fv=fx=(*f)(x); 
     fp=(*fret);    for (iter=1;iter<=ITMAX;iter++) { 
     ibig=0;      xm=0.5*(a+b); 
     del=0.0;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for (i=1;i<=n;i++)      printf(".");fflush(stdout);
       printf(" %d %.12f",i, p[i]);      fprintf(ficlog,".");fflush(ficlog);
     printf("\n");  #ifdef DEBUG
     for (i=1;i<=n;i++) {      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      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);
       fptt=(*fret);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 #ifdef DEBUG  #endif
       printf("fret=%lf \n",*fret);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 #endif        *xmin=x; 
       printf("%d",i);fflush(stdout);        return fx; 
       linmin(p,xit,n,fret,func);      } 
       if (fabs(fptt-(*fret)) > del) {      ftemp=fu;
         del=fabs(fptt-(*fret));      if (fabs(e) > tol1) { 
         ibig=i;        r=(x-w)*(fx-fv); 
       }        q=(x-v)*(fx-fw); 
 #ifdef DEBUG        p=(x-v)*q-(x-w)*r; 
       printf("%d %.12e",i,(*fret));        q=2.0*(q-r); 
       for (j=1;j<=n;j++) {        if (q > 0.0) p = -p; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);        q=fabs(q); 
         printf(" x(%d)=%.12e",j,xit[j]);        etemp=e; 
       }        e=d; 
       for(j=1;j<=n;j++)        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         printf(" p=%.12e",p[j]);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       printf("\n");        else { 
 #endif          d=p/q; 
     }          u=x+d; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {          if (u-a < tol2 || b-u < tol2) 
 #ifdef DEBUG            d=SIGN(tol1,xm-x); 
       int k[2],l;        } 
       k[0]=1;      } else { 
       k[1]=-1;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       printf("Max: %.12e",(*func)(p));      } 
       for (j=1;j<=n;j++)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         printf(" %.12e",p[j]);      fu=(*f)(u); 
       printf("\n");      if (fu <= fx) { 
       for(l=0;l<=1;l++) {        if (u >= x) a=x; else b=x; 
         for (j=1;j<=n;j++) {        SHFT(v,w,x,u) 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];          SHFT(fv,fw,fx,fu) 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);          } else { 
         }            if (u < x) a=u; else b=u; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));            if (fu <= fw || w == x) { 
       }              v=w; 
 #endif              w=u; 
               fv=fw; 
               fw=fu; 
       free_vector(xit,1,n);            } else if (fu <= fv || v == x || v == w) { 
       free_vector(xits,1,n);              v=u; 
       free_vector(ptt,1,n);              fv=fu; 
       free_vector(pt,1,n);            } 
       return;          } 
     }    } 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    nrerror("Too many iterations in brent"); 
     for (j=1;j<=n;j++) {    *xmin=x; 
       ptt[j]=2.0*p[j]-pt[j];    return fx; 
       xit[j]=p[j]-pt[j];  } 
       pt[j]=p[j];  
     }  /****************** mnbrak ***********************/
     fptt=(*func)(ptt);  
     if (fptt < fp) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);              double (*func)(double)) 
       if (t < 0.0) {  { 
         linmin(p,xit,n,fret,func);    double ulim,u,r,q, dum;
         for (j=1;j<=n;j++) {    double fu; 
           xi[j][ibig]=xi[j][n];   
           xi[j][n]=xit[j];    *fa=(*func)(*ax); 
         }    *fb=(*func)(*bx); 
 #ifdef DEBUG    if (*fb > *fa) { 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      SHFT(dum,*ax,*bx,dum) 
         for(j=1;j<=n;j++)        SHFT(dum,*fb,*fa,dum) 
           printf(" %.12e",xit[j]);        } 
         printf("\n");    *cx=(*bx)+GOLD*(*bx-*ax); 
 #endif    *fc=(*func)(*cx); 
       }    while (*fb > *fc) { 
     }      r=(*bx-*ax)*(*fb-*fc); 
   }      q=(*bx-*cx)*(*fb-*fa); 
 }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 /**** Prevalence limit ****************/      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        fu=(*func)(u); 
 {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        fu=(*func)(u); 
      matrix by transitions matrix until convergence is reached */        if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   int i, ii,j,k;            SHFT(*fb,*fc,fu,(*func)(u)) 
   double min, max, maxmin, maxmax,sumnew=0.;            } 
   double **matprod2();      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   double **out, cov[NCOVMAX], **pmij();        u=ulim; 
   double **newm;        fu=(*func)(u); 
   double agefin, delaymax=50 ; /* Max number of years to converge */      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        fu=(*func)(u); 
     for (j=1;j<=nlstate+ndeath;j++){      } 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      SHFT(*ax,*bx,*cx,u) 
     }        SHFT(*fa,*fb,*fc,fu) 
         } 
    cov[1]=1.;  } 
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*************** linmin ************************/
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  int ncom; 
     /* Covariates have to be included here again */  double *pcom,*xicom;
      cov[2]=agefin;  double (*nrfunc)(double []); 
     
       for (k=1; k<=cptcovn;k++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];  { 
     double brent(double ax, double bx, double cx, 
 /*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/                 double (*f)(double), double tol, double *xmin); 
       }    double f1dim(double x); 
       for (k=1; k<=cptcovage;k++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];                double *fc, double (*func)(double)); 
        int j; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    double xx,xmin,bx,ax; 
     double fx,fb,fa;
     savm=oldm;   
     oldm=newm;    ncom=n; 
     maxmax=0.;    pcom=vector(1,n); 
     for(j=1;j<=nlstate;j++){    xicom=vector(1,n); 
       min=1.;    nrfunc=func; 
       max=0.;    for (j=1;j<=n;j++) { 
       for(i=1; i<=nlstate; i++) {      pcom[j]=p[j]; 
         sumnew=0;      xicom[j]=xi[j]; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    } 
         prlim[i][j]= newm[i][j]/(1-sumnew);    ax=0.0; 
         max=FMAX(max,prlim[i][j]);    xx=1.0; 
         min=FMIN(min,prlim[i][j]);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       maxmin=max-min;  #ifdef DEBUG
       maxmax=FMAX(maxmax,maxmin);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if(maxmax < ftolpl){  #endif
       return prlim;    for (j=1;j<=n;j++) { 
     }      xi[j] *= xmin; 
   }      p[j] += xi[j]; 
 }    } 
     free_vector(xicom,1,n); 
 /*************** transition probabilities **********/    free_vector(pcom,1,n); 
   } 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  /*************** powell ************************/
   double s1, s2;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   /*double t34;*/              double (*func)(double [])) 
   int i,j,j1, nc, ii, jj;  { 
     void linmin(double p[], double xi[], int n, double *fret, 
     for(i=1; i<= nlstate; i++){                double (*func)(double [])); 
     for(j=1; j<i;j++){    int i,ibig,j; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double del,t,*pt,*ptt,*xit;
         /*s2 += param[i][j][nc]*cov[nc];*/    double fp,fptt;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double *xits;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    pt=vector(1,n); 
       }    ptt=vector(1,n); 
       ps[i][j]=s2;    xit=vector(1,n); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    xits=vector(1,n); 
     }    *fret=(*func)(p); 
     for(j=i+1; j<=nlstate+ndeath;j++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    for (*iter=1;;++(*iter)) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      fp=(*fret); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      ibig=0; 
       }      del=0.0; 
       ps[i][j]=s2;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   }      fprintf(ficrespow,"%d %.12f",*iter,*fret);
   for(i=1; i<= nlstate; i++){      for (i=1;i<=n;i++) {
      s1=0;        printf(" %d %.12f",i, p[i]);
     for(j=1; j<i; j++)        fprintf(ficlog," %d %.12lf",i, p[i]);
       s1+=exp(ps[i][j]);        fprintf(ficrespow," %.12lf", p[i]);
     for(j=i+1; j<=nlstate+ndeath; j++)      }
       s1+=exp(ps[i][j]);      printf("\n");
     ps[i][i]=1./(s1+1.);      fprintf(ficlog,"\n");
     for(j=1; j<i; j++)      fprintf(ficrespow,"\n");
       ps[i][j]= exp(ps[i][j])*ps[i][i];      for (i=1;i<=n;i++) { 
     for(j=i+1; j<=nlstate+ndeath; j++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        fptt=(*fret); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #ifdef DEBUG
   } /* end i */        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #endif
     for(jj=1; jj<= nlstate+ndeath; jj++){        printf("%d",i);fflush(stdout);
       ps[ii][jj]=0;        fprintf(ficlog,"%d",i);fflush(ficlog);
       ps[ii][ii]=1;        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
           ibig=i; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        } 
     for(jj=1; jj<= nlstate+ndeath; jj++){  #ifdef DEBUG
      printf("%lf ",ps[ii][jj]);        printf("%d %.12e",i,(*fret));
    }        fprintf(ficlog,"%d %.12e",i,(*fret));
     printf("\n ");        for (j=1;j<=n;j++) {
     }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     printf("\n ");printf("%lf ",cov[2]);*/          printf(" x(%d)=%.12e",j,xit[j]);
 /*          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        }
   goto end;*/        for(j=1;j<=n;j++) {
     return ps;          printf(" p=%.12e",p[j]);
 }          fprintf(ficlog," p=%.12e",p[j]);
         }
 /**************** Product of 2 matrices ******************/        printf("\n");
         fprintf(ficlog,"\n");
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  #endif
 {      } 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  #ifdef DEBUG
   /* in, b, out are matrice of pointers which should have been initialized        int k[2],l;
      before: only the contents of out is modified. The function returns        k[0]=1;
      a pointer to pointers identical to out */        k[1]=-1;
   long i, j, k;        printf("Max: %.12e",(*func)(p));
   for(i=nrl; i<= nrh; i++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for(k=ncolol; k<=ncoloh; k++)        for (j=1;j<=n;j++) {
       for(j=ncl,out[i][k]=0.; j<=nch; j++)          printf(" %.12e",p[j]);
         out[i][k] +=in[i][j]*b[j][k];          fprintf(ficlog," %.12e",p[j]);
         }
   return out;        printf("\n");
 }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
 /************* Higher Matrix Product ***************/            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]);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 {          }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      duration (i.e. until          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        }
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  #endif
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be  
      included manually here.        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
      */        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
   int i, j, d, h, k;        return; 
   double **out, cov[NCOVMAX];      } 
   double **newm;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
   /* Hstepm could be zero and should return the unit matrix */        ptt[j]=2.0*p[j]-pt[j]; 
   for (i=1;i<=nlstate+ndeath;i++)        xit[j]=p[j]-pt[j]; 
     for (j=1;j<=nlstate+ndeath;j++){        pt[j]=p[j]; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      } 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      fptt=(*func)(ptt); 
     }      if (fptt < fp) { 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   for(h=1; h <=nhstepm; h++){        if (t < 0.0) { 
     for(d=1; d <=hstepm; d++){          linmin(p,xit,n,fret,func); 
       newm=savm;          for (j=1;j<=n;j++) { 
       /* Covariates have to be included here again */            xi[j][ibig]=xi[j][n]; 
       cov[1]=1.;            xi[j][n]=xit[j]; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          }
       if (cptcovn>0){  #ifdef DEBUG
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          for(j=1;j<=n;j++){
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/            printf(" %.12e",xit[j]);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,            fprintf(ficlog," %.12e",xit[j]);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          }
       savm=oldm;          printf("\n");
       oldm=newm;          fprintf(ficlog,"\n");
     }  #endif
     for(i=1; i<=nlstate+ndeath; i++)        }
       for(j=1;j<=nlstate+ndeath;j++) {      } 
         po[i][j][h]=newm[i][j];    } 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  } 
          */  
       }  /**** Prevalence limit (stable prevalence)  ****************/
   } /* end h */  
   return po;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 }  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
 /*************** log-likelihood *************/  
 double func( double *x)    int i, ii,j,k;
 {    double min, max, maxmin, maxmax,sumnew=0.;
   int i, ii, j, k, mi, d, kk;    double **matprod2();
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double **out, cov[NCOVMAX], **pmij();
   double **out;    double **newm;
   double sw; /* Sum of weights */    double agefin, delaymax=50 ; /* Max number of years to converge */
   double lli; /* Individual log likelihood */  
   long ipmx;    for (ii=1;ii<=nlstate+ndeath;ii++)
   /*extern weight */      for (j=1;j<=nlstate+ndeath;j++){
   /* We are differentiating ll according to initial status */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      }
   /*for(i=1;i<imx;i++)  
 printf(" %d\n",s[4][i]);     cov[1]=1.;
   */   
   cov[1]=1.;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for(k=1; k<=nlstate; k++) ll[k]=0.;      newm=savm;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      /* Covariates have to be included here again */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];       cov[2]=agefin;
        for(mi=1; mi<= wav[i]-1; mi++){    
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (k=1; k<=cptcovn;k++) {
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
             for(d=0; d<dh[mi][i]; d++){          /*      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]]);*/
               newm=savm;        }
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
               for (kk=1; kk<=cptcovage;kk++) {        for (k=1; k<=cptcovprod;k++)
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                  /*printf("%d %d",kk,Tage[kk]);*/  
               }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
               /*cov[3]=pow(cov[2],2)/1000.;*/        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      savm=oldm;
           savm=oldm;      oldm=newm;
           oldm=newm;      maxmax=0.;
       for(j=1;j<=nlstate;j++){
         min=1.;
       } /* end mult */        max=0.;
            for(i=1; i<=nlstate; i++) {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          sumnew=0;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       ipmx +=1;          prlim[i][j]= newm[i][j]/(1-sumnew);
       sw += weight[i];          max=FMAX(max,prlim[i][j]);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          min=FMIN(min,prlim[i][j]);
     } /* end of wave */        }
   } /* end of individual */        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      if(maxmax < ftolpl){
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        return prlim;
   return -l;      }
 }    }
   }
   
 /*********** Maximum Likelihood Estimation ***************/  /*************** transition probabilities ***************/ 
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
   int i,j, iter;    double s1, s2;
   double **xi,*delti;    /*double t34;*/
   double fret;    int i,j,j1, nc, ii, jj;
   xi=matrix(1,npar,1,npar);  
   for (i=1;i<=npar;i++)      for(i=1; i<= nlstate; i++){
     for (j=1;j<=npar;j++)      for(j=1; j<i;j++){
       xi[i][j]=(i==j ? 1.0 : 0.0);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   printf("Powell\n");          /*s2 += param[i][j][nc]*cov[nc];*/
   powell(p,xi,npar,ftol,&iter,&fret,func);          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 }      }
       for(j=i+1; j<=nlstate+ndeath;j++){
 /**** Computes Hessian and covariance matrix ***/        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          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);*/
   double  **a,**y,*x,pd;        }
   double **hess;        ps[i][j]=s2;
   int i, j,jk;      }
   int *indx;    }
       /*ps[3][2]=1;*/
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);    for(i=1; i<= nlstate; i++){
   void lubksb(double **a, int npar, int *indx, double b[]) ;       s1=0;
   void ludcmp(double **a, int npar, int *indx, double *d) ;      for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
   hess=matrix(1,npar,1,npar);        s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
   printf("\nCalculation of the hessian matrix. Wait...\n");      for(j=1; j<i; j++)
   for (i=1;i<=npar;i++){        ps[i][j]= exp(ps[i][j])*ps[i][i];
     printf("%d",i);fflush(stdout);      for(j=i+1; j<=nlstate+ndeath; j++)
     hess[i][i]=hessii(p,ftolhess,i,delti);        ps[i][j]= exp(ps[i][j])*ps[i][i];
     /*printf(" %f ",p[i]);*/      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   }    } /* end i */
   
   for (i=1;i<=npar;i++) {    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for (j=1;j<=npar;j++)  {      for(jj=1; jj<= nlstate+ndeath; jj++){
       if (j>i) {        ps[ii][jj]=0;
         printf(".%d%d",i,j);fflush(stdout);        ps[ii][ii]=1;
         hess[i][j]=hessij(p,delti,i,j);      }
         hess[j][i]=hess[i][j];    }
       }  
     }  
   }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   printf("\n");      for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");     }
        printf("\n ");
   a=matrix(1,npar,1,npar);      }
   y=matrix(1,npar,1,npar);      printf("\n ");printf("%lf ",cov[2]);*/
   x=vector(1,npar);  /*
   indx=ivector(1,npar);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for (i=1;i<=npar;i++)    goto end;*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      return ps;
   ludcmp(a,npar,indx,&pd);  }
   
   for (j=1;j<=npar;j++) {  /**************** Product of 2 matrices ******************/
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     lubksb(a,npar,indx,x);  {
     for (i=1;i<=npar;i++){    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       matcov[i][j]=x[i];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     }    /* in, b, out are matrice of pointers which should have been initialized 
   }       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
   printf("\n#Hessian matrix#\n");    long i, j, k;
   for (i=1;i<=npar;i++) {    for(i=nrl; i<= nrh; i++)
     for (j=1;j<=npar;j++) {      for(k=ncolol; k<=ncoloh; k++)
       printf("%.3e ",hess[i][j]);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     }          out[i][k] +=in[i][j]*b[j][k];
     printf("\n");  
   }    return out;
   }
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  /************* Higher Matrix Product ***************/
   ludcmp(a,npar,indx,&pd);  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   /*  printf("\n#Hessian matrix recomputed#\n");  {
     /* Computes the transition matrix starting at age 'age' over 
   for (j=1;j<=npar;j++) {       'nhstepm*hstepm*stepm' months (i.e. until
     for (i=1;i<=npar;i++) x[i]=0;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     x[j]=1;       nhstepm*hstepm matrices. 
     lubksb(a,npar,indx,x);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     for (i=1;i<=npar;i++){       (typically every 2 years instead of every month which is too big 
       y[i][j]=x[i];       for the memory).
       printf("%.3e ",y[i][j]);       Model is determined by parameters x and covariates have to be 
     }       included manually here. 
     printf("\n");  
   }       */
   */  
     int i, j, d, h, k;
   free_matrix(a,1,npar,1,npar);    double **out, cov[NCOVMAX];
   free_matrix(y,1,npar,1,npar);    double **newm;
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);    /* Hstepm could be zero and should return the unit matrix */
   free_matrix(hess,1,npar,1,npar);    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
 }        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
 /*************** hessian matrix ****************/    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 double hessii( double x[], double delta, int theta, double delti[])    for(h=1; h <=nhstepm; h++){
 {      for(d=1; d <=hstepm; d++){
   int i;        newm=savm;
   int l=1, lmax=20;        /* Covariates have to be included here again */
   double k1,k2;        cov[1]=1.;
   double p2[NPARMAX+1];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double res;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        for (k=1; k<=cptcovage;k++)
   double fx;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   int k=0,kmax=10;        for (k=1; k<=cptcovprod;k++)
   double l1;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   for(l=0 ; l <=lmax; l++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     l1=pow(10,l);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     delts=delt;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(k=1 ; k <kmax; k=k+1){        savm=oldm;
       delt = delta*(l1*k);        oldm=newm;
       p2[theta]=x[theta] +delt;      }
       k1=func(p2)-fx;      for(i=1; i<=nlstate+ndeath; i++)
       p2[theta]=x[theta]-delt;        for(j=1;j<=nlstate+ndeath;j++) {
       k2=func(p2)-fx;          po[i][j][h]=newm[i][j];
       /*res= (k1-2.0*fx+k2)/delt/delt; */          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */           */
              }
 #ifdef DEBUG    } /* end h */
       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);    return po;
 #endif  }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;  /*************** log-likelihood *************/
       }  double func( double *x)
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  {
         k=kmax; l=lmax*10.;    int i, ii, j, k, mi, d, kk;
       }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    double **out;
         delts=delt;    double sw; /* Sum of weights */
       }    double lli; /* Individual log likelihood */
     }    int s1, s2;
   }    double bbh, survp;
   delti[theta]=delts;    long ipmx;
   return res;    /*extern weight */
      /* We are differentiating ll according to initial status */
 }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
 double hessij( double x[], double delti[], int thetai,int thetaj)      printf(" %d\n",s[4][i]);
 {    */
   int i;    cov[1]=1.;
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double p2[NPARMAX+1];  
   int k;    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fx=func(x);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (k=1; k<=2; k++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1;i<=npar;i++) p2[i]=x[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
     p2[thetai]=x[thetai]+delti[thetai]/k;            for (j=1;j<=nlstate+ndeath;j++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     k1=func(p2)-fx;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
     p2[thetai]=x[thetai]+delti[thetai]/k;          for(d=0; d<dh[mi][i]; d++){
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            newm=savm;
     k2=func(p2)-fx;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
     p2[thetai]=x[thetai]-delti[thetai]/k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            }
     k3=func(p2)-fx;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     p2[thetai]=x[thetai]-delti[thetai]/k;            savm=oldm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            oldm=newm;
     k4=func(p2)-fx;          } /* end mult */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        
 #ifdef DEBUG          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     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);          /* But now since version 0.9 we anticipate for bias and large stepm.
 #endif           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   }           * (in months) between two waves is not a multiple of stepm, we rounded to 
   return res;           * the nearest (and in case of equal distance, to the lowest) interval but now
 }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 /************** Inverse of matrix **************/           * probability in order to take into account the bias as a fraction of the way
 void ludcmp(double **a, int n, int *indx, double *d)           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 {           * -stepm/2 to stepm/2 .
   int i,imax,j,k;           * For stepm=1 the results are the same as for previous versions of Imach.
   double big,dum,sum,temp;           * For stepm > 1 the results are less biased than in previous versions. 
   double *vv;           */
            s1=s[mw[mi][i]][i];
   vv=vector(1,n);          s2=s[mw[mi+1][i]][i];
   *d=1.0;          bbh=(double)bh[mi][i]/(double)stepm; 
   for (i=1;i<=n;i++) {          /* bias is positive if real duration
     big=0.0;           * is higher than the multiple of stepm and negative otherwise.
     for (j=1;j<=n;j++)           */
       if ((temp=fabs(a[i][j])) > big) big=temp;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          if( s2 > nlstate){ 
     vv[i]=1.0/big;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   }               to the likelihood is the probability to die between last step unit time and current 
   for (j=1;j<=n;j++) {               step unit time, which is also the differences between probability to die before dh 
     for (i=1;i<j;i++) {               and probability to die before dh-stepm . 
       sum=a[i][j];               In version up to 0.92 likelihood was computed
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          as if date of death was unknown. Death was treated as any other
       a[i][j]=sum;          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
     big=0.0;          to consider that at each interview the state was recorded
     for (i=j;i<=n;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<j;k++)          the contribution of an exact death to the likelihood. This new
         sum -= a[i][k]*a[k][j];          contribution is smaller and very dependent of the step unit
       a[i][j]=sum;          stepm. It is no more the probability to die between last interview
       if ( (dum=vv[i]*fabs(sum)) >= big) {          and month of death but the probability to survive from last
         big=dum;          interview up to one month before death multiplied by the
         imax=i;          probability to die within a month. Thanks to Chris
       }          Jackson for correcting this bug.  Former versions increased
     }          mortality artificially. The bad side is that we add another loop
     if (j != imax) {          which slows down the processing. The difference can be up to 10%
       for (k=1;k<=n;k++) {          lower mortality.
         dum=a[imax][k];            */
         a[imax][k]=a[j][k];            lli=log(out[s1][s2] - savm[s1][s2]);
         a[j][k]=dum;          }else{
       }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       *d = -(*d);            /*  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 */
       vv[imax]=vv[j];          } 
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     indx[j]=imax;          /*if(lli ==000.0)*/
     if (a[j][j] == 0.0) a[j][j]=TINY;          /*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 (j != n) {          ipmx +=1;
       dum=1.0/(a[j][j]);          sw += weight[i];
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
   }      } /* end of individual */
   free_vector(vv,1,n);  /* Doesn't work */    }  else if(mle==2){
 ;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 void lubksb(double **a, int n, int *indx, double b[])          for (ii=1;ii<=nlstate+ndeath;ii++)
 {            for (j=1;j<=nlstate+ndeath;j++){
   int i,ii=0,ip,j;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double sum;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   for (i=1;i<=n;i++) {          for(d=0; d<=dh[mi][i]; d++){
     ip=indx[i];            newm=savm;
     sum=b[ip];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     b[ip]=b[i];            for (kk=1; kk<=cptcovage;kk++) {
     if (ii)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            }
     else if (sum) ii=i;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     b[i]=sum;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   for (i=n;i>=1;i--) {            oldm=newm;
     sum=b[i];          } /* end mult */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        
     b[i]=sum/a[i][i];          /*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.
 }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
 /************ Frequencies ********************/           * the nearest (and in case of equal distance, to the lowest) interval but now
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 {  /* Some frequencies */           * (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
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   double ***freq; /* Frequencies */           * -stepm/2 to stepm/2 .
   double *pp;           * For stepm=1 the results are the same as for previous versions of Imach.
   double pos;           * For stepm > 1 the results are less biased than in previous versions. 
   FILE *ficresp;           */
   char fileresp[FILENAMELENGTH];          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   pp=vector(1,nlstate);          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
   strcpy(fileresp,"p");           * is higher than the multiple of stepm and negative otherwise.
   strcat(fileresp,fileres);           */
   if((ficresp=fopen(fileresp,"w"))==NULL) {          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 */
     printf("Problem with prevalence resultfile: %s\n", fileresp);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     exit(0);          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
   }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          /*if(lli ==000.0)*/
   j1=0;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
   j=cptcovn;          sw += weight[i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
   for(k1=1; k1<=j;k1++){      } /* end of individual */
    for(i1=1; i1<=ncodemax[k1];i1++){    }  else if(mle==3){  /* exponential inter-extrapolation */
        j1++;      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=-1; i<=nlstate+ndeath; i++)          for(mi=1; mi<= wav[i]-1; mi++){
          for (jk=-1; jk<=nlstate+ndeath; jk++)            for (ii=1;ii<=nlstate+ndeath;ii++)
            for(m=agemin; m <= agemax+3; m++)            for (j=1;j<=nlstate+ndeath;j++){
              freq[i][jk][m]=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                      savm[ii][j]=(ii==j ? 1.0 : 0.0);
        for (i=1; i<=imx; i++) {            }
          bool=1;          for(d=0; d<dh[mi][i]; d++){
          if  (cptcovn>0) {            newm=savm;
            for (z1=1; z1<=cptcovn; z1++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;            for (kk=1; kk<=cptcovage;kk++) {
          }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if (bool==1) {            }
            for(m=firstpass; m<=lastpass-1; m++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
              if(agev[m][i]==0) agev[m][i]=agemax+1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              if(agev[m][i]==1) agev[m][i]=agemax+2;            savm=oldm;
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            oldm=newm;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          } /* end mult */
            }        
          }          /*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.
         if  (cptcovn>0) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
          fprintf(ficresp, "\n#Variable");           * (in months) between two waves is not a multiple of stepm, we rounded to 
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);           * the nearest (and in case of equal distance, to the lowest) interval but now
        }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
        fprintf(ficresp, "\n#");           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
        for(i=1; i<=nlstate;i++)           * probability in order to take into account the bias as a fraction of the way
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
        fprintf(ficresp, "\n");           * -stepm/2 to stepm/2 .
                   * For stepm=1 the results are the same as for previous versions of Imach.
   for(i=(int)agemin; i <= (int)agemax+3; i++){           * For stepm > 1 the results are less biased than in previous versions. 
     if(i==(int)agemax+3)           */
       printf("Total");          s1=s[mw[mi][i]][i];
     else          s2=s[mw[mi+1][i]][i];
       printf("Age %d", i);          bbh=(double)bh[mi][i]/(double)stepm; 
     for(jk=1; jk <=nlstate ; jk++){          /* bias is positive if real duration
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)           * is higher than the multiple of stepm and negative otherwise.
         pp[jk] += freq[jk][m][i];           */
     }          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
     for(jk=1; jk <=nlstate ; jk++){          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 */
       for(m=-1, pos=0; m <=0 ; m++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         pos += freq[jk][m][i];          /*if(lli ==000.0)*/
       if(pp[jk]>=1.e-10)          /*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); */
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          ipmx +=1;
       else          sw += weight[i];
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     for(jk=1; jk <=nlstate ; jk++){      } /* end of individual */
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         pp[jk] += freq[jk][m][i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(jk=1,pos=0; jk <=nlstate ; jk++)        for(mi=1; mi<= wav[i]-1; mi++){
       pos += pp[jk];          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(jk=1; jk <=nlstate ; jk++){            for (j=1;j<=nlstate+ndeath;j++){
       if(pos>=1.e-5)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       else            }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          for(d=0; d<dh[mi][i]; d++){
       if( i <= (int) agemax){            newm=savm;
         if(pos>=1.e-5)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            for (kk=1; kk<=cptcovage;kk++) {
       else              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            }
       }          
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(jk=-1; jk <=nlstate+ndeath; jk++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(m=-1; m <=nlstate+ndeath; m++)            savm=oldm;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            oldm=newm;
     if(i <= (int) agemax)          } /* end mult */
       fprintf(ficresp,"\n");        
     printf("\n");          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
     }          if( s2 > nlstate){ 
  }            lli=log(out[s1][s2] - savm[s1][s2]);
            }else{
   fclose(ficresp);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          }
   free_vector(pp,1,nlstate);          ipmx +=1;
           sw += weight[i];
 }  /* End of Freq */          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]); */
 /************* Waves Concatenation ***************/        } /* end of wave */
       } /* end of individual */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      Death is a valid wave (if date is known).        for(mi=1; mi<= wav[i]-1; mi++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          for (ii=1;ii<=nlstate+ndeath;ii++)
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            for (j=1;j<=nlstate+ndeath;j++){
      and mw[mi+1][i]. dh depends on stepm.              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   int i, mi, m;          for(d=0; d<dh[mi][i]; d++){
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            newm=savm;
 float sum=0.;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=imx; i++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     mi=0;            }
     m=firstpass;          
     while(s[m][i] <= nlstate){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if(s[m][i]>=1)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         mw[++mi][i]=m;            savm=oldm;
       if(m >=lastpass)            oldm=newm;
         break;          } /* end mult */
       else        
         m++;          s1=s[mw[mi][i]][i];
     }/* end while */          s2=s[mw[mi+1][i]][i];
     if (s[m][i] > nlstate){          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       mi++;     /* Death is another wave */          ipmx +=1;
       /* if(mi==0)  never been interviewed correctly before death */          sw += weight[i];
          /* Only death is a correct wave */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       mw[mi][i]=m;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     }        } /* end of wave */
       } /* end of individual */
     wav[i]=mi;    } /* End of if */
     if(mi==0)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    /* 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 */
     return -l;
   for(i=1; i<=imx; i++){  }
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)  /*************** log-likelihood *************/
         dh[mi][i]=1;  double funcone( double *x)
       else{  {
         if (s[mw[mi+1][i]][i] > nlstate) {    int i, ii, j, k, mi, d, kk;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
           if(j=0) j=1;  /* Survives at least one month after exam */    double **out;
         }    double lli; /* Individual log likelihood */
         else{    int s1, s2;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    double bbh, survp;
           k=k+1;    /*extern weight */
           if (j >= jmax) jmax=j;    /* We are differentiating ll according to initial status */
           else if (j <= jmin)jmin=j;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           sum=sum+j;    /*for(i=1;i<imx;i++) 
         }      printf(" %d\n",s[4][i]);
         jk= j/stepm;    */
         jl= j -jk*stepm;    cov[1]=1.;
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)    for(k=1; k<=nlstate; k++) ll[k]=0.;
           dh[mi][i]=jk;  
         else    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           dh[mi][i]=jk+1;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if(dh[mi][i]==0)      for(mi=1; mi<= wav[i]-1; mi++){
           dh[mi][i]=1; /* At least one step */        for (ii=1;ii<=nlstate+ndeath;ii++)
       }          for (j=1;j<=nlstate+ndeath;j++){
     }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);          }
 }        for(d=0; d<dh[mi][i]; d++){
 /*********** Tricode ****************************/          newm=savm;
 void tricode(int *Tvar, int **nbcode, int imx)          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {          for (kk=1; kk<=cptcovage;kk++) {
   int Ndum[80],ij=1, k, j, i, Ntvar[20];            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int cptcode=0;          }
   for (k=0; k<79; k++) Ndum[k]=0;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (k=1; k<=7; k++) ncodemax[k]=0;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
   for (j=1; j<=cptcovn; j++) {          oldm=newm;
     for (i=1; i<=imx; i++) {        } /* end mult */
       ij=(int)(covar[Tvar[j]][i]);        
       Ndum[ij]++;        s1=s[mw[mi][i]][i];
       if (ij > cptcode) cptcode=ij;        s2=s[mw[mi+1][i]][i];
     }        bbh=(double)bh[mi][i]/(double)stepm; 
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/        /* bias is positive if real duration
     for (i=0; i<=cptcode; i++) {         * is higher than the multiple of stepm and negative otherwise.
       if(Ndum[i]!=0) ncodemax[j]++;         */
     }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
            lli=log(out[s1][s2] - savm[s1][s2]);
     ij=1;        } else if (mle==1){
     for (i=1; i<=ncodemax[j]; i++) {          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for (k=0; k<=79; k++) {        } else if(mle==2){
         if (Ndum[k] != 0) {          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 */
           nbcode[Tvar[j]][ij]=k;        } else if(mle==3){  /* exponential inter-extrapolation */
           ij++;          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 */
         if (ij > ncodemax[j]) break;          lli=log(out[s1][s2]); /* Original formula */
       }          } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     }          lli=log(out[s1][s2]); /* Original formula */
   }          } /* End of if */
          ipmx +=1;
 }        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /*********** Health Expectancies ****************/  /*       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){
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
 {   %10.6f %10.6f %10.6f ", \
   /* Health expectancies */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   int i, j, nhstepm, hstepm, h;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   double age, agelim,hf;          for(k=1,l=0.; k<=nlstate; k++) 
   double ***p3mat;            fprintf(ficresilk," %10.6f",ll[k]);
            fprintf(ficresilk,"\n");
   fprintf(ficreseij,"# Health expectancies\n");        }
   fprintf(ficreseij,"# Age");      } /* end of wave */
   for(i=1; i<=nlstate;i++)    } /* end of individual */
     for(j=1; j<=nlstate;j++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       fprintf(ficreseij," %1d-%1d",i,j);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   fprintf(ficreseij,"\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
   hstepm=1*YEARM; /*  Every j years of age (in month) */  }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   
   agelim=AGESUP;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpr, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  {
     /* nhstepm age range expressed in number of stepm */    /* This routine should help understanding what is done with the selection of individuals/waves and
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);       to check the exact contribution to the likelihood.
     /* Typically if 20 years = 20*12/6=40 stepm */       Plotting could be done.
     if (stepm >= YEARM) hstepm=1;     */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    int k;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if(globpr !=0){ /* Just counts and sums no printings */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      strcpy(fileresilk,"ilk"); 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      strcat(fileresilk,fileres);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     for(i=1; i<=nlstate;i++)      }
       for(j=1; j<=nlstate;j++)      fprintf(ficresilk, "#individual(line's record) s1 s2 wave# effective_wave# number_of_product_matrix pij weight 2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state\n");
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight out sav ");
           eij[i][j][(int)age] +=p3mat[i][j][h];      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         }      for(k=1; k<=nlstate; k++) 
            fprintf(ficresilk," ll[%d]",k);
     hf=1;      fprintf(ficresilk,"\n");
     if (stepm >= YEARM) hf=stepm/YEARM;    }
     fprintf(ficreseij,"%.0f",age );  
     for(i=1; i<=nlstate;i++)    *fretone=(*funcone)(p);
       for(j=1; j<=nlstate;j++){    if(globpr !=0){
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);      fclose(ficresilk);
       }      if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     fprintf(ficreseij,"\n");        printf("Problem with html file: %s\n", optionfilehtm);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   }        exit(0);
 }      }
       else{
 /************ Variance ******************/        fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",fileresilk);
 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)        fclose(fichtm);
 {      }
   /* Variance of health expectancies */    }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    return;
   double **newm;  }
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h;  /*********** Maximum Likelihood Estimation ***************/
   int k, cptcode;  
    double *xp;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   double **gp, **gm;  {
   double ***gradg, ***trgradg;    int i,j, iter;
   double ***p3mat;    double **xi;
   double age,agelim;    double fret;
   int theta;    double fretone; /* Only one call to likelihood */
     char filerespow[FILENAMELENGTH];
    fprintf(ficresvij,"# Covariances of life expectancies\n");    xi=matrix(1,npar,1,npar);
   fprintf(ficresvij,"# Age");    for (i=1;i<=npar;i++)
   for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++)
     for(j=1; j<=nlstate;j++)        xi[i][j]=(i==j ? 1.0 : 0.0);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   fprintf(ficresvij,"\n");    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
   xp=vector(1,npar);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   dnewm=matrix(1,nlstate,1,npar);      printf("Problem with resultfile: %s\n", filerespow);
   doldm=matrix(1,nlstate,1,nlstate);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      }
   hstepm=1*YEARM; /* Every year of age */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for (i=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)fprintf(ficrespow," p%1d%1d",i,j);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(ficrespow,"\n");
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    powell(p,xi,npar,ftol,&iter,&fret,func);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    fclose(ficrespow);
     gp=matrix(0,nhstepm,1,nlstate);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     gm=matrix(0,nhstepm,1,nlstate);    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));
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }  /**** Computes Hessian and covariance matrix ***/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
       for(j=1; j<= nlstate; j++){    double  **a,**y,*x,pd;
         for(h=0; h<=nhstepm; h++){    double **hess;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    int i, j,jk;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    int *indx;
         }  
       }    double hessii(double p[], double delta, int theta, double delti[]);
        double hessij(double p[], double delti[], int i, int j);
       for(i=1; i<=npar; i++) /* Computes gradient */    void lubksb(double **a, int npar, int *indx, double b[]) ;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    void ludcmp(double **a, int npar, int *indx, double *d) ;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    hess=matrix(1,npar,1,npar);
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    printf("\nCalculation of the hessian matrix. Wait...\n");
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    for (i=1;i<=npar;i++){
         }      printf("%d",i);fflush(stdout);
       }      fprintf(ficlog,"%d",i);fflush(ficlog);
       for(j=1; j<= nlstate; j++)      hess[i][i]=hessii(p,ftolhess,i,delti);
         for(h=0; h<=nhstepm; h++){      /*printf(" %f ",p[i]);*/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      /*printf(" %lf ",hess[i][i]);*/
         }    }
     } /* End theta */    
     for (i=1;i<=npar;i++) {
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      for (j=1;j<=npar;j++)  {
         if (j>i) { 
     for(h=0; h<=nhstepm; h++)          printf(".%d%d",i,j);fflush(stdout);
       for(j=1; j<=nlstate;j++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         for(theta=1; theta <=npar; theta++)          hess[i][j]=hessij(p,delti,i,j);
           trgradg[h][j][theta]=gradg[h][theta][j];          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
     for(i=1;i<=nlstate;i++)        }
       for(j=1;j<=nlstate;j++)      }
         vareij[i][j][(int)age] =0.;    }
     for(h=0;h<=nhstepm;h++){    printf("\n");
       for(k=0;k<=nhstepm;k++){    fprintf(ficlog,"\n");
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         for(i=1;i<=nlstate;i++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           for(j=1;j<=nlstate;j++)    
             vareij[i][j][(int)age] += doldm[i][j];    a=matrix(1,npar,1,npar);
       }    y=matrix(1,npar,1,npar);
     }    x=vector(1,npar);
     h=1;    indx=ivector(1,npar);
     if (stepm >= YEARM) h=stepm/YEARM;    for (i=1;i<=npar;i++)
     fprintf(ficresvij,"%.0f ",age );      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     for(i=1; i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    for (j=1;j<=npar;j++) {
       }      for (i=1;i<=npar;i++) x[i]=0;
     fprintf(ficresvij,"\n");      x[j]=1;
     free_matrix(gp,0,nhstepm,1,nlstate);      lubksb(a,npar,indx,x);
     free_matrix(gm,0,nhstepm,1,nlstate);      for (i=1;i<=npar;i++){ 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        matcov[i][j]=x[i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
   } /* End age */  
      printf("\n#Hessian matrix#\n");
   free_vector(xp,1,npar);    fprintf(ficlog,"\n#Hessian matrix#\n");
   free_matrix(doldm,1,nlstate,1,npar);    for (i=1;i<=npar;i++) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
 }        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
 /************ Variance of prevlim ******************/      printf("\n");
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      fprintf(ficlog,"\n");
 {    }
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /* Recompute Inverse */
   double **newm;    for (i=1;i<=npar;i++)
   double **dnewm,**doldm;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   int i, j, nhstepm, hstepm;    ludcmp(a,npar,indx,&pd);
   int k, cptcode;  
   double *xp;    /*  printf("\n#Hessian matrix recomputed#\n");
   double *gp, *gm;  
   double **gradg, **trgradg;    for (j=1;j<=npar;j++) {
   double age,agelim;      for (i=1;i<=npar;i++) x[i]=0;
   int theta;      x[j]=1;
          lubksb(a,npar,indx,x);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      for (i=1;i<=npar;i++){ 
   fprintf(ficresvpl,"# Age");        y[i][j]=x[i];
   for(i=1; i<=nlstate;i++)        printf("%.3e ",y[i][j]);
       fprintf(ficresvpl," %1d-%1d",i,i);        fprintf(ficlog,"%.3e ",y[i][j]);
   fprintf(ficresvpl,"\n");      }
       printf("\n");
   xp=vector(1,npar);      fprintf(ficlog,"\n");
   dnewm=matrix(1,nlstate,1,npar);    }
   doldm=matrix(1,nlstate,1,nlstate);    */
    
   hstepm=1*YEARM; /* Every year of age */    free_matrix(a,1,npar,1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    free_matrix(y,1,npar,1,npar);
   agelim = AGESUP;    free_vector(x,1,npar);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    free_ivector(indx,1,npar);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_matrix(hess,1,npar,1,npar);
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);  }
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);  /*************** hessian matrix ****************/
   double hessii( double x[], double delta, int theta, double delti[])
     for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++){ /* Computes gradient */    int i;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int l=1, lmax=20;
       }    double k1,k2;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double p2[NPARMAX+1];
       for(i=1;i<=nlstate;i++)    double res;
         gp[i] = prlim[i][i];    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
        double fx;
       for(i=1; i<=npar; i++) /* Computes gradient */    int k=0,kmax=10;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double l1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    fx=func(x);
         gm[i] = prlim[i][i];    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
       for(i=1;i<=nlstate;i++)      l1=pow(10,l);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      delts=delt;
     } /* End theta */      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
     trgradg =matrix(1,nlstate,1,npar);        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
     for(j=1; j<=nlstate;j++)        p2[theta]=x[theta]-delt;
       for(theta=1; theta <=npar; theta++)        k2=func(p2)-fx;
         trgradg[j][theta]=gradg[theta][j];        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     for(i=1;i<=nlstate;i++)        
       varpl[i][(int)age] =0.;  #ifdef DEBUG
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        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);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        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);
     for(i=1;i<=nlstate;i++)  #endif
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     fprintf(ficresvpl,"%.0f ",age );          k=kmax;
     for(i=1; i<=nlstate;i++)        }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     fprintf(ficresvpl,"\n");          k=kmax; l=lmax*10.;
     free_vector(gp,1,nlstate);        }
     free_vector(gm,1,nlstate);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     free_matrix(gradg,1,npar,1,nlstate);          delts=delt;
     free_matrix(trgradg,1,nlstate,1,npar);        }
   } /* End age */      }
     }
   free_vector(xp,1,npar);    delti[theta]=delts;
   free_matrix(doldm,1,nlstate,1,npar);    return res; 
   free_matrix(dnewm,1,nlstate,1,nlstate);    
   }
 }  
   double hessij( double x[], double delti[], int thetai,int thetaj)
   {
     int i;
 /***********************************************/    int l=1, l1, lmax=20;
 /**************** Main Program *****************/    double k1,k2,k3,k4,res,fx;
 /***********************************************/    double p2[NPARMAX+1];
     int k;
 /*int main(int argc, char *argv[])*/  
 int main()    fx=func(x);
 {    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double agedeb, agefin,hf;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double agemin=1.e20, agemax=-1.e20;      k1=func(p2)-fx;
     
   double fret;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double **xi,tmp,delta;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
   double dum; /* Dummy variable */    
   double ***p3mat;      p2[thetai]=x[thetai]-delti[thetai]/k;
   int *indx;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   char line[MAXLINE], linepar[MAXLINE];      k3=func(p2)-fx;
   char title[MAXLINE];    
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      p2[thetai]=x[thetai]-delti[thetai]/k;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   char filerest[FILENAMELENGTH];      k4=func(p2)-fx;
   char fileregp[FILENAMELENGTH];      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  #ifdef DEBUG
   int firstobs=1, lastobs=10;      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);
   int sdeb, sfin; /* Status at beginning and end */      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);
   int c,  h , cpt,l;  #endif
   int ju,jl, mi;    }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize;    return res;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  }
    
   int hstepm, nhstepm;  /************** Inverse of matrix **************/
   double bage, fage, age, agelim, agebase;  void ludcmp(double **a, int n, int *indx, double *d) 
   double ftolpl=FTOL;  { 
   double **prlim;    int i,imax,j,k; 
   double *severity;    double big,dum,sum,temp; 
   double ***param; /* Matrix of parameters */    double *vv; 
   double  *p;   
   double **matcov; /* Matrix of covariance */    vv=vector(1,n); 
   double ***delti3; /* Scale */    *d=1.0; 
   double *delti; /* Scale */    for (i=1;i<=n;i++) { 
   double ***eij, ***vareij;      big=0.0; 
   double **varpl; /* Variances of prevalence limits by age */      for (j=1;j<=n;j++) 
   double *epj, vepp;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   char *alph[]={"a","a","b","c","d","e"}, str[4];      vv[i]=1.0/big; 
     } 
   char z[1]="c", occ;    for (j=1;j<=n;j++) { 
 #include <sys/time.h>      for (i=1;i<j;i++) { 
 #include <time.h>        sum=a[i][j]; 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   /* long total_usecs;        a[i][j]=sum; 
   struct timeval start_time, end_time;      } 
        big=0.0; 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
         for (k=1;k<j;k++) 
   printf("\nIMACH, Version 0.64a");          sum -= a[i][k]*a[k][j]; 
   printf("\nEnter the parameter file name: ");        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
 #ifdef windows          big=dum; 
   scanf("%s",pathtot);          imax=i; 
   getcwd(pathcd, size);        } 
   /*cygwin_split_path(pathtot,path,optionfile);      } 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      if (j != imax) { 
   /* cutv(path,optionfile,pathtot,'\\');*/        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
 split(pathtot, path,optionfile);          a[imax][k]=a[j][k]; 
   chdir(path);          a[j][k]=dum; 
   replace(pathc,path);        } 
 #endif        *d = -(*d); 
 #ifdef unix        vv[imax]=vv[j]; 
   scanf("%s",optionfile);      } 
 #endif      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
 /*-------- arguments in the command line --------*/      if (j != n) { 
         dum=1.0/(a[j][j]); 
   strcpy(fileres,"r");        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   strcat(fileres, optionfile);      } 
     } 
   /*---------arguments file --------*/    free_vector(vv,1,n);  /* Doesn't work */
   ;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  } 
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;  void lubksb(double **a, int n, int *indx, double b[]) 
   }  { 
     int i,ii=0,ip,j; 
   strcpy(filereso,"o");    double sum; 
   strcat(filereso,fileres);   
   if((ficparo=fopen(filereso,"w"))==NULL) {    for (i=1;i<=n;i++) { 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      ip=indx[i]; 
   }      sum=b[ip]; 
       b[ip]=b[i]; 
   /* Reads comments: lines beginning with '#' */      if (ii) 
   while((c=getc(ficpar))=='#' && c!= EOF){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     ungetc(c,ficpar);      else if (sum) ii=i; 
     fgets(line, MAXLINE, ficpar);      b[i]=sum; 
     puts(line);    } 
     fputs(line,ficparo);    for (i=n;i>=1;i--) { 
   }      sum=b[i]; 
   ungetc(c,ficpar);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
   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);    } 
   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);  } 
   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);  
   /************ Frequencies ********************/
   covar=matrix(0,NCOVMAX,1,n);      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)
   if (strlen(model)<=1) cptcovn=0;  {  /* Some frequencies */
   else {    
     j=0;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     j=nbocc(model,'+');    int first;
     cptcovn=j+1;    double ***freq; /* Frequencies */
   }    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
   ncovmodel=2+cptcovn;    FILE *ficresp;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    char fileresp[FILENAMELENGTH];
      
   /* Read guess parameters */    pp=vector(1,nlstate);
   /* Reads comments: lines beginning with '#' */    prop=matrix(1,nlstate,iagemin,iagemax+3);
   while((c=getc(ficpar))=='#' && c!= EOF){    strcpy(fileresp,"p");
     ungetc(c,ficpar);    strcat(fileresp,fileres);
     fgets(line, MAXLINE, ficpar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
     puts(line);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     fputs(line,ficparo);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   }      exit(0);
   ungetc(c,ficpar);    }
      freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    j1=0;
     for(i=1; i <=nlstate; i++)    
     for(j=1; j <=nlstate+ndeath-1; j++){    j=cptcoveff;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);    first=1;
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);    for(k1=1; k1<=j;k1++){
         printf(" %lf",param[i][j][k]);      for(i1=1; i1<=ncodemax[k1];i1++){
         fprintf(ficparo," %lf",param[i][j][k]);        j1++;
       }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       fscanf(ficpar,"\n");          scanf("%d", i);*/
       printf("\n");        for (i=-1; i<=nlstate+ndeath; i++)  
       fprintf(ficparo,"\n");          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     }            for(m=iagemin; m <= iagemax+3; m++)
                freq[i][jk][m]=0;
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
   p=param[1][1];      for (i=1; i<=nlstate; i++)  
          for(m=iagemin; m <= iagemax+3; m++)
   /* Reads comments: lines beginning with '#' */          prop[i][m]=0;
   while((c=getc(ficpar))=='#' && c!= EOF){        
     ungetc(c,ficpar);        dateintsum=0;
     fgets(line, MAXLINE, ficpar);        k2cpt=0;
     puts(line);        for (i=1; i<=imx; i++) {
     fputs(line,ficparo);          bool=1;
   }          if  (cptcovn>0) {
   ungetc(c,ficpar);            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                bool=0;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          }
   for(i=1; i <=nlstate; i++){          if (bool==1){
     for(j=1; j <=nlstate+ndeath-1; j++){            for(m=firstpass; m<=lastpass; m++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);              k2=anint[m][i]+(mint[m][i]/12.);
       printf("%1d%1d",i,j);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       fprintf(ficparo,"%1d%1d",i1,j1);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       for(k=1; k<=ncovmodel;k++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         fscanf(ficpar,"%le",&delti3[i][j][k]);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         printf(" %le",delti3[i][j][k]);                if (m<lastpass) {
         fprintf(ficparo," %le",delti3[i][j][k]);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       fscanf(ficpar,"\n");                }
       printf("\n");                
       fprintf(ficparo,"\n");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     }                  dateintsum=dateintsum+k2;
   }                  k2cpt++;
   delti=delti3[1][1];                }
                  /*}*/
   /* Reads comments: lines beginning with '#' */            }
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);         
     puts(line);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     fputs(line,ficparo);  
   }        if  (cptcovn>0) {
   ungetc(c,ficpar);          fprintf(ficresp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   matcov=matrix(1,npar,1,npar);          fprintf(ficresp, "**********\n#");
   for(i=1; i <=npar; i++){        }
     fscanf(ficpar,"%s",&str);        for(i=1; i<=nlstate;i++) 
     printf("%s",str);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     fprintf(ficparo,"%s",str);        fprintf(ficresp, "\n");
     for(j=1; j <=i; j++){        
       fscanf(ficpar," %le",&matcov[i][j]);        for(i=iagemin; i <= iagemax+3; i++){
       printf(" %.5le",matcov[i][j]);          if(i==iagemax+3){
       fprintf(ficparo," %.5le",matcov[i][j]);            fprintf(ficlog,"Total");
     }          }else{
     fscanf(ficpar,"\n");            if(first==1){
     printf("\n");              first=0;
     fprintf(ficparo,"\n");              printf("See log file for details...\n");
   }            }
   for(i=1; i <=npar; i++)            fprintf(ficlog,"Age %d", i);
     for(j=i+1;j<=npar;j++)          }
       matcov[i][j]=matcov[j][i];          for(jk=1; jk <=nlstate ; jk++){
                for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   printf("\n");              pp[jk] += freq[jk][m][i]; 
           }
           for(jk=1; jk <=nlstate ; jk++){
     /*-------- data file ----------*/            for(m=-1, pos=0; m <=0 ; m++)
     if((ficres =fopen(fileres,"w"))==NULL) {              pos += freq[jk][m][i];
       printf("Problem with resultfile: %s\n", fileres);goto end;            if(pp[jk]>=1.e-10){
     }              if(first==1){
     fprintf(ficres,"#%s\n",version);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                  }
     if((fic=fopen(datafile,"r"))==NULL)    {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       printf("Problem with datafile: %s\n", datafile);goto end;            }else{
     }              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     n= lastobs;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     severity = vector(1,maxwav);            }
     outcome=imatrix(1,maxwav+1,1,n);          }
     num=ivector(1,n);  
     moisnais=vector(1,n);          for(jk=1; jk <=nlstate ; jk++){
     annais=vector(1,n);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     moisdc=vector(1,n);              pp[jk] += freq[jk][m][i];
     andc=vector(1,n);          }       
     agedc=vector(1,n);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     cod=ivector(1,n);            pos += pp[jk];
     weight=vector(1,n);            posprop += prop[jk][i];
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          }
     mint=matrix(1,maxwav,1,n);          for(jk=1; jk <=nlstate ; jk++){
     anint=matrix(1,maxwav,1,n);            if(pos>=1.e-5){
     s=imatrix(1,maxwav+1,1,n);              if(first==1)
     adl=imatrix(1,maxwav+1,1,n);                    printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     tab=ivector(1,NCOVMAX);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     ncodemax=ivector(1,8);            }else{
               if(first==1)
     i=1;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     while (fgets(line, MAXLINE, fic) != NULL)    {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       if ((i >= firstobs) && (i <=lastobs)) {            }
                    if( i <= iagemax){
         for (j=maxwav;j>=1;j--){              if(pos>=1.e-5){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           strcpy(line,stra);                /*probs[i][jk][j1]= pp[jk]/pos;*/
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              }
         }              else
                        fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         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);          for(jk=-1; jk <=nlstate+ndeath; jk++)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              if(first==1)
         for (j=ncov;j>=1;j--){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         }              }
         num[i]=atol(stra);          if(i <= iagemax)
             fprintf(ficresp,"\n");
         /*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]));*/          if(first==1)
             printf("Others in log...\n");
         i=i+1;          fprintf(ficlog,"\n");
       }        }
     }      }
     }
     /*scanf("%d",i);*/    dateintmean=dateintsum/k2cpt; 
   imx=i-1; /* Number of individuals */   
     fclose(ficresp);
   /* Calculation of the number of parameter from char model*/    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   Tvar=ivector(1,15);        free_vector(pp,1,nlstate);
   Tage=ivector(1,15);          free_matrix(prop,1,nlstate,iagemin, iagemax+3);
        /* End of Freq */
   if (strlen(model) >1){  }
     j=0, j1=0;  
     j=nbocc(model,'+');  /************ Prevalence ********************/
     j1=nbocc(model,'*');  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)
     cptcovn=j+1;  {  
        /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     strcpy(modelsav,model);       in each health status at the date of interview (if between dateprev1 and dateprev2).
     if (j==0) {       We still use firstpass and lastpass as another selection.
       if (j1==0){    */
        cutv(stra,strb,modelsav,'V');   
        Tvar[1]=atoi(strb);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       }    double ***freq; /* Frequencies */
       else if (j1==1) {    double *pp, **prop;
        cutv(stra,strb,modelsav,'*');    double pos,posprop; 
        /*      printf("stra=%s strb=%s modelsav=%s ",stra,strb,modelsav);*/    double  y2; /* in fractional years */
        Tage[1]=1; cptcovage++;    int iagemin, iagemax;
        if (strcmp(stra,"age")==0) {  
          cutv(strd,strc,strb,'V');    iagemin= (int) agemin;
          Tvar[1]=atoi(strc);    iagemax= (int) agemax;
        }    /*pp=vector(1,nlstate);*/
        else if (strcmp(strb,"age")==0) {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
          cutv(strd,strc,stra,'V');    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
          Tvar[1]=atoi(strc);    j1=0;
        }    
        else {printf("Error"); exit(0);}    j=cptcoveff;
       }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     }    
     else {    for(k1=1; k1<=j;k1++){
       for(i=j; i>=1;i--){      for(i1=1; i1<=ncodemax[k1];i1++){
         cutv(stra,strb,modelsav,'+');        j1++;
         /*printf("%s %s %s\n", stra,strb,modelsav);*/        
         if (strchr(strb,'*')) {        for (i=1; i<=nlstate; i++)  
           cutv(strd,strc,strb,'*');          for(m=iagemin; m <= iagemax+3; m++)
           if (strcmp(strc,"age")==0) {            prop[i][m]=0.0;
             cutv(strb,stre,strd,'V');       
             Tvar[i+1]=atoi(stre);        for (i=1; i<=imx; i++) { /* Each individual */
             cptcovage++;          bool=1;
             Tage[cptcovage]=i+1;          if  (cptcovn>0) {
             printf("stre=%s ", stre);            for (z1=1; z1<=cptcoveff; z1++) 
           }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           else if (strcmp(strd,"age")==0) {                bool=0;
             cutv(strb,stre,strc,'V');          } 
             Tvar[i+1]=atoi(stre);          if (bool==1) { 
             cptcovage++;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
             Tage[cptcovage]=i+1;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           else {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             cutv(strb,stre,strc,'V');                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             Tvar[i+1]=ncov+1;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
             cutv(strb,strc,strd,'V');                if (s[m][i]>0 && s[m][i]<=nlstate) { 
             for (k=1; k<=lastobs;k++)                  /*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]]);*/
               covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
           }                  prop[s[m][i]][iagemax+3] += weight[i]; 
         }                } 
         else {              }
           cutv(strd,strc,strb,'V');            } /* end selection of waves */
           /* printf("%s %s %s", strd,strc,strb);*/          }
         }
         Tvar[i+1]=atoi(strc);        for(i=iagemin; i <= iagemax+3; i++){  
         }          
         strcpy(modelsav,stra);            for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       }            posprop += prop[jk][i]; 
       cutv(strd,strc,stra,'V');          } 
       Tvar[1]=atoi(strc);  
     }          for(jk=1; jk <=nlstate ; jk++){     
   }            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);                probs[i][jk][j1]= prop[jk][i]/posprop;
      scanf("%d ",i);*/              } 
     fclose(fic);            } 
           }/* end jk */ 
    if(mle==1){        }/* end i */ 
     if (weightopt != 1) { /* Maximisation without weights*/      } /* end i1 */
       for(i=1;i<=n;i++) weight[i]=1.0;    } /* end k1 */
     }    
     /*-calculation of age at interview from date of interview and age at death -*/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     agev=matrix(1,maxwav,1,imx);    /*free_vector(pp,1,nlstate);*/
        free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     for (i=1; i<=imx; i++)  {  }  /* End of prevalence */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){  /************* Waves Concatenation ***************/
         if(s[m][i] >0){  
           if (s[m][i] == nlstate+1) {  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)
             if(agedc[i]>0)  {
               if(moisdc[i]!=99 && andc[i]!=9999)    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
               agev[m][i]=agedc[i];       Death is a valid wave (if date is known).
             else{       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
               printf("Warning negative age at death: %d line:%d\n",num[i],i);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
               agev[m][i]=-1;       and mw[mi+1][i]. dh depends on stepm.
             }       */
           }  
           else if(s[m][i] !=9){ /* Should no more exist */    int i, mi, m;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
             if(mint[m][i]==99 || anint[m][i]==9999)       double sum=0., jmean=0.;*/
               agev[m][i]=1;    int first;
             else if(agev[m][i] <agemin){    int j, k=0,jk, ju, jl;
               agemin=agev[m][i];    double sum=0.;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    first=0;
             }    jmin=1e+5;
             else if(agev[m][i] >agemax){    jmax=-1;
               agemax=agev[m][i];    jmean=0.;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    for(i=1; i<=imx; i++){
             }      mi=0;
             /*agev[m][i]=anint[m][i]-annais[i];*/      m=firstpass;
             /*   agev[m][i] = age[i]+2*m;*/      while(s[m][i] <= nlstate){
           }        if(s[m][i]>=1)
           else { /* =9 */          mw[++mi][i]=m;
             agev[m][i]=1;        if(m >=lastpass)
             s[m][i]=-1;          break;
           }        else
         }          m++;
         else /*= 0 Unknown */      }/* end while */
           agev[m][i]=1;      if (s[m][i] > nlstate){
       }        mi++;     /* Death is another wave */
            /* if(mi==0)  never been interviewed correctly before death */
     }           /* Only death is a correct wave */
     for (i=1; i<=imx; i++)  {        mw[mi][i]=m;
       for(m=1; (m<= maxwav); m++){      }
         if (s[m][i] > (nlstate+ndeath)) {  
           printf("Error: Wrong value in nlstate or ndeath\n");        wav[i]=mi;
           goto end;      if(mi==0){
         }        if(first==0){
       }          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     }          first=1;
         }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        if(first==1){
           fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
     free_vector(severity,1,maxwav);        }
     free_imatrix(outcome,1,maxwav+1,1,n);      } /* end mi==0 */
     free_vector(moisnais,1,n);    } /* End individuals */
     free_vector(annais,1,n);  
     free_matrix(mint,1,maxwav,1,n);    for(i=1; i<=imx; i++){
     free_matrix(anint,1,maxwav,1,n);      for(mi=1; mi<wav[i];mi++){
     free_vector(moisdc,1,n);        if (stepm <=0)
     free_vector(andc,1,n);          dh[mi][i]=1;
         else{
              if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     wav=ivector(1,imx);            if (agedc[i] < 2*AGESUP) {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              if(j==0) j=1;  /* Survives at least one month after exam */
                  else if(j<0){
     /* Concatenates waves */                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]);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);                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);
                 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]);
       Tcode=ivector(1,100);                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);
    nbcode=imatrix(1,nvar,1,8);                }
    ncodemax[1]=1;              k=k+1;
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);              if (j >= jmax) jmax=j;
                if (j <= jmin) jmin=j;
    codtab=imatrix(1,100,1,10);              sum=sum+j;
    h=0;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
    m=pow(2,cptcovn);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
              }
    for(k=1;k<=cptcovn; k++){          }
      for(i=1; i <=(m/pow(2,k));i++){          else{
        for(j=1; j <= ncodemax[k]; j++){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
            h++;            k=k+1;
            if (h>m) h=1;codtab[h][k]=j;            if (j >= jmax) jmax=j;
          }            else if (j <= jmin)jmin=j;
        }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
      }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
    }            if(j<0){
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
    /* for(i=1; i <=m ;i++){              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      for(k=1; k <=cptcovn; k++){            }
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);            sum=sum+j;
      }          }
      printf("\n");          jk= j/stepm;
    }          jl= j -jk*stepm;
    scanf("%d",i);*/          ju= j -(jk+1)*stepm;
              if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
    /* Calculates basic frequencies. Computes observed prevalence at single age            if(jl==0){
        and prints on file fileres'p'. */              dh[mi][i]=jk;
    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    * at the price of an extra matrix product in likelihood */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              dh[mi][i]=jk+1;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              bh[mi][i]=ju;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          }else{
                if(jl <= -ju){
     /* For Powell, parameters are in a vector p[] starting at p[1]              dh[mi][i]=jk;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */              bh[mi][i]=jl;       /* bias is positive if real duration
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */                                   * is higher than the multiple of stepm and negative otherwise.
                                       */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            }
             else{
                  dh[mi][i]=jk+1;
     /*--------- results files --------------*/              bh[mi][i]=ju;
     fprintf(ficres,"\ntitle=%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(dh[mi][i]==0){
    jk=1;              dh[mi][i]=1; /* At least one step */
    fprintf(ficres,"# Parameters\n");              bh[mi][i]=ju; /* At least one step */
    printf("# Parameters\n");              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
    for(i=1,jk=1; i <=nlstate; i++){            }
      for(k=1; k <=(nlstate+ndeath); k++){          } /* end if mle */
        if (k != i)        }
          {      } /* end wave */
            printf("%d%d ",i,k);    }
            fprintf(ficres,"%1d%1d ",i,k);    jmean=sum/k;
            for(j=1; j <=ncovmodel; j++){    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
              printf("%f ",p[jk]);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
              fprintf(ficres,"%f ",p[jk]);   }
              jk++;  
            }  /*********** Tricode ****************************/
            printf("\n");  void tricode(int *Tvar, int **nbcode, int imx)
            fprintf(ficres,"\n");  {
          }    
      }    int Ndum[20],ij=1, k, j, i, maxncov=19;
    }    int cptcode=0;
     cptcoveff=0; 
     /* Computing hessian and covariance matrix */   
     ftolhess=ftol; /* Usually correct */    for (k=0; k<maxncov; k++) Ndum[k]=0;
     hesscov(matcov, p, npar, delti, ftolhess, func);    for (k=1; k<=7; k++) ncodemax[k]=0;
     fprintf(ficres,"# Scales\n");  
     printf("# Scales\n");    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
      for(i=1,jk=1; i <=nlstate; i++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       for(j=1; j <=nlstate+ndeath; j++){                                 modality*/ 
         if (j!=i) {        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
           fprintf(ficres,"%1d%1d",i,j);        Ndum[ij]++; /*store the modality */
           printf("%1d%1d",i,j);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           for(k=1; k<=ncovmodel;k++){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
             printf(" %.5e",delti[jk]);                                         Tvar[j]. If V=sex and male is 0 and 
             fprintf(ficres," %.5e",delti[jk]);                                         female is 1, then  cptcode=1.*/
             jk++;      }
           }  
           printf("\n");      for (i=0; i<=cptcode; i++) {
           fprintf(ficres,"\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 */
         }      }
       }  
       }      ij=1; 
          for (i=1; i<=ncodemax[j]; i++) {
     k=1;        for (k=0; k<= maxncov; k++) {
     fprintf(ficres,"# Covariance\n");          if (Ndum[k] != 0) {
     printf("# Covariance\n");            nbcode[Tvar[j]][ij]=k; 
     for(i=1;i<=npar;i++){            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       /*  if (k>nlstate) k=1;            
       i1=(i-1)/(ncovmodel*nlstate)+1;            ij++;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          }
       printf("%s%d%d",alph[k],i1,tab[i]);*/          if (ij > ncodemax[j]) break; 
       fprintf(ficres,"%3d",i);        }  
       printf("%3d",i);      } 
       for(j=1; j<=i;j++){    }  
         fprintf(ficres," %.5e",matcov[i][j]);  
         printf(" %.5e",matcov[i][j]);   for (k=0; k< maxncov; k++) Ndum[k]=0;
       }  
       fprintf(ficres,"\n");   for (i=1; i<=ncovmodel-2; i++) { 
       printf("\n");     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       k++;     ij=Tvar[i];
     }     Ndum[ij]++;
       }
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);   ij=1;
       fgets(line, MAXLINE, ficpar);   for (i=1; i<= maxncov; i++) {
       puts(line);     if((Ndum[i]!=0) && (i<=ncovcol)){
       fputs(line,ficparo);       Tvaraff[ij]=i; /*For printing */
     }       ij++;
     ungetc(c,ficpar);     }
     }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);   
       cptcoveff=ij-1; /*Number of simple covariates*/
     if (fage <= 2) {  }
       bage = agemin;  
       fage = agemax;  /*********** Health Expectancies ****************/
     }  
   void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
     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\n",agemin,agemax,bage,fage);  {
 /*------------ gnuplot -------------*/    /* Health expectancies */
 chdir(pathcd);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   if((ficgp=fopen("graph.plt","w"))==NULL) {    double age, agelim, hf;
     printf("Problem with file graph.gp");goto end;    double ***p3mat,***varhe;
   }    double **dnewm,**doldm;
 #ifdef windows    double *xp;
   fprintf(ficgp,"cd \"%s\" \n",pathc);    double **gp, **gm;
 #endif    double ***gradg, ***trgradg;
 m=pow(2,cptcovn);    int theta;
    
  /* 1eme*/    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   for (cpt=1; cpt<= nlstate ; cpt ++) {    xp=vector(1,npar);
    for (k1=1; k1<= m ; k1 ++) {    dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
 #ifdef windows    
     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);    fprintf(ficreseij,"# Health expectancies\n");
 #endif    fprintf(ficreseij,"# Age");
 #ifdef unix    for(i=1; i<=nlstate;i++)
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      for(j=1; j<=nlstate;j++)
 #endif        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    if(estepm < stepm){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      printf ("Problem %d lower than %d\n",estepm, stepm);
 }    }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    else  hstepm=estepm;   
     for (i=1; i<= nlstate ; i ++) {    /* We compute the life expectancy from trapezoids spaced every estepm months
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");     * This is mainly to measure the difference between two models: for example
   else fprintf(ficgp," \%%*lf (\%%*lf)");     * if stepm=24 months pijx are given only every 2 years and by summing them
 }     * we are calculating an estimate of the Life Expectancy assuming a linear 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);     * progression in between and thus overestimating or underestimating according
      for (i=1; i<= nlstate ; i ++) {     * to the curvature of the survival function. If, for the same date, we 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   else fprintf(ficgp," \%%*lf (\%%*lf)");     * to compare the new estimate of Life expectancy with the same linear 
 }       * hypothesis. A more precise result, taking into account a more precise
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));     * curvature will be obtained if estepm is as small as stepm. */
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");    /* For example we decided to compute the life expectancy with the smallest unit */
 #endif    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       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
   /*2 eme*/       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   for (k1=1; k1<= m ; k1 ++) {       survival function given by stepm (the optimization length). Unfortunately it
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);       means that if the survival funtion is printed only each two years of age and if
           you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     for (i=1; i<= nlstate+1 ; i ++) {       results. So we changed our mind and took the option of the best precision.
       k=2*i;    */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    agelim=AGESUP;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 }        /* nhstepm age range expressed in number of stepm */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      /* if (stepm >= YEARM) hstepm=1;*/
       for (j=1; j<= nlstate+1 ; j ++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         else fprintf(ficgp," \%%*lf (\%%*lf)");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 }        gp=matrix(0,nhstepm,1,nlstate*nlstate);
       fprintf(ficgp,"\" t\"\" w l 0,");      gm=matrix(0,nhstepm,1,nlstate*nlstate);
      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 ++) {      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 }     
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      /* Computing Variances of health expectancies */
   }  
         for(theta=1; theta <=npar; theta++){
   /*3eme*/        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   for (k1=1; k1<= m ; k1 ++) {        }
     for (cpt=1; cpt<= nlstate ; cpt ++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       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);        cptj=0;
       for (i=1; i< nlstate ; i ++) {        for(j=1; j<= nlstate; j++){
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          for(i=1; i<=nlstate; i++){
       }            cptj=cptj+1;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   }            }
            }
   /* CV preval stat */        }
   for (k1=1; k1<= m ; k1 ++) {       
     for (cpt=1; cpt<nlstate ; cpt ++) {       
       k=3;        for(i=1; i<=npar; i++) 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       for (i=1; i< nlstate ; i ++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficgp,"+$%d",k+i+1);        
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        cptj=0;
              for(j=1; j<= nlstate; j++){
       l=3+(nlstate+ndeath)*cpt;          for(i=1;i<=nlstate;i++){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            cptj=cptj+1;
       for (i=1; i< nlstate ; i ++) {            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       }            }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        }
     }        for(j=1; j<= nlstate*nlstate; j++)
   }          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   /* proba elementaires */          }
    for(i=1,jk=1; i <=nlstate; i++){       } 
     for(k=1; k <=(nlstate+ndeath); k++){     
       if (k != i) {  /* End theta */
         for(j=1; j <=ncovmodel; j++){  
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           /*fprintf(ficgp,"%s",alph[1]);*/  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);       for(h=0; h<=nhstepm-1; h++)
           jk++;        for(j=1; j<=nlstate*nlstate;j++)
           fprintf(ficgp,"\n");          for(theta=1; theta <=npar; theta++)
         }            trgradg[h][j][theta]=gradg[h][theta][j];
       }       
     }  
     }       for(i=1;i<=nlstate*nlstate;i++)
         for(j=1;j<=nlstate*nlstate;j++)
   for(jk=1; jk <=m; jk++) {          varhe[i][j][(int)age] =0.;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);  
    i=1;       printf("%d|",(int)age);fflush(stdout);
    for(k2=1; k2<=nlstate; k2++) {       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      k3=i;       for(h=0;h<=nhstepm-1;h++){
      for(k=1; k<=(nlstate+ndeath); k++) {        for(k=0;k<=nhstepm-1;k++){
        if (k != k2){          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(i=1;i<=nlstate*nlstate;i++)
         for(j=3; j <=ncovmodel; j++)            for(j=1;j<=nlstate*nlstate;j++)
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         fprintf(ficgp,")/(1");        }
              }
         for(k1=1; k1 <=nlstate; k1++){        /* Computing expectancies */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      for(i=1; i<=nlstate;i++)
           for(j=3; j <=ncovmodel; j++)        for(j=1; j<=nlstate;j++)
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           fprintf(ficgp,")");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         }            
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
         i=i+ncovmodel;          }
        }  
      }      fprintf(ficreseij,"%3.0f",age );
    }      cptj=0;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++){
              cptj++;
   fclose(ficgp);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
            }
 chdir(path);      fprintf(ficreseij,"\n");
     free_matrix(agev,1,maxwav,1,imx);     
     free_ivector(wav,1,imx);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
          free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_imatrix(s,1,maxwav+1,1,n);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        }
        printf("\n");
     free_ivector(num,1,n);    fprintf(ficlog,"\n");
     free_vector(agedc,1,n);  
     free_vector(weight,1,n);    free_vector(xp,1,npar);
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     fclose(ficparo);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     fclose(ficres);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    }  }
      
    /*________fin mle=1_________*/  /************ Variance ******************/
      void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
   {
      /* Variance of health expectancies */
     /* No more information from the sample is required now */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   /* Reads comments: lines beginning with '#' */    /* double **newm;*/
   while((c=getc(ficpar))=='#' && c!= EOF){    double **dnewm,**doldm;
     ungetc(c,ficpar);    double **dnewmp,**doldmp;
     fgets(line, MAXLINE, ficpar);    int i, j, nhstepm, hstepm, h, nstepm ;
     puts(line);    int k, cptcode;
     fputs(line,ficparo);    double *xp;
   }    double **gp, **gm;  /* for var eij */
   ungetc(c,ficpar);    double ***gradg, ***trgradg; /*for var eij */
      double **gradgp, **trgradgp; /* for var p point j */
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    double *gpp, *gmp; /* for var p point j */
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    double ***p3mat;
 /*--------- index.htm --------*/    double age,agelim, hf;
     double ***mobaverage;
   if((fichtm=fopen("index.htm","w"))==NULL)    {    int theta;
     printf("Problem with index.htm \n");goto end;    char digit[4];
   }    char digitp[25];
   
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n    char fileresprobmorprev[FILENAMELENGTH];
         - 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>    if(popbased==1){
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      if(mobilav!=0)
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        strcpy(digitp,"-populbased-mobilav-");
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>      else strcpy(digitp,"-populbased-nomobil-");
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    }
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    else 
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      strcpy(digitp,"-stablbased-");
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  
     if (mobilav!=0) {
  fprintf(fichtm," <li>Graphs</li>\n<p>");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
  m=cptcovn;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
  j1=0;    }
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){    strcpy(fileresprobmorprev,"prmorprev"); 
        j1++;    sprintf(digit,"%-d",ij);
        if (cptcovn > 0) {    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
          fprintf(fichtm,"<hr>************ Results for covariates");    strcat(fileresprobmorprev,digit); /* Tvar to be done */
          for (cpt=1; cpt<=cptcovn;cpt++)    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);    strcat(fileresprobmorprev,fileres);
          fprintf(fichtm," ************\n<hr>");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
        }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        }
        for(cpt=1; cpt<nlstate;cpt++){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
        }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(cpt=1; cpt<=nlstate;cpt++) {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      fprintf(ficresprobmorprev," p.%-d SE",j);
 interval) in state (%d): v%s%d%d.gif <br>      for(i=1; i<=nlstate;i++)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }    }  
      for(cpt=1; cpt<=nlstate;cpt++) {    fprintf(ficresprobmorprev,"\n");
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
      }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      exit(0);
 health expectancies in states (1) and (2): e%s%d.gif<br>    }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    else{
 fprintf(fichtm,"\n</body>");      fprintf(ficgp,"\n# Routine varevsij");
    }    }
  }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
 fclose(fichtm);      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   /*--------------- Prevalence limit --------------*/      exit(0);
      }
   strcpy(filerespl,"pl");    else{
   strcat(filerespl,fileres);      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");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    }
   }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   fprintf(ficrespl,"#Age ");    fprintf(ficresvij,"# Age");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++)
   fprintf(ficrespl,"\n");      for(j=1; j<=nlstate;j++)
          fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   prlim=matrix(1,nlstate,1,nlstate);    fprintf(ficresvij,"\n");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    xp=vector(1,npar);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    dnewm=matrix(1,nlstate,1,npar);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    doldm=matrix(1,nlstate,1,nlstate);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   k=0;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   agebase=agemin;  
   agelim=agemax;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   ftolpl=1.e-10;    gpp=vector(nlstate+1,nlstate+ndeath);
   i1=cptcovn;    gmp=vector(nlstate+1,nlstate+ndeath);
   if (cptcovn < 1){i1=1;}    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
   for(cptcov=1;cptcov<=i1;cptcov++){    if(estepm < stepm){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf ("Problem %d lower than %d\n",estepm, stepm);
         k=k+1;    }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    else  hstepm=estepm;   
         fprintf(ficrespl,"\n#******");    /* For example we decided to compute the life expectancy with the smallest unit */
         for(j=1;j<=cptcovn;j++)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           fprintf(ficrespl," V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);       nhstepm is the number of hstepm from age to agelim 
         fprintf(ficrespl,"******\n");       nstepm is the number of stepm from age to agelin. 
               Look at hpijx to understand the reason of that which relies in memory size
         for (age=agebase; age<=agelim; age++){       and note for a fixed period like k years */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           fprintf(ficrespl,"%.0f",age );       survival function given by stepm (the optimization length). Unfortunately it
           for(i=1; i<=nlstate;i++)       means that if the survival funtion is printed every two years of age and if
           fprintf(ficrespl," %.5f", prlim[i][i]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           fprintf(ficrespl,"\n");       results. So we changed our mind and took the option of the best precision.
         }    */
       }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     }    agelim = AGESUP;
   fclose(ficrespl);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /*------------- h Pij x at various ages ------------*/      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      gp=matrix(0,nhstepm,1,nlstate);
   }      gm=matrix(0,nhstepm,1,nlstate);
   printf("Computing pij: result on file '%s' \n", filerespij);  
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;      for(theta=1; theta <=npar; theta++){
   if (stepm<=24) stepsize=2;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   agelim=AGESUP;        }
   hstepm=stepsize*YEARM; /* Every year of age */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   k=0;        if (popbased==1) {
   for(cptcov=1;cptcov<=i1;cptcov++){          if(mobilav ==0){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for(i=1; i<=nlstate;i++)
       k=k+1;              prlim[i][i]=probs[(int)age][i][ij];
         fprintf(ficrespij,"\n#****** ");          }else{ /* mobilav */ 
         for(j=1;j<=cptcovn;j++)            for(i=1; i<=nlstate;i++)
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);              prlim[i][i]=mobaverage[(int)age][i][ij];
         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 */        for(j=1; j<= nlstate; j++){
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          for(h=0; h<=nhstepm; h++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
           oldm=oldms;savm=savms;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
           fprintf(ficrespij,"# Age");        }
           for(i=1; i<=nlstate;i++)        /* This for computing probability of death (h=1 means
             for(j=1; j<=nlstate+ndeath;j++)           computed over hstepm matrices product = hstepm*stepm months) 
               fprintf(ficrespij," %1d-%1d",i,j);           as a weighted average of prlim.
           fprintf(ficrespij,"\n");        */
           for (h=0; h<=nhstepm; h++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             for(i=1; i<=nlstate;i++)            gpp[j] += prlim[i][i]*p3mat[i][j][1];
               for(j=1; j<=nlstate+ndeath;j++)        }    
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        /* end probability of death */
             fprintf(ficrespij,"\n");  
           }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           fprintf(ficrespij,"\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }   
   }        if (popbased==1) {
           if(mobilav ==0){
   fclose(ficrespij);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   /*---------- Health expectancies and variances ------------*/          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   strcpy(filerest,"t");              prlim[i][i]=mobaverage[(int)age][i][ij];
   strcat(filerest,fileres);          }
   if((ficrest=fopen(filerest,"w"))==NULL) {        }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }        for(j=1; j<= nlstate; j++){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   strcpy(filerese,"e");          }
   strcat(filerese,fileres);        }
   if((ficreseij=fopen(filerese,"w"))==NULL) {        /* This for computing probability of death (h=1 means
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
  strcpy(fileresv,"v");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   strcat(fileresv,fileres);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        }    
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        /* end probability of death */
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
   k=0;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   for(cptcov=1;cptcov<=i1;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       fprintf(ficrest,"\n#****** ");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       for(j=1;j<=cptcovn;j++)        }
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);  
       fprintf(ficrest,"******\n");      } /* End theta */
   
       fprintf(ficreseij,"\n#****** ");      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       for(j=1;j<=cptcovn;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      for(h=0; h<=nhstepm; h++) /* veij */
       fprintf(ficreseij,"******\n");        for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
       fprintf(ficresvij,"\n#****** ");            trgradg[h][j][theta]=gradg[h][theta][j];
       for(j=1;j<=cptcovn;j++)  
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       fprintf(ficresvij,"******\n");        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
       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);        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      for(i=1;i<=nlstate;i++)
       oldm=oldms;savm=savms;        for(j=1;j<=nlstate;j++)
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          vareij[i][j][(int)age] =0.;
        
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      for(h=0;h<=nhstepm;h++){
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        for(k=0;k<=nhstepm;k++){
       fprintf(ficrest,"\n");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                  matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       hf=1;          for(i=1;i<=nlstate;i++)
       if (stepm >= YEARM) hf=stepm/YEARM;            for(j=1;j<=nlstate;j++)
       epj=vector(1,nlstate+1);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       for(age=bage; age <=fage ;age++){        }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      }
         fprintf(ficrest," %.0f",age);    
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      /* pptj */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           epj[nlstate+1] +=epj[j];        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         }          varppt[j][i]=doldmp[j][i];
         for(i=1, vepp=0.;i <=nlstate;i++)      /* end ppptj */
           for(j=1;j <=nlstate;j++)      /*  x centered again */
             vepp += vareij[i][j][(int)age];      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         for(j=1;j <=nlstate;j++){   
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));      if (popbased==1) {
         }        if(mobilav ==0){
         fprintf(ficrest,"\n");          for(i=1; i<=nlstate;i++)
       }            prlim[i][i]=probs[(int)age][i][ij];
     }        }else{ /* mobilav */ 
   }          for(i=1; i<=nlstate;i++)
                    prlim[i][i]=mobaverage[(int)age][i][ij];
  fclose(ficreseij);        }
  fclose(ficresvij);      }
   fclose(ficrest);               
   fclose(ficpar);      /* This for computing probability of death (h=1 means
   free_vector(epj,1,nlstate+1);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   /*  scanf("%d ",i); */         as a weighted average of prlim.
       */
   /*------- Variance limit prevalence------*/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
 strcpy(fileresvpl,"vpl");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   strcat(fileresvpl,fileres);      }    
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      /* end probability of death */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
  k=0;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
  for(cptcov=1;cptcov<=i1;cptcov++){        }
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      } 
      k=k+1;      fprintf(ficresprobmorprev,"\n");
      fprintf(ficresvpl,"\n#****** ");  
      for(j=1;j<=cptcovn;j++)      fprintf(ficresvij,"%.0f ",age );
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);      for(i=1; i<=nlstate;i++)
      fprintf(ficresvpl,"******\n");        for(j=1; j<=nlstate;j++){
                fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);        }
      oldm=oldms;savm=savms;      fprintf(ficresvij,"\n");
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      free_matrix(gp,0,nhstepm,1,nlstate);
    }      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);
   fclose(ficresvpl);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
   /*---------- End : free ----------------*/    free_vector(gpp,nlstate+1,nlstate+ndeath);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    free_vector(gmp,nlstate+1,nlstate+ndeath);
      free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
      /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
   free_matrix(matcov,1,npar,1,npar);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
   free_vector(delti,1,npar);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
      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);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   printf("End of Imach\n");    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
      free_vector(xp,1,npar);
   /* 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);*/    free_matrix(doldm,1,nlstate,1,nlstate);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    free_matrix(dnewm,1,nlstate,1,npar);
   /*------ End -----------*/    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
  end:    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 #ifdef windows    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  chdir(pathcd);    fclose(ficresprobmorprev);
 #endif    fclose(ficgp);
  system("wgnuplot graph.plt");    fclose(fichtm);
   }  /* end varevsij */
 #ifdef windows  
   while (z[0] != 'q') {  /************ Variance of prevlim ******************/
     chdir(pathcd);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  {
     scanf("%s",z);    /* Variance of prevalence limit */
     if (z[0] == 'c') system("./imach");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     else if (z[0] == 'e') {    double **newm;
       chdir(path);    double **dnewm,**doldm;
       system("index.htm");    int i, j, nhstepm, hstepm;
     }    int k, cptcode;
     else if (z[0] == 'q') exit(0);    double *xp;
   }    double *gp, *gm;
 #endif    double **gradg, **trgradg;
 }    double age,agelim;
     int theta;
      
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     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 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
     }
     else{
       fprintf(ficgp,"\n# Routine varprob");
     }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
       exit(0);
     }
     else{
       fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(fichtm,"\n");
   
       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");
       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");
   
     }
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           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]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           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];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           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);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       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);
                     }
                     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) */
                     /* 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");
                       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);
                       fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fclose(ficgp);
     fclose(fichtm);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
     if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     }
   
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n \
    - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
    - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <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(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        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]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        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);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> \
   <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
        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 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
    - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
    - 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\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
    - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
    - 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);
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        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]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
   interval) in state (%d): v%s%d%d.png <br>\
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   fclose(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   
     /*#ifdef windows */
       fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   m=pow(2,cptcoveff);
     
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"v%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] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        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);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%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 *optionfile)
   {
     if((fichier=fopen(optionfile,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfile);
       fprintf(ficlog,"Problem with file: %s\n", optionfile);
       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 */
     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,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <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>\n\
    - Date and time at start: %s</ul>\n",\
             version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
             model,fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strt);
     fclose(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(fileappend(fichtm, optionfilehtm)){
       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.1.6  
changed lines
  Added in v.1.86


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