imach/src/imach.c - diff

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Diff for /imach/src/imach.c between versions 1.55 and 1.96

-version 1.55, 2002/07/24 17:00:55
+version 1.96, 2003/07/15 15:38:55
  Line 1
  /* $Id$
+   $State$
+   $Log$
+   Revision 1.96  2003/07/15 15:38:55  brouard
+   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
+   rewritten within the same printf. Workaround: many printfs.
+   Revision 1.95  2003/07/08 07:54:34  brouard
+   * imach.c (Repository):
+   (Repository): Using imachwizard code to output a more meaningful covariance
+   matrix (cov(a12,c31) instead of numbers.
+   Revision 1.94  2003/06/27 13:00:02  brouard
+   Just cleaning
+   Revision 1.93  2003/06/25 16:33:55  brouard
+   (Module): On windows (cygwin) function asctime_r doesn't
+   exist so I changed back to asctime which exists.
+   (Module): Version 0.96b
+   Revision 1.92  2003/06/25 16:30:45  brouard
+   (Module): On windows (cygwin) function asctime_r doesn't
+   exist so I changed back to asctime which exists.
+   Revision 1.91  2003/06/25 15:30:29  brouard
+   * imach.c (Repository): Duplicated warning errors corrected.
+   (Repository): Elapsed time after each iteration is now output. It
+   helps to forecast when convergence will be reached. Elapsed time
+   is stamped in powell.  We created a new html file for the graphs
+   concerning matrix of covariance. It has extension -cov.htm.
+   Revision 1.90  2003/06/24 12:34:15  brouard
+   (Module): Some bugs corrected for windows. Also, when
+   mle=-1 a template is output in file "or"mypar.txt with the design
+   of the covariance matrix to be input.
+   Revision 1.89  2003/06/24 12:30:52  brouard
+   (Module): Some bugs corrected for windows. Also, when
+   mle=-1 a template is output in file "or"mypar.txt with the design
+   of the covariance matrix to be input.
+   Revision 1.88  2003/06/23 17:54:56  brouard
+   * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
+   Revision 1.87  2003/06/18 12:26:01  brouard
+   Version 0.96
+   Revision 1.86  2003/06/17 20:04:08  brouard
+   (Module): Change position of html and gnuplot routines and added
+   routine fileappend.
+   Revision 1.85  2003/06/17 13:12:43  brouard
+   * imach.c (Repository): Check when date of death was earlier that
+   current date of interview. It may happen when the death was just
+   prior to the death. In this case, dh was negative and likelihood
+   was wrong (infinity). We still send an "Error" but patch by
+   assuming that the date of death was just one stepm after the
+   interview.
+   (Repository): Because some people have very long ID (first column)
+   we changed int to long in num[] and we added a new lvector for
+   memory allocation. But we also truncated to 8 characters (left
+   truncation)
+   (Repository): No more line truncation errors.
+   Revision 1.84  2003/06/13 21:44:43  brouard
+   * imach.c (Repository): Replace "freqsummary" at a correct
+   place. It differs from routine "prevalence" which may be called
+   many times. Probs is memory consuming and must be used with
+   parcimony.
+   Version 0.95a3 (should output exactly the same maximization than 0.8a2)
+   Revision 1.83  2003/06/10 13:39:11  lievre
+   *** empty log message ***
+   Revision 1.82  2003/06/05 15:57:20  brouard
+   Add log in  imach.c and  fullversion number is now printed.
+ */
+ /*
     Interpolated Markov Chain
    Short summary of the programme:
- Line 32
+ Line 110
    hPijx is the probability to be observed in state i at age x+h
    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 or quarter trimester,
+   states. This elementary transition (by month, quarter,
-   semester or year) is model as a multinomial logistic.  The hPx
+   semester or year) is modelled as a multinomial logistic.  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.
- Line 48
+ Line 126
    It is copyrighted identically to a GNU software product, ie programme and
    software can be distributed freely for non commercial use. Latest version
    can be accessed at http://euroreves.ined.fr/imach .
+   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
+   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    **********************************************************************/
+ /*
+   main
+   read parameterfile
+   read datafile
+   concatwav
+   freqsummary
+   if (mle >= 1)
+     mlikeli
+   print results files
+   if mle==1
+      computes hessian
+   read end of parameter file: agemin, agemax, bage, fage, estepm
+       begin-prev-date,...
+   open gnuplot file
+   open html file
+   stable prevalence
+    for age prevalim()
+   h Pij x
+   variance of p varprob
+   forecasting if prevfcast==1 prevforecast call prevalence()
+   health expectancies
+   Variance-covariance of DFLE
+   prevalence()
+    movingaverage()
+   varevsij()
+   if popbased==1 varevsij(,popbased)
+   total life expectancies
+   Variance of stable prevalence
+  end
+ */
  #include <math.h>
  #include <stdio.h>
  #include <stdlib.h>
  #include <unistd.h>
+ #include <sys/time.h>
+ #include <time.h>
+ #include "timeval.h"
+ /* #include <libintl.h> */
+ /* #define _(String) gettext (String) */
  #define MAXLINE 256
  #define GNUPLOTPROGRAM "gnuplot"
  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- #define FILENAMELENGTH 80
+ #define FILENAMELENGTH 132
  /*#define DEBUG*/
- #define windows
+ /*#define windows*/
  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- Line 75
+ Line 197
  #define YEARM 12. /* Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
- #ifdef windows
+ #ifdef unix
- #define DIRSEPARATOR '\\'
- #define ODIRSEPARATOR '/'
- #else
  #define DIRSEPARATOR '/'
  #define ODIRSEPARATOR '\\'
+ #else
+ #define DIRSEPARATOR '\\'
+ #define ODIRSEPARATOR '/'
  #endif
- char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";
+ /* $Id$ */
- int erreur; /* Error number */
+ /* $State$ */
+ char version[]="Imach version 0.96c, July 2003, INED-EUROREVES ";
+ char fullversion[]="$Revision$ $Date$";
+ int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
  int nvar;
  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
  int npar=NPARMAX;
- Line 96  int popbased=0;
+ Line 222  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
  int maxwav; /* Maxim number of waves */
  int jmin, jmax; /* min, max spacing between 2 waves */
+ int gipmx, gsw; /* Global variables on the number of contributions
+                    to the likelihood and the sum of weights (done by funcone)*/
  int mle, weightopt;
  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
  double jmean; /* Mean space between 2 waves */
  double **oldm, **newm, **savm; /* Working pointers to matrices */
  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- FILE *ficlog;
+ FILE *ficlog, *ficrespow;
+ int globpr; /* Global variable for printing or not */
+ double fretone; /* Only one call to likelihood */
+ long ipmx; /* Number of contributions */
+ double sw; /* Sum of weights */
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ FILE *ficresilk;
  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
  FILE *ficresprobmorprev;
- FILE *fichtm; /* Html File */
+ FILE *fichtm, *fichtmcov; /* Html File */
  FILE *ficreseij;
  char filerese[FILENAMELENGTH];
  FILE  *ficresvij;
- Line 116  char fileresvpl[FILENAMELENGTH];
+ Line 252  char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ char command[FILENAMELENGTH];
+ int  outcmd=0;
  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
  char filelog[FILENAMELENGTH]; /* Log file */
  char filerest[FILENAMELENGTH];
  char fileregp[FILENAMELENGTH];
  char popfile[FILENAMELENGTH];
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ struct timezone tzp;
+ extern int gettimeofday();
+ struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ long time_value;
+ extern long time();
+ char strcurr[80], strfor[80];
  #define NR_END 1
  #define FREE_ARG char*
- Line 161  int estepm;
+ Line 309  int estepm;
  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
  int m,nb;
- int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
+ long *num;
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  double **pmmij, ***probs;
  double dateintmean=0;
- Line 177  double ftolhess; /* Tolerance for comput
+ Line 326  double ftolhess; /* Tolerance for comput
  /**************** split *************************/
  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
  {
-    char *s;                             /* pointer */
+   char  *ss;                            /* pointer */
-    int  l1, l2;                         /* length counters */
+   int   l1, l2;                         /* length counters */
-    l1 = strlen( path );                 /* length of path */
-    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-    s= strrchr( path, DIRSEPARATOR );            /* find last / */
-    if ( s == NULL ) {                   /* no directory, so use current */
-      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
- #if     defined(__bsd__)                /* get current working directory */
-       extern char       *getwd( );
-       if ( getwd( dirc ) == NULL ) {
- #else
-       extern char       *getcwd( );
-       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+   l1 = strlen(path );                   /* length of path */
- #endif
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-          return( GLOCK_ERROR_GETCWD );
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-       }
+   if ( ss == NULL ) {                   /* no directory, so use current */
-       strcpy( name, path );             /* we've got it */
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-    } else {                             /* strip direcotry from path */
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-       s++;                              /* after this, the filename */
+     /* get current working directory */
-       l2 = strlen( s );                 /* length of filename */
+     /*    extern  char* getcwd ( char *buf , int len);*/
-       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
-       strcpy( name, s );                /* save file name */
+       return( GLOCK_ERROR_GETCWD );
-       strncpy( dirc, path, l1 - l2 );   /* now the directory */
+     }
-       dirc[l1-l2] = 0;                  /* add zero */
+     strcpy( name, path );               /* we've got it */
-    }
+   } else {                              /* strip direcotry from path */
-    l1 = strlen( dirc );                 /* length of directory */
+     ss++;                               /* after this, the filename */
- #ifdef windows
+     l2 = strlen( ss );                  /* length of filename */
-    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+     strcpy( name, ss );         /* save file name */
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+     dirc[l1-l2] = 0;                    /* add zero */
+   }
+   l1 = strlen( dirc );                  /* length of directory */
+   /*#ifdef windows
+   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
  #else
-    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
+   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
  #endif
-    s = strrchr( name, '.' );            /* find last / */
+   */
-    s++;
+   ss = strrchr( name, '.' );            /* find last / */
-    strcpy(ext,s);                       /* save extension */
+   ss++;
-    l1= strlen( name);
+   strcpy(ext,ss);                       /* save extension */
-    l2= strlen( s)+1;
+   l1= strlen( name);
-    strncpy( finame, name, l1-l2);
+   l2= strlen(ss)+1;
-    finame[l1-l2]= 0;
+   strncpy( finame, name, l1-l2);
-    return( 0 );                         /* we're done */
+   finame[l1-l2]= 0;
+   return( 0 );                          /* we're done */
  }
  /******************************************/
- void replace(char *s, char*t)
+ void replace_back_to_slash(char *s, char*t)
  {
    int i;
-   int lg=20;
+   int lg=0;
    i=0;
    lg=strlen(t);
    for(i=0; i<= lg; i++) {
- Line 277  void nrerror(char error_text[])
+ Line 421  void nrerror(char error_text[])
  {
    fprintf(stderr,"ERREUR ...\n");
    fprintf(stderr,"%s\n",error_text);
-   exit(1);
+   exit(EXIT_FAILURE);
  }
  /*********************** vector *******************/
  double *vector(int nl, int nh)
- Line 309  void free_ivector(int *v, long nl, long
+ Line 453  void free_ivector(int *v, long nl, long
    free((FREE_ARG)(v+nl-NR_END));
  }
+ /************************lvector *******************************/
+ long *lvector(long nl,long nh)
+ {
+   long *v;
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+   if (!v) nrerror("allocation failure in ivector");
+   return v-nl+NR_END;
+ }
+ /******************free lvector **************************/
+ void free_lvector(long *v, long nl, long nh)
+ {
+   free((FREE_ARG)(v+nl-NR_END));
+ }
  /******************* imatrix *******************************/
  int **imatrix(long nrl, long nrh, long ncl, long nch)
       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
- Line 363  double **matrix(long nrl, long nrh, long
+ Line 522  double **matrix(long nrl, long nrh, long
    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    return m;
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+    */
  }
  /*************************free matrix ************************/
- Line 402  double ***ma3x(long nrl, long nrh, long
+ Line 563  double ***ma3x(long nrl, long nrh, long
      for (j=ncl+1; j<=nch; j++)
        m[i][j]=m[i][j-1]+nlay;
    }
    return m;
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   */
  }
  /*************************free ma3x ************************/
- Line 413  void free_ma3x(double ***m, long nrl, lo
+ Line 577  void free_ma3x(double ***m, long nrl, lo
    free((FREE_ARG)(m+nrl-NR_END));
  }
+ /*************** function subdirf ***********/
+ char *subdirf(char fileres[])
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/"); /* Add to the right */
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
+ /*************** function subdirf2 ***********/
+ char *subdirf2(char fileres[], char *preop)
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
+ /*************** function subdirf3 ***********/
+ char *subdirf3(char fileres[], char *preop, char *preop2)
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
+   strcat(tmpout,preop2);
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
  /***************** f1dim *************************/
  extern int ncom;
  extern double *pcom,*xicom;
- Line 588  void linmin(double p[], double xi[], int
+ Line 787  void linmin(double p[], double xi[], int
    free_vector(pcom,1,n);
  }
+ char *asc_diff_time(long time_sec, char ascdiff[])
+ {
+   long sec_left, days, hours, minutes;
+   days = (time_sec) / (60*60*24);
+   sec_left = (time_sec) % (60*60*24);
+   hours = (sec_left) / (60*60) ;
+   sec_left = (sec_left) %(60*60);
+   minutes = (sec_left) /60;
+   sec_left = (sec_left) % (60);
+   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+   return ascdiff;
+ }
  /*************** powell ************************/
  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
              double (*func)(double []))
- Line 598  void powell(double p[], double **xi, int
+ Line 810  void powell(double p[], double **xi, int
    double del,t,*pt,*ptt,*xit;
    double fp,fptt;
    double *xits;
+   int niterf, itmp;
    pt=vector(1,n);
    ptt=vector(1,n);
    xit=vector(1,n);
- Line 608  void powell(double p[], double **xi, int
+ Line 822  void powell(double p[], double **xi, int
      fp=(*fret);
      ibig=0;
      del=0.0;
-     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+     last_time=curr_time;
-     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+     (void) gettimeofday(&curr_time,&tzp);
-     for (i=1;i<=n;i++)
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
+     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
+     for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
-     fprintf(ficlog," %d %.12f",i, p[i]);
+       fprintf(ficlog," %d %.12lf",i, p[i]);
+       fprintf(ficrespow," %.12lf", p[i]);
+     }
      printf("\n");
      fprintf(ficlog,"\n");
+     fprintf(ficrespow,"\n");fflush(ficrespow);
+     if(*iter <=3){
+       tm = *localtime(&curr_time.tv_sec);
+       strcpy(strcurr,asctime(&tmf));
+ /*       asctime_r(&tm,strcurr); */
+       forecast_time=curr_time;
+       itmp = strlen(strcurr);
+       if(strcurr[itmp-1]=='\n')
+         strcurr[itmp-1]='\0';
+       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       for(niterf=10;niterf<=30;niterf+=10){
+         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+         tmf = *localtime(&forecast_time.tv_sec);
+ /*      asctime_r(&tmf,strfor); */
+         strcpy(strfor,asctime(&tmf));
+         itmp = strlen(strfor);
+         if(strfor[itmp-1]=='\n')
+         strfor[itmp-1]='\0';
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+       }
+     }
      for (i=1;i<=n;i++) {
        for (j=1;j<=n;j++) xit[j]=xi[j][i];
        fptt=(*fret);
- Line 854  double **matprod2(double **out, double *
+ Line 1096  double **matprod2(double **out, double *
  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
  {
-   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
+   /* Computes the transition matrix starting at age 'age' over
-      duration (i.e. until
+      'nhstepm*hstepm*stepm' months (i.e. until
-      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+      nhstepm*hstepm matrices.
       Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-      (typically every 2 years instead of every month which is too big).
+      (typically every 2 years instead of every month which is too big
+      for the memory).
       Model is determined by parameters x and covariates have to be
       included manually here.
- Line 914  double func( double *x)
+ Line 1158  double func( double *x)
    double **out;
    double sw; /* Sum of weights */
    double lli; /* Individual log likelihood */
+   int s1, s2;
+   double bbh, survp;
    long ipmx;
    /*extern weight */
    /* We are differentiating ll according to initial status */
- Line 924  double func( double *x)
+ Line 1170  double func( double *x)
    cov[1]=1.;
    for(k=1; k<=nlstate; k++) ll[k]=0.;
+   if(mle==1){
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
+         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);
+           }
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
+         } /* 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 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
+          * the nearest (and in case of equal distance, to the lowest) interval but now
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
+          * probability in order to take into account the bias as a fraction of the way
+          * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
+          * -stepm/2 to stepm/2 .
+          * For stepm=1 the results are the same as for previous versions of Imach.
+          * For stepm > 1 the results are less biased than in previous versions.
+          */
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
+         /* bias is positive if real duration
+          * is higher than the multiple of stepm and negative otherwise.
+          */
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+         if( s2 > nlstate){
+           /* i.e. if s2 is a death state and if the date of death is known then the contribution
+              to the likelihood is the probability to die between last step unit time and current
+              step unit time, which is also the differences between probability to die before dh
+              and probability to die before dh-stepm .
+              In version up to 0.92 likelihood was computed
+         as if date of death was unknown. Death was treated as any other
+         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
+         to consider that at each interview the state was recorded
+         (healthy, disable or death) and IMaCh was corrected; but when we
+         introduced the exact date of death then we should have modified
+         the contribution of an exact death to the likelihood. This new
+         contribution is smaller and very dependent of the step unit
+         stepm. It is no more the probability to die between last interview
+         and month of death but the probability to survive from last
+         interview up to one month before death multiplied by the
+         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
+         which slows down the processing. The difference can be up to 10%
+         lower mortality.
+           */
+           lli=log(out[s1][s2] - savm[s1][s2]);
+         }else{
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
+         }
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+         /*if(lli ==000.0)*/
+         /*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;
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
+     } /* end of individual */
+   }  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++){
+         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);
+           }
+         for(d=0; d<=dh[mi][i]; d++){
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
+         } /* end mult */
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
+         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 */
+         ipmx +=1;
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
+     } /* end of individual */
+   }  else if(mle==3){  /* exponential inter-extrapolation */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
+         } /* end mult */
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
+         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 */
+         ipmx +=1;
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
+     } /* end of individual */
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
+         } /* end mult */
+         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{
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         }
+         ipmx +=1;
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       } /* end of wave */
+     } /* end of individual */
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
+         } /* end mult */
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         ipmx +=1;
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+       } /* end of wave */
+     } /* end of individual */
+   } /* End of if */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   return -l;
+ }
+ /*************** log-likelihood *************/
+ double funcone( double *x)
+ {
+   /* Same as likeli but slower because of a lot of printf and if */
+   int i, ii, j, k, mi, d, kk;
+   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   double **out;
+   double lli; /* Individual log likelihood */
+   double llt;
+   int s1, s2;
+   double bbh, survp;
+   /*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++)
+     printf(" %d\n",s[4][i]);
+   */
+   cov[1]=1.;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      for(mi=1; mi<= wav[i]-1; mi++){
        for (ii=1;ii<=nlstate+ndeath;ii++)
-         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         for (j=1;j<=nlstate+ndeath;j++){
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         }
        for(d=0; d<dh[mi][i]; d++){
          newm=savm;
          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
          for (kk=1; kk<=cptcovage;kk++) {
            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          }
          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          savm=oldm;
          oldm=newm;
        } /* end mult */
-       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
+       s1=s[mw[mi][i]][i];
-       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
+       s2=s[mw[mi+1][i]][i];
+       bbh=(double)bh[mi][i]/(double)stepm;
+       /* bias is positive if real duration
+        * is higher than the multiple of stepm and negative otherwise.
+        */
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         lli=log(out[s1][s2] - savm[s1][s2]);
+       } else if (mle==1){
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+       } else if(mle==2){
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+       } else if(mle==3){  /* exponential inter-extrapolation */
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+         lli=log(out[s1][s2]); /* Original formula */
+       } 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;
+ /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       if(globpr){
+         fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
+  %10.6f %10.6f %10.6f ", \
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+           llt +=ll[k]*gipmx/gsw;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         }
+         fprintf(ficresilk," %10.6f\n", -llt);
+       }
      } /* end of wave */
    } /* end of individual */
    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   if(globpr==0){ /* First time we count the contributions and weights */
+     gipmx=ipmx;
+     gsw=sw;
+   }
    return -l;
  }
+ /*************** function likelione ***********/
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+ {
+   /* This routine should help understanding what is done with
+      the selection of individuals/waves and
+      to check the exact contribution to the likelihood.
+      Plotting could be done.
+    */
+   int k;
+   if(*globpri !=0){ /* Just counts and sums, no printings */
+     strcpy(fileresilk,"ilk");
+     strcat(fileresilk,fileres);
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", fileresilk);
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+     }
+     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+     /*  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," -2*gipw/gsw*weight*ll[%d]++",k);
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+   }
+   *fretone=(*funcone)(p);
+   if(*globpri !=0){
+     fclose(ficresilk);
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     fflush(fichtm);
+   }
+   return;
+ }
  /*********** Maximum Likelihood Estimation ***************/
  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
  {
    int i,j, iter;
-   double **xi,*delti;
+   double **xi;
    double fret;
+   double fretone; /* Only one call to likelihood */
+   char filerespow[FILENAMELENGTH];
    xi=matrix(1,npar,1,npar);
    for (i=1;i<=npar;i++)
      for (j=1;j<=npar;j++)
        xi[i][j]=(i==j ? 1.0 : 0.0);
    printf("Powell\n");  fprintf(ficlog,"Powell\n");
+   strcpy(filerespow,"pow");
+   strcat(filerespow,fileres);
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", filerespow);
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+   }
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   for (i=1;i<=nlstate;i++)
+     for(j=1;j<=nlstate+ndeath;j++)
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   fprintf(ficrespow,"\n");
    powell(p,xi,npar,ftol,&iter,&fret,func);
-    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+   fclose(ficrespow);
-   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
  }
- Line 1237  void lubksb(double **a, int n, int *indx
+ Line 1797  void lubksb(double **a, int n, int *indx
  }
  /************ Frequencies ********************/
- void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
+ 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)
  {  /* Some frequencies */
    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
    int first;
    double ***freq; /* Frequencies */
-   double *pp;
+   double *pp, **prop;
-   double pos, k2, dateintsum=0,k2cpt=0;
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
    FILE *ficresp;
    char fileresp[FILENAMELENGTH];
    pp=vector(1,nlstate);
-   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
    strcpy(fileresp,"p");
    strcat(fileresp,fileres);
    if((ficresp=fopen(fileresp,"w"))==NULL) {
- Line 1257  void  freqsummary(char fileres[], int ag
+ Line 1817  void  freqsummary(char fileres[], int ag
      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      exit(0);
    }
-   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
+   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
    j1=0;
    j=cptcoveff;
- Line 1272  void  freqsummary(char fileres[], int ag
+ Line 1832  void  freqsummary(char fileres[], int ag
          scanf("%d", i);*/
        for (i=-1; i<=nlstate+ndeath; i++)
          for (jk=-1; jk<=nlstate+ndeath; jk++)
-           for(m=agemin; m <= agemax+3; m++)
+           for(m=iagemin; m <= iagemax+3; m++)
              freq[i][jk][m]=0;
+     for (i=1; i<=nlstate; i++)
+       for(m=iagemin; m <= iagemax+3; m++)
+         prop[i][m]=0;
        dateintsum=0;
        k2cpt=0;
- Line 1284  void  freqsummary(char fileres[], int ag
+ Line 1848  void  freqsummary(char fileres[], int ag
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
                bool=0;
          }
-         if (bool==1) {
+         if (bool==1){
            for(m=firstpass; m<=lastpass; m++){
              k2=anint[m][i]+(mint[m][i]/12.);
-             if ((k2>=dateprev1) && (k2<=dateprev2)) {
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-               if(agev[m][i]==0) agev[m][i]=agemax+1;
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-               if(agev[m][i]==1) agev[m][i]=agemax+2;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                if (m<lastpass) {
                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                }
-               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                  dateintsum=dateintsum+k2;
                  k2cpt++;
                }
-             }
+               /*}*/
            }
          }
        }
-       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
        if  (cptcovn>0) {
          fprintf(ficresp, "\n#********** Variable ");
- Line 1315  void  freqsummary(char fileres[], int ag
+ Line 1880  void  freqsummary(char fileres[], int ag
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        fprintf(ficresp, "\n");
-       for(i=(int)agemin; i <= (int)agemax+3; i++){
+       for(i=iagemin; i <= iagemax+3; i++){
-         if(i==(int)agemax+3){
+         if(i==iagemax+3){
            fprintf(ficlog,"Total");
          }else{
            if(first==1){
- Line 1347  void  freqsummary(char fileres[], int ag
+ Line 1912  void  freqsummary(char fileres[], int ag
          for(jk=1; jk <=nlstate ; jk++){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
              pp[jk] += freq[jk][m][i];
          }
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-         for(jk=1,pos=0; jk <=nlstate ; jk++)
            pos += pp[jk];
+           posprop += prop[jk][i];
+         }
          for(jk=1; jk <=nlstate ; jk++){
            if(pos>=1.e-5){
              if(first==1)
- Line 1361  void  freqsummary(char fileres[], int ag
+ Line 1927  void  freqsummary(char fileres[], int ag
                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
            }
-           if( i <= (int) agemax){
+           if( i <= iagemax){
              if(pos>=1.e-5){
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-               probs[i][jk][j1]= pp[jk]/pos;
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
              }
              else
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
            }
          }
- Line 1379  void  freqsummary(char fileres[], int ag
+ Line 1945  void  freqsummary(char fileres[], int ag
                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
              }
-         if(i <= (int) agemax)
+         if(i <= iagemax)
            fprintf(ficresp,"\n");
          if(first==1)
            printf("Others in log...\n");
- Line 1390  void  freqsummary(char fileres[], int ag
+ Line 1956  void  freqsummary(char fileres[], int ag
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
-   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
+   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
    free_vector(pp,1,nlstate);
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
    /* End of Freq */
  }
  /************ Prevalence ********************/
- void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
+ 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)
- {  /* Some frequencies */
+ {
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
+      We still use firstpass and lastpass as another selection.
+   */
    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
    double ***freq; /* Frequencies */
-   double *pp;
+   double *pp, **prop;
-   double pos, k2;
+   double pos,posprop;
+   double  y2; /* in fractional years */
-   pp=vector(1,nlstate);
+   int iagemin, iagemax;
-   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
+   iagemin= (int) agemin;
+   iagemax= (int) agemax;
+   /*pp=vector(1,nlstate);*/
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    j1=0;
    j=cptcoveff;
- Line 1417  void prevalence(int agemin, float agemax
+ Line 1991  void prevalence(int agemin, float agemax
      for(i1=1; i1<=ncodemax[k1];i1++){
        j1++;
-       for (i=-1; i<=nlstate+ndeath; i++)
+       for (i=1; i<=nlstate; i++)
-         for (jk=-1; jk<=nlstate+ndeath; jk++)
+         for(m=iagemin; m <= iagemax+3; m++)
-           for(m=agemin; m <= agemax+3; m++)
+           prop[i][m]=0.0;
-             freq[i][jk][m]=0;
-       for (i=1; i<=imx; i++) {
+       for (i=1; i<=imx; i++) { /* Each individual */
          bool=1;
          if  (cptcovn>0) {
            for (z1=1; z1<=cptcoveff; z1++)
- Line 1430  void prevalence(int agemin, float agemax
+ Line 2003  void prevalence(int agemin, float agemax
                bool=0;
          }
          if (bool==1) {
-           for(m=firstpass; m<=lastpass; m++){
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-             k2=anint[m][i]+(mint[m][i]/12.);
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-             if ((k2>=dateprev1) && (k2<=dateprev2)) {
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-               if(agev[m][i]==0) agev[m][i]=agemax+1;
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-               if(agev[m][i]==1) agev[m][i]=agemax+2;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-               if (m<lastpass) {
+               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
-                 if (calagedate>0)
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
+                 /*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]]);*/
-                 else
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+                 prop[s[m][i]][iagemax+3] += weight[i];
-                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
+               }
-               }
              }
-           }
+           } /* end selection of waves */
          }
        }
-       for(i=(int)agemin; i <= (int)agemax+3; i++){
+       for(i=iagemin; i <= iagemax+3; i++){
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-             pp[jk] += freq[jk][m][i];
-         }
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=-1, pos=0; m <=0 ; m++)
-             pos += freq[jk][m][i];
-         }
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-             pp[jk] += freq[jk][m][i];
-         }
-         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
-         for(jk=1; jk <=nlstate ; jk++){
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-           if( i <= (int) agemax){
+           posprop += prop[jk][i];
-             if(pos>=1.e-5){
+         }
-               probs[i][jk][j1]= pp[jk]/pos;
-             }
+         for(jk=1; jk <=nlstate ; jk++){
-           }
+           if( i <=  iagemax){
-         }/* end jk */
+             if(posprop>=1.e-5){
-       }/* end i */
+               probs[i][jk][j1]= prop[jk][i]/posprop;
+             }
+           }
+         }/* end jk */
+       }/* end i */
      } /* end i1 */
    } /* end k1 */
-   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-   free_vector(pp,1,nlstate);
+   /*free_vector(pp,1,nlstate);*/
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
- }  /* End of Freq */
+ }  /* End of prevalence */
  /************* Waves Concatenation ***************/
- void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
+ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
  {
    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       Death is a valid wave (if date is known).
       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       and mw[mi+1][i]. dh depends on stepm.
       */
- Line 1521  void  concatwav(int wav[], int **dh, int
+ Line 2081  void  concatwav(int wav[], int **dh, int
      wav[i]=mi;
      if(mi==0){
+       nbwarn++;
        if(first==0){
-         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
+         printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
          first=1;
        }
        if(first==1){
-         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
+         fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
        }
      } /* end mi==0 */
-   }
+   } /* End individuals */
    for(i=1; i<=imx; i++){
      for(mi=1; mi<wav[i];mi++){
        if (stepm <=0)
          dh[mi][i]=1;
        else{
-         if (s[mw[mi+1][i]][i] > nlstate) {
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
            if (agedc[i] < 2*AGESUP) {
-           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-           if(j==0) j=1;  /* Survives at least one month after exam */
+             if(j==0) j=1;  /* Survives at least one month after exam */
-           k=k+1;
+             else if(j<0){
-           if (j >= jmax) jmax=j;
+               nberr++;
-           if (j <= jmin) jmin=j;
+               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]);
-           sum=sum+j;
+               j=1; /* Temporary Dangerous patch */
-           /*if (j<0) printf("j=%d num=%d \n",j,i); */
+               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);
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+               fprintf(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);
+             }
+             k=k+1;
+             if (j >= jmax) jmax=j;
+             if (j <= jmin) jmin=j;
+             sum=sum+j;
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
            }
          }
          else{
            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+           /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
            k=k+1;
            if (j >= jmax) jmax=j;
            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){
+             nberr++;
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+           }
            sum=sum+j;
          }
          jk= j/stepm;
          jl= j -jk*stepm;
          ju= j -(jk+1)*stepm;
-         if(jl <= -ju)
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-           dh[mi][i]=jk;
+           if(jl==0){
-         else
+             dh[mi][i]=jk;
-           dh[mi][i]=jk+1;
+             bh[mi][i]=0;
-         if(dh[mi][i]==0)
+           }else{ /* We want a negative bias in order to only have interpolation ie
-           dh[mi][i]=1; /* At least one step */
+                   * at the price of an extra matrix product in likelihood */
+             dh[mi][i]=jk+1;
+             bh[mi][i]=ju;
+           }
+         }else{
+           if(jl <= -ju){
+             dh[mi][i]=jk;
+             bh[mi][i]=jl;       /* bias is positive if real duration
+                                  * is higher than the multiple of stepm and negative otherwise.
+                                  */
+           }
+           else{
+             dh[mi][i]=jk+1;
+             bh[mi][i]=ju;
+           }
+           if(dh[mi][i]==0){
+             dh[mi][i]=1; /* At least one step */
+             bh[mi][i]=ju; /* At least one step */
+             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+           }
+         } /* end if mle */
        }
-     }
+     } /* end wave */
    }
    jmean=sum/k;
    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
- Line 1575  void  concatwav(int wav[], int **dh, int
+ Line 2172  void  concatwav(int wav[], int **dh, int
  /*********** Tricode ****************************/
  void tricode(int *Tvar, int **nbcode, int imx)
  {
-   int Ndum[20],ij=1, k, j, i;
+   int Ndum[20],ij=1, k, j, i, maxncov=19;
    int cptcode=0;
    cptcoveff=0;
-   for (k=0; k<19; k++) Ndum[k]=0;
+   for (k=0; k<maxncov; k++) Ndum[k]=0;
    for (k=1; k<=7; k++) ncodemax[k]=0;
    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
-     for (i=1; i<=imx; i++) {
+     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
-       ij=(int)(covar[Tvar[j]][i]);
+                                modality*/
-       Ndum[ij]++;
+       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+       Ndum[ij]++; /*store the modality */
        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-       if (ij > cptcode) cptcode=ij;
+       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+                                        Tvar[j]. If V=sex and male is 0 and
+                                        female is 1, then  cptcode=1.*/
      }
      for (i=0; i<=cptcode; i++) {
-       if(Ndum[i]!=0) ncodemax[j]++;
+       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;
+     ij=1;
      for (i=1; i<=ncodemax[j]; i++) {
-       for (k=0; k<=19; k++) {
+       for (k=0; k<= maxncov; k++) {
          if (Ndum[k] != 0) {
            nbcode[Tvar[j]][ij]=k;
+           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
            ij++;
          }
- Line 1608  void tricode(int *Tvar, int **nbcode, in
+ Line 2209  void tricode(int *Tvar, int **nbcode, in
      }
    }
-  for (k=0; k<19; k++) Ndum[k]=0;
+  for (k=0; k< maxncov; k++) Ndum[k]=0;
   for (i=1; i<=ncovmodel-2; i++) {
+    /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     ij=Tvar[i];
     Ndum[ij]++;
   }
   ij=1;
-  for (i=1; i<=10; i++) {
+  for (i=1; i<= maxncov; i++) {
     if((Ndum[i]!=0) && (i<=ncovcol)){
-      Tvaraff[ij]=i;
+      Tvaraff[ij]=i; /*For printing */
       ij++;
     }
   }
-  cptcoveff=ij-1;
+  cptcoveff=ij-1; /*Number of simple covariates*/
  }
  /*********** Health Expectancies ****************/
- Line 1641  void evsij(char fileres[], double ***eij
+ Line 2243  void evsij(char fileres[], double ***eij
    double ***gradg, ***trgradg;
    int theta;
-   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
    xp=vector(1,npar);
-   dnewm=matrix(1,nlstate*2,1,npar);
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   doldm=matrix(1,nlstate*2,1,nlstate*2);
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
    fprintf(ficreseij,"# Health expectancies\n");
    fprintf(ficreseij,"# Age");
- Line 1661  void evsij(char fileres[], double ***eij
+ Line 2263  void evsij(char fileres[], double ***eij
     * This is mainly to measure the difference between two models: for example
     * if stepm=24 months pijx are given only every 2 years and by summing them
     * we are calculating an estimate of the Life Expectancy assuming a linear
-    * progression inbetween and thus overestimating or underestimating according
+    * progression in between and thus overestimating or underestimating according
     * to the curvature of the survival function. If, for the same date, we
     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     * to compare the new estimate of Life expectancy with the same linear
- Line 1690  void evsij(char fileres[], double ***eij
+ Line 2292  void evsij(char fileres[], double ***eij
      /* if (stepm >= YEARM) hstepm=1;*/
      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-     gp=matrix(0,nhstepm,1,nlstate*2);
+     gp=matrix(0,nhstepm,1,nlstate*nlstate);
-     gm=matrix(0,nhstepm,1,nlstate*2);
+     gm=matrix(0,nhstepm,1,nlstate*nlstate);
      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
- Line 1701  void evsij(char fileres[], double ***eij
+ Line 2303  void evsij(char fileres[], double ***eij
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     /* Computing Variances of health expectancies */
+     /* Computing  Variances of health expectancies */
       for(theta=1; theta <=npar; theta++){
        for(i=1; i<=npar; i++){
- Line 1729  void evsij(char fileres[], double ***eij
+ Line 2331  void evsij(char fileres[], double ***eij
          for(i=1;i<=nlstate;i++){
            cptj=cptj+1;
            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
            }
          }
        }
-       for(j=1; j<= nlstate*2; j++)
+       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];
          }
- Line 1741  void evsij(char fileres[], double ***eij
+ Line 2344  void evsij(char fileres[], double ***eij
  /* End theta */
-      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
+      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       for(h=0; h<=nhstepm-1; h++)
-       for(j=1; j<=nlstate*2;j++)
+       for(j=1; j<=nlstate*nlstate;j++)
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
-      for(i=1;i<=nlstate*2;i++)
+      for(i=1;i<=nlstate*nlstate;i++)
-       for(j=1;j<=nlstate*2;j++)
+       for(j=1;j<=nlstate*nlstate;j++)
          varhe[i][j][(int)age] =0.;
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       for(h=0;h<=nhstepm-1;h++){
        for(k=0;k<=nhstepm-1;k++){
-         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-         for(i=1;i<=nlstate*2;i++)
+         for(i=1;i<=nlstate*nlstate;i++)
-           for(j=1;j<=nlstate*2;j++)
+           for(j=1;j<=nlstate*nlstate;j++)
              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
        }
      }
- Line 1783  void evsij(char fileres[], double ***eij
+ Line 2386  void evsij(char fileres[], double ***eij
        }
      fprintf(ficreseij,"\n");
-     free_matrix(gm,0,nhstepm,1,nlstate*2);
+     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-     free_matrix(gp,0,nhstepm,1,nlstate*2);
+     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
+     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }
    printf("\n");
    fprintf(ficlog,"\n");
    free_vector(xp,1,npar);
-   free_matrix(dnewm,1,nlstate*2,1,npar);
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-   free_matrix(doldm,1,nlstate*2,1,nlstate*2);
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  }
  /************ Variance ******************/
- Line 1824  void varevsij(char optionfilefiname[], d
+ Line 2427  void varevsij(char optionfilefiname[], d
    char fileresprobmorprev[FILENAMELENGTH];
    if(popbased==1){
-     if(mobilav==1)
+     if(mobilav!=0)
        strcpy(digitp,"-populbased-mobilav-");
      else strcpy(digitp,"-populbased-nomobil-");
    }
    else
      strcpy(digitp,"-stablbased-");
- <<<<<<< imach.c
-   if (mobilav!=0) {
- =======
-   if(mobilav!=0)
-     strcat(digitp,"mobilav-");
-   else
-     strcat(digitp,"nomobil-");
    if (mobilav!=0) {
- >>>>>>> 1.54
      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);
- Line 1858  void varevsij(char optionfilefiname[], d
+ Line 2454  void varevsij(char optionfilefiname[], d
    }
    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
+   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
      fprintf(ficresprobmorprev," p.%-d SE",j);
- Line 1866  void varevsij(char optionfilefiname[], d
+ Line 2462  void varevsij(char optionfilefiname[], d
        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
    }
    fprintf(ficresprobmorprev,"\n");
-   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+   fprintf(ficgp,"\n# Routine varevsij");
-     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+   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");
-     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-     exit(0);
+ /*   } */
-   }
-   else{
-     fprintf(ficgp,"\n# Routine varevsij");
-   }
-   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 probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-     fprintf(fichtm,"\n<br>%s (� revoir) <br>\n",digitp);
-   }
    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
- Line 1915  void varevsij(char optionfilefiname[], d
+ Line 2498  void varevsij(char optionfilefiname[], d
       and note for a fixed period like k years */
    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       survival function given by stepm (the optimization length). Unfortunately it
-      means that if the survival funtion is printed only each two years of age and if
+      means that if the survival funtion is printed every two years of age and if
       you sum them up and add 1 year (area under the trapezoids) you won't get the same
       results. So we changed our mind and took the option of the best precision.
    */
- Line 1931  void varevsij(char optionfilefiname[], d
+ Line 2514  void varevsij(char optionfilefiname[], d
      for(theta=1; theta <=npar; theta++){
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
- Line 1953  void varevsij(char optionfilefiname[], d
+ Line 2536  void varevsij(char optionfilefiname[], d
              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
          }
        }
-       /* This for computing forces of mortality (h=1)as a weighted average */
+       /* This for computing probability of death (h=1 means
-       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
+          computed over hstepm matrices product = hstepm*stepm months)
-         for(i=1; i<= nlstate; i++)
+          as a weighted average of prlim.
+       */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
            gpp[j] += prlim[i][i]*p3mat[i][j][1];
        }
-       /* end force of mortality */
+       /* end probability of death */
-       for(i=1; i<=npar; i++) /* Computes gradient */
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
- Line 1981  void varevsij(char optionfilefiname[], d
+ Line 2567  void varevsij(char optionfilefiname[], d
              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
          }
        }
-       /* This for computing force of mortality (h=1)as a weighted average */
+       /* This for computing probability of death (h=1 means
-       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
+          computed over hstepm matrices product = hstepm*stepm months)
-         for(i=1; i<= nlstate; i++)
+          as a weighted average of prlim.
-           gmp[j] += prlim[i][i]*p3mat[i][j][1];
+       */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
        }
-       /* end force of mortality */
+       /* end probability of death */
        for(j=1; j<= nlstate; j++) /* vareij */
          for(h=0; h<=nhstepm; h++){
            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
          }
        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
        }
- Line 2008  void varevsij(char optionfilefiname[], d
+ Line 2598  void varevsij(char optionfilefiname[], d
      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
        for(theta=1; theta <=npar; theta++)
          trgradgp[j][theta]=gradgp[theta][j];
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(i=1;i<=nlstate;i++)
- Line 2023  void varevsij(char optionfilefiname[], d
+ Line 2614  void varevsij(char optionfilefiname[], d
              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
        }
      }
      /* pptj */
      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
- Line 2031  void varevsij(char optionfilefiname[], d
+ Line 2622  void varevsij(char optionfilefiname[], d
        for(i=nlstate+1;i<=nlstate+ndeath;i++)
          varppt[j][i]=doldmp[j][i];
      /* end ppptj */
+     /*  x centered again */
      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
- Line 2043  void varevsij(char optionfilefiname[], d
+ Line 2635  void varevsij(char optionfilefiname[], d
            prlim[i][i]=mobaverage[(int)age][i][ij];
        }
      }
-     /* This for computing force of mortality (h=1)as a weighted average */
+     /* This for computing probability of death (h=1 means
-     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-       for(i=1; i<= nlstate; i++)
+        as a weighted average of prlim.
+     */
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
          gmp[j] += prlim[i][i]*p3mat[i][j][1];
      }
-     /* end force of mortality */
+     /* end probability of death */
      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
- Line 2079  void varevsij(char optionfilefiname[], d
+ Line 2674  void varevsij(char optionfilefiname[], d
    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)\";");
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    /*  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);
  */
-   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    free_vector(xp,1,npar);
    free_matrix(doldm,1,nlstate,1,nlstate);
- Line 2096  void varevsij(char optionfilefiname[], d
+ Line 2695  void varevsij(char optionfilefiname[], d
    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    fclose(ficresprobmorprev);
-   fclose(ficgp);
+   fflush(ficgp);
-   fclose(fichtm);
+   fflush(fichtm);
- }
+ }  /* end varevsij */
  /************ Variance of prevlim ******************/
  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
  {
    /* Variance of prevalence limit */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
    double **newm;
    double **dnewm,**doldm;
    int i, j, nhstepm, hstepm;
- Line 2244  void varprob(char optionfilefiname[], do
+ Line 2843  void varprob(char optionfilefiname[], do
        fprintf(ficresprobcov," p%1d-%1d ",i,j);
        fprintf(ficresprobcor," p%1d-%1d ",i,j);
      }
-   fprintf(ficresprob,"\n");
+  /* fprintf(ficresprob,"\n");
    fprintf(ficresprobcov,"\n");
    fprintf(ficresprobcor,"\n");
-   xp=vector(1,npar);
+  */
+  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) {
+   fprintf(ficgp,"\n# Routine varprob");
-     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+   fprintf(fichtm,"\n");
-     exit(0);
-   }
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   else{
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-     fprintf(ficgp,"\n# Routine varprob");
+   file %s<br>\n",optionfilehtmcov);
-   }
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+ and drawn. It helps understanding how is the covariance between two incidences.\
-     printf("Problem with html file: %s\n", optionfilehtm);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
-     exit(0);
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-   }
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-   else{
+ standard deviations wide on each axis. <br>\
-     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-     fprintf(fichtm,"\n");
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \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;}
- Line 2284  void varprob(char optionfilefiname[], do
+ Line 2878  void varprob(char optionfilefiname[], do
    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#");
+         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#");
+         fprintf(ficresprobcov, "**********\n#\n");
          fprintf(ficgp, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficgp, "**********\n#");
+         fprintf(ficgp, "**********\n#\n");
-         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+         fprintf(fichtmcov, "\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(fichtmcov, "**********\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(ficgp, "**********\n#");
+         fprintf(ficresprobcor, "**********\n#");
        }
        for (age=bage; age<=fage; age ++){
- Line 2323  void varprob(char optionfilefiname[], do
+ Line 2916  void varprob(char optionfilefiname[], do
          for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++)
-             xp[i] = x[i] + (i==theta ?delti[theta]:0);
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
            pmij(pmmij,cov,ncovmodel,xp,nlstate);
- Line 2336  void varprob(char optionfilefiname[], do
+ Line 2929  void varprob(char optionfilefiname[], do
            }
            for(i=1; i<=npar; i++)
-             xp[i] = x[i] - (i==theta ?delti[theta]:0);
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
            pmij(pmmij,cov,ncovmodel,xp,nlstate);
            k=0;
- Line 2348  void varprob(char optionfilefiname[], do
+ Line 2941  void varprob(char optionfilefiname[], do
            }
            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
          }
          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
- Line 2357  void varprob(char optionfilefiname[], do
+ Line 2950  void varprob(char optionfilefiname[], do
          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;
- Line 2372  void varprob(char optionfilefiname[], do
+ Line 2969  void varprob(char optionfilefiname[], do
              varpij[i][j][(int)age] = doldm[i][j];
          /*printf("\n%d ",(int)age);
-      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           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]));
+           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(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);
- Line 2403  void varprob(char optionfilefiname[], do
+ Line 3000  void varprob(char optionfilefiname[], do
        /* Confidence intervalle of pij  */
        /*
-       fprintf(ficgp,"\nset noparametric;unset label");
+         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 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(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>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(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-       fprintf(ficgp,"\nset out \"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);
+         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)*/
- Line 2454  void varprob(char optionfilefiname[], do
+ Line 3051  void varprob(char optionfilefiname[], do
                      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(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
- Line 2465  void varprob(char optionfilefiname[], do
+ Line 3066  void varprob(char optionfilefiname[], do
                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                    }else{
                      first=0;
-                     fprintf(fichtm," %d (%.3f),",(int) age, c12);
+                     fprintf(fichtmcov," %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",\
- Line 2474  void varprob(char optionfilefiname[], do
+ Line 3075  void varprob(char optionfilefiname[], do
                    }/* 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);
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), 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_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    }
+   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);
+   fflush(ficgp);
-   fclose(fichtm);
+   fflush(fichtmcov);
  }
- Line 2505  void printinghtml(char fileres[], char t
+ Line 3102  void printinghtml(char fileres[], char t
                    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
+    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
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
+    fprintf(fichtm,"\
-  - Life expectancies by age and initial health status (estepm=%2d months):
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-    <a href=\"e%s\">e%s</a> <br>\n</li>", \
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
+    fprintf(fichtm,"\
+  - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+    fprintf(fichtm,"\
+  - Life expectancies by age and initial health status (estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
- Line 2535  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3133  fprintf(fichtm," \n<ul><li><b>Graphs</b>
         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>
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
- <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+ <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
       /* Quasi-incidences */
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
+ <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
         /* 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>
+          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);
+ <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),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>
+         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
- <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),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
+  fprintf(fichtm,"\
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
+ \n<br><li><h4> Result files (second order: variances)</h4>\n\
-  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-  - 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
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
+  fprintf(fichtm,"\
-  - 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);
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-  if(popforecast==1) fprintf(fichtm,"\n
-  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
+  fprintf(fichtm,"\
-  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-         <br>",fileres,fileres,fileres,fileres);
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-  else
+  fprintf(fichtm,"\
-    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);
+  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
- fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+  fprintf(fichtm,"\
+  - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+  fprintf(fichtm,"\
+  - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+ /*  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); */
+  fflush(fichtm);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   m=cptcoveff;
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- Line 2588  fprintf(fichtm," <ul><li><b>Graphs</b></
+ Line 3199  fprintf(fichtm," <ul><li><b>Graphs</b></
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- interval) in state (%d): v%s%d%d.png <br>
+ prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
- <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
       }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+ health expectancies in states (1) and (2): %s%d.png<br>\
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     } /* end i1 */
   }/* End k1 */
   fprintf(fichtm,"</ul>");
- fclose(fichtm);
+  fflush(fichtm);
  }
  /******************* Gnuplot file **************/
- void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   char dirfileres[132],optfileres[132];
    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
    int ng;
-   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-     printf("Problem with file %s",optionfilegnuplot);
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-   }
+ /*   } */
    /*#ifdef windows */
-     fprintf(ficgp,"cd \"%s\" \n",pathc);
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
      /*#endif */
- m=pow(2,cptcoveff);
+   m=pow(2,cptcoveff);
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
   /* 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,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),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);
+      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+      fprintf(ficgp,"set xlabel \"Age\" \n\
+ set ylabel \"Probability\" \n\
+ set ter png small\n\
+ set size 0.65,0.65\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
       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+2*$3) \"\%%lf",fileres,k1-1,k1-1);
+      fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (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:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
+      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }
-      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
+      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     }
    }
    /*2 eme*/
    for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),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);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        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);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"\" w l 0,");
-       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
- Line 2672  m=pow(2,cptcoveff);
+ Line 3294  m=pow(2,cptcoveff);
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<= nlstate ; cpt ++) {
        k=2+nlstate*(2*cpt-2);
-       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+       fprintf(ficgp,"set ter png small\n\
+ set size 0.65,0.65\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
- Line 2683  m=pow(2,cptcoveff);
+ Line 3307  m=pow(2,cptcoveff);
        */
        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);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
        }
      }
    }
-   /* CV preval stat */
+   /* CV preval stable (period) */
    for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<nlstate ; cpt ++) {
+     for (cpt=1; cpt<=nlstate ; cpt ++) {
        k=3;
-       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),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);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter png small\nset size 0.65,0.65\n\
+ unset log y\n\
+ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
        for (i=1; i< nlstate ; i ++)
          fprintf(ficgp,"+$%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);
+       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
        for (i=1; i< nlstate ; i ++) {
          l=3+(nlstate+ndeath)*cpt;
          fprintf(ficgp,"+$%d",l+i+1);
- Line 2725  m=pow(2,cptcoveff);
+ Line 3352  m=pow(2,cptcoveff);
     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);
+        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
         if (ng==2)
           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
         else
- Line 2772  m=pow(2,cptcoveff);
+ Line 3399  m=pow(2,cptcoveff);
         } /* end k2 */
       } /* end jk */
     } /* end ng */
-    fclose(ficgp);
+    fflush(ficgp);
  }  /* end gnuplot */
- Line 2780  m=pow(2,cptcoveff);
+ Line 3407  m=pow(2,cptcoveff);
  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<=ncodemax[cptcov];cptcod++)
+         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
- Line 2796  int movingaverage(double ***probs, doubl
+ Line 3429  int movingaverage(double ***probs, doubl
      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<=ncodemax[cptcoveff];cptcod++){
+           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];
- Line 2813  int movingaverage(double ***probs, doubl
+ Line 3446  int movingaverage(double ***probs, doubl
  /************** Forecasting ******************/
- prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
+ 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
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+      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 calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   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;
+   agelim=AGESUP;
- calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
    strcpy(fileresf,"f");
    strcat(fileresf,fileres);
- Line 2850  calagedate=(anproj1+mproj1/12.+jproj1/36
+ Line 3485  calagedate=(anproj1+mproj1/12.+jproj1/36
    stepsize=(int) (stepm+YEARM-1)/YEARM;
    if (stepm<=12) stepsize=1;
+   if(estepm < stepm){
-   agelim=AGESUP;
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
-   hstepm=1;
+   else  hstepm=estepm;
    hstepm=hstepm/stepm;
-   yp1=modf(dateintmean,&yp);
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+                                fractional in yp1 */
    anprojmean=yp;
    yp2=modf((yp1*12),&yp);
    mprojmean=yp;
- Line 2863  calagedate=(anproj1+mproj1/12.+jproj1/36
+ Line 3500  calagedate=(anproj1+mproj1/12.+jproj1/36
    jprojmean=yp;
    if(jprojmean==0) jprojmean=1;
    if(mprojmean==0) jprojmean=1;
+   i1=cptcoveff;
+   if (cptcovn < 1){i1=1;}
-   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-   for(cptcov=1;cptcov<=i2;cptcov++){
+   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 ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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,"# StartingAge FinalAge");
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
+       for(j=1; j<=nlstate+ndeath;j++){
+         for(i=1; i<=nlstate;i++)
+           fprintf(ficresf," p%d%d",i,j);
-       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
+         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+cpt);
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+         for (agec=fage; agec>=(ageminpar-1); agec--){
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           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,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
            for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedate+YEARM*cpt)) {
+             if (h*hstepm/YEARM*stepm ==yearp) {
-               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
+               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++) {
-               kk1=0.;kk2=0;
+               ppij=0.;
                for(i=1; i<=nlstate;i++) {
                  if (mobilav==1)
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                  else {
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                  }
+                 if (h*hstepm/YEARM*stepm== yearp) {
-               }
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-               if (h==(int)(calagedate+12*cpt)){
+                 }
-                 fprintf(ficresf," %.3f", kk1);
+               } /* 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 ******************/
+ /************** 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 calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double calagedatem, agelim, kk1, kk2;
    double *popeffectif,*popcount;
    double ***p3mat,***tabpop,***tabpopprev;
    double ***mobaverage;
- Line 2934  populforecast(char fileres[], double anp
+ Line 3583  populforecast(char fileres[], double anp
    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    agelim=AGESUP;
-   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    strcpy(filerespop,"pop");
- Line 2982  populforecast(char fileres[], double anp
+ Line 3631  populforecast(char fileres[], double anp
      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
    }
-   for(cptcov=1;cptcov<=i2;cptcov++){
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
        k=k+1;
        fprintf(ficrespop,"\n#******");
- Line 2997  populforecast(char fileres[], double anp
+ Line 3646  populforecast(char fileres[], double anp
        for (cpt=0; cpt<=0;cpt++) {
          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
            nhstepm = nhstepm/hstepm;
- Line 3006  populforecast(char fileres[], double anp
+ Line 3655  populforecast(char fileres[], double anp
            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
            for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedate+YEARM*cpt)) {
+             if (h==(int) (calagedatem+YEARM*cpt)) {
                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
              }
              for(j=1; j<=nlstate+ndeath;j++) {
- Line 3018  populforecast(char fileres[], double anp
+ Line 3667  populforecast(char fileres[], double anp
                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                  }
                }
-               if (h==(int)(calagedate+12*cpt)){
+               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]);*/
- Line 3029  populforecast(char fileres[], double anp
+ Line 3678  populforecast(char fileres[], double anp
                  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+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
              }
-             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
+             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);
- Line 3043  populforecast(char fileres[], double anp
+ Line 3692  populforecast(char fileres[], double anp
        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)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
            nhstepm = nhstepm/hstepm;
- Line 3051  populforecast(char fileres[], double anp
+ Line 3700  populforecast(char fileres[], double anp
            oldm=oldms;savm=savms;
            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
            for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedate+YEARM*cpt)) {
+             if (h==(int) (calagedatem+YEARM*cpt)) {
                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
              }
              for(j=1; j<=nlstate+ndeath;j++) {
- Line 3059  populforecast(char fileres[], double anp
+ Line 3708  populforecast(char fileres[], double anp
                for(i=1; i<=nlstate;i++) {
                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
                }
-               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
              }
            }
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- Line 3078  populforecast(char fileres[], double anp
+ Line 3727  populforecast(char fileres[], double anp
    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    fclose(ficrespop);
+ } /* End of popforecast */
+ int fileappend(FILE *fichier, char *optionfich)
+ {
+   if((fichier=fopen(optionfich,"a"))==NULL) {
+     printf("Problem with file: %s\n", optionfich);
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+     return (0);
+   }
+   fflush(fichier);
+   return (1);
  }
+ /**************** function prwizard **********************/
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+ {
+   /* Wizard to print covariance matrix template */
+   char ca[32], cb[32], cc[32];
+   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+   int numlinepar;
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   for(i=1; i <=nlstate; i++){
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
+       jj++;
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+       printf("%1d%1d",i,j);
+       fprintf(ficparo,"%1d%1d",i,j);
+       for(k=1; k<=ncovmodel;k++){
+         /*        printf(" %lf",param[i][j][k]); */
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+         printf(" 0.");
+         fprintf(ficparo," 0.");
+       }
+       printf("\n");
+       fprintf(ficparo,"\n");
+     }
+   }
+   printf("# Scales (for hessian or gradient estimation)\n");
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   for(i=1; i <=nlstate; i++){
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
+       jj++;
+       fprintf(ficparo,"%1d%1d",i,j);
+       printf("%1d%1d",i,j);
+       fflush(stdout);
+       for(k=1; k<=ncovmodel;k++){
+         /*      printf(" %le",delti3[i][j][k]); */
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+         printf(" 0.");
+         fprintf(ficparo," 0.");
+       }
+       numlinepar++;
+       printf("\n");
+       fprintf(ficparo,"\n");
+     }
+   }
+   printf("# Covariance matrix\n");
+ /* # 121 Var(a12)\n\ */
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   fflush(stdout);
+   fprintf(ficparo,"# Covariance matrix\n");
+   /* # 121 Var(a12)\n\ */
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   /* #   ...\n\ */
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+   for(itimes=1;itimes<=2;itimes++){
+     jj=0;
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j==i) continue;
+         for(k=1; k<=ncovmodel;k++){
+           jj++;
+           ca[0]= k+'a'-1;ca[1]='\0';
+           if(itimes==1){
+             printf("#%1d%1d%d",i,j,k);
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+           }else{
+             printf("%1d%1d%d",i,j,k);
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
+             /*  printf(" %.5le",matcov[i][j]); */
+           }
+           ll=0;
+           for(li=1;li <=nlstate; li++){
+             for(lj=1;lj <=nlstate+ndeath; lj++){
+               if(lj==li) continue;
+               for(lk=1;lk<=ncovmodel;lk++){
+                 ll++;
+                 if(ll<=jj){
+                   cb[0]= lk +'a'-1;cb[1]='\0';
+                   if(ll<jj){
+                     if(itimes==1){
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                     }else{
+                       printf(" 0.");
+                       fprintf(ficparo," 0.");
+                     }
+                   }else{
+                     if(itimes==1){
+                       printf(" Var(%s%1d%1d)",ca,i,j);
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+                     }else{
+                       printf(" 0.");
+                       fprintf(ficparo," 0.");
+                     }
+                   }
+                 }
+               } /* end lk */
+             } /* end lj */
+           } /* end li */
+           printf("\n");
+           fprintf(ficparo,"\n");
+           numlinepar++;
+         } /* end k*/
+       } /*end j */
+     } /* end i */
+   } /* end itimes */
+ } /* end of prwizard */
  /***********************************************/
  /**************** Main Program *****************/
  /***********************************************/
  int main(int argc, char *argv[])
  {
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+   int jj, ll, li, lj, lk, imk;
+   int numlinepar=0; /* Current linenumber of parameter file */
+   int itimes;
+   char ca[32], cb[32], cc[32];
+   /*  FILE *fichtm; *//* Html File */
+   /* FILE *ficgp;*/ /*Gnuplot File */
    double agedeb, agefin,hf;
    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
- Line 3099  int main(int argc, char *argv[])
+ Line 3891  int main(int argc, char *argv[])
    double ***mobaverage;
    int *indx;
    char line[MAXLINE], linepar[MAXLINE];
-   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   char pathr[MAXLINE];
    int firstobs=1, lastobs=10;
    int sdeb, sfin; /* Status at beginning and end */
    int c,  h , cpt,l;
    int ju,jl, mi;
    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
+   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, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
+   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;
- Line 3123  int main(int argc, char *argv[])
+ Line 3918  int main(int argc, char *argv[])
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
    double kk1, kk2;
-   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
+   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;
- #include <sys/time.h>
- #include <time.h>
    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+   char strstart[80], *strt, strtend[80];
+   char *stratrunc;
+   int lstra;
+   long total_usecs;
-   /* long total_usecs;
+ /*   setlocale (LC_ALL, ""); */
-   struct timeval start_time, end_time;
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
-   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   (void) gettimeofday(&start_time,&tzp);
+   curr_time=start_time;
+   tm = *localtime(&start_time.tv_sec);
+   tmg = *gmtime(&start_time.tv_sec);
+   strcpy(strstart,asctime(&tm));
+ /*  printf("Localtime (at start)=%s",strstart); */
+ /*  tp.tv_sec = tp.tv_sec +86400; */
+ /*  tm = *localtime(&start_time.tv_sec); */
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ /*   tp.tv_sec = mktime(&tmg); */
+ /*   strt=asctime(&tmg); */
+ /*   printf("Time(after) =%s",strstart);  */
+ /*  (void) time (&time_value);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+ *  tm = *localtime(&time_value);
+ *  strstart=asctime(&tm);
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+ */
+   nberr=0; /* Number of errors and warnings */
+   nbwarn=0;
    getcwd(pathcd, size);
-   printf("\n%s",version);
+   printf("\n%s\n%s",version,fullversion);
    if(argc <=1){
      printf("\nEnter the parameter file name: ");
      scanf("%s",pathtot);
- Line 3148  int main(int argc, char *argv[])
+ Line 3973  int main(int argc, char *argv[])
    else{
      strcpy(pathtot,argv[1]);
    }
-   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
    /*cygwin_split_path(pathtot,path,optionfile);
      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
    /* cutv(path,optionfile,pathtot,'\\');*/
    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",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);
+   strcpy(command,"mkdir ");
+   strcat(command,optionfilefiname);
+   if((outcmd=system(command)) != 0){
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+     /* fclose(ficlog); */
+ /*     exit(1); */
+   }
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
+ /*     perror("mkdir"); */
+ /*   } */
- /*-------- arguments in the command line --------*/
+   /*-------- arguments in the command line --------*/
    /* Log file */
    strcat(filelog, optionfilefiname);
- Line 3168  int main(int argc, char *argv[])
+ Line 4003  int main(int argc, char *argv[])
      goto end;
    }
    fprintf(ficlog,"Log filename:%s\n",filelog);
-   fprintf(ficlog,"\n%s",version);
+   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);
+   fprintf(ficlog,"pathtot=%s\n\
+  path=%s \n\
+  optionfile=%s\n\
+  optionfilext=%s\n\
+  optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("Local time (at start):%s",strstart);
+   fprintf(ficlog,"Local time (at start): %s",strstart);
    fflush(ficlog);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
    /* */
    strcpy(fileres,"r");
- Line 3183  int main(int argc, char *argv[])
+ Line 4027  int main(int argc, char *argv[])
    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) {
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
      printf("Problem with Output resultfile: %s\n", filereso);
      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     fflush(ficlog);
      goto end;
    }
    /* Reads comments: lines beginning with '#' */
+   numlinepar=0;
    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
+     numlinepar++;
      puts(line);
      fputs(line,ficparo);
+     fputs(line,ficlog);
    }
    ungetc(c,ficpar);
    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   numlinepar++;
    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
- while((c=getc(ficpar))=='#' && c!= EOF){
+   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;
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
-   ncovmodel=2+cptcovn;
+   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     fclose (ficparo);
+     fclose (ficlog);
+     exit(0);
+   }
    /* Read guess parameters */
    /* Reads comments: lines beginning with '#' */
    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
+     numlinepar++;
      puts(line);
      fputs(line,ficparo);
+     fputs(line,ficlog);
    }
    ungetc(c,ficpar);
    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     for(i=1; i <=nlstate; i++)
+   for(i=1; i <=nlstate; i++){
-     for(j=1; j <=nlstate+ndeath-1; j++){
+     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);
- Line 3251  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4124  while((c=getc(ficpar))=='#' && c!= EOF){
          fprintf(ficparo," %lf",param[i][j][k]);
        }
        fscanf(ficpar,"\n");
+       numlinepar++;
        if(mle==1)
          printf("\n");
        fprintf(ficlog,"\n");
        fprintf(ficparo,"\n");
      }
+   }
-     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
+   fflush(ficlog);
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
    p=param[1][1];
- Line 3265  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4141  while((c=getc(ficpar))=='#' && c!= EOF){
    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) */
+   /* 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);
- Line 3309  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4202  while((c=getc(ficpar))=='#' && c!= EOF){
        fscanf(ficpar," %le",&matcov[i][j]);
        if(mle==1){
          printf(" %.5le",matcov[i][j]);
-         fprintf(ficlog," %.5le",matcov[i][j]);
        }
-       else
+       fprintf(ficlog," %.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");
- Line 3329  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4221  while((c=getc(ficpar))=='#' && c!= EOF){
      printf("\n");
    fprintf(ficlog,"\n");
+   fflush(ficlog);
-     /*-------- Rewriting paramater file ----------*/
+   /*-------- Rewriting paramater file ----------*/
-      strcpy(rfileres,"r");    /* "Rparameterfile */
+   strcpy(rfileres,"r");    /* "Rparameterfile */
-      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+   strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-      strcat(rfileres,".");    /* */
+   strcat(rfileres,".");    /* */
-      strcat(rfileres,optionfilext);    /* Other files have txt extension */
+   strcat(rfileres,optionfilext);    /* Other files have txt extension */
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+   if((ficres =fopen(rfileres,"w"))==NULL) {
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+     printf("Problem writing new parameter file: %s\n", fileres);goto end;
-       fprintf(ficlog,"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);
+   fprintf(ficres,"#%s\n",version);
-     /*-------- data file ----------*/
+   /*-------- data file ----------*/
-     if((fic=fopen(datafile,"r"))==NULL)    {
+   if((fic=fopen(datafile,"r"))==NULL)    {
-       printf("Problem with datafile: %s\n", datafile);goto end;
+     printf("Problem with datafile: %s\n", datafile);goto end;
-       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
+     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
-     }
+   }
-     n= lastobs;
+   n= lastobs;
-     severity = vector(1,maxwav);
+   severity = vector(1,maxwav);
-     outcome=imatrix(1,maxwav+1,1,n);
+   outcome=imatrix(1,maxwav+1,1,n);
-     num=ivector(1,n);
+   num=lvector(1,n);
-     moisnais=vector(1,n);
+   moisnais=vector(1,n);
-     annais=vector(1,n);
+   annais=vector(1,n);
-     moisdc=vector(1,n);
+   moisdc=vector(1,n);
-     andc=vector(1,n);
+   andc=vector(1,n);
-     agedc=vector(1,n);
+   agedc=vector(1,n);
-     cod=ivector(1,n);
+   cod=ivector(1,n);
-     weight=vector(1,n);
+   weight=vector(1,n);
-     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-     mint=matrix(1,maxwav,1,n);
+   mint=matrix(1,maxwav,1,n);
-     anint=matrix(1,maxwav,1,n);
+   anint=matrix(1,maxwav,1,n);
-     s=imatrix(1,maxwav+1,1,n);
+   s=imatrix(1,maxwav+1,1,n);
-     adl=imatrix(1,maxwav+1,1,n);
+   tab=ivector(1,NCOVMAX);
-     tab=ivector(1,NCOVMAX);
+   ncodemax=ivector(1,8);
-     ncodemax=ivector(1,8);
+   i=1;
-     i=1;
+   while (fgets(line, MAXLINE, fic) != NULL)    {
-     while (fgets(line, MAXLINE, fic) != NULL)    {
+     if ((i >= firstobs) && (i <=lastobs)) {
-       if ((i >= firstobs) && (i <=lastobs)) {
-         for (j=maxwav;j>=1;j--){
+       for (j=maxwav;j>=1;j--){
-           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
+         cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
-           strcpy(line,stra);
+         strcpy(line,stra);
-           cutv(stra, strb,line,'/'); anint[j][i]=(double)(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,' '); 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,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
-         cutv(stra, strb,line,' '); moisdc[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,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
-         cutv(stra, strb,line,' '); moisnais[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);
+       cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
-         for (j=ncovcol;j>=1;j--){
+       for (j=ncovcol;j>=1;j--){
-           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+         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)){
+       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+         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;
+       i=i+1;
-       }
+     }
-     }
+   }
-     /* printf("ii=%d", ij);
+   /* printf("ii=%d", ij);
-        scanf("%d",i);*/
+      scanf("%d",i);*/
    imx=i-1; /* Number of individuals */
    /* for (i=1; i<=imx; i++){
- Line 3406  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4304  while((c=getc(ficpar))=='#' && c!= EOF){
      }*/
     /*  for (i=1; i<=imx; i++){
       if (s[4][i]==9)  s[4][i]=-1;
-      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+      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);
- Line 3416  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4318  while((c=getc(ficpar))=='#' && c!= EOF){
    Tvard=imatrix(1,15,1,2);
    Tage=ivector(1,15);
-   if (strlen(model) >1){
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
      j=0, j1=0, k1=1, k2=1;
-     j=nbocc(model,'+');
+     j=nbocc(model,'+'); /* j=Number of '+' */
-     j1=nbocc(model,'*');
+     j1=nbocc(model,'*'); /* j1=Number of '*' */
      cptcovn=j+1;
-     cptcovprod=j1;
+     cptcovprod=j1; /*Number of products */
      strcpy(modelsav,model);
      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
- Line 3430  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4332  while((c=getc(ficpar))=='#' && c!= EOF){
        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 analyze it */
+       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 */
- Line 3479  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4383  while((c=getc(ficpar))=='#' && c!= EOF){
      } /* 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);
+   scanf("%d ",i);
+   fclose(fic);*/
      /*  if(mle==1){*/
-     if (weightopt != 1) { /* Maximisation without weights*/
+   if (weightopt != 1) { /* Maximisation without weights*/
-       for(i=1;i<=n;i++) weight[i]=1.0;
+     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);
+   agev=matrix(1,maxwav,1,imx);
-     for (i=1; i<=imx; i++) {
+   for (i=1; i<=imx; i++) {
-       for(m=2; (m<= maxwav); m++) {
+     for(m=2; (m<= maxwav); m++) {
-        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-          anint[m][i]=9999;
+         anint[m][i]=9999;
-          s[m][i]=-1;
+         s[m][i]=-1;
-        }
+       }
-      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+         nberr++;
+         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){
+         nberr++;
+         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++)  {
+   for (i=1; i<=imx; i++)  {
-       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-       for(m=1; (m<= maxwav); m++){
+     for(m=firstpass; (m<= lastpass); m++){
-         if(s[m][i] >0){
+       if(s[m][i] >0){
-           if (s[m][i] >= nlstate+1) {
+         if (s[m][i] >= nlstate+1) {
-             if(agedc[i]>0)
+           if(agedc[i]>0)
-               if(moisdc[i]!=99 && andc[i]!=9999)
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-                 agev[m][i]=agedc[i];
+               agev[m][i]=agedc[i];
-             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-            else {
+             else {
-               if (andc[i]!=9999){
+               if ((int)andc[i]!=9999){
-               printf("Warning negative age at death: %d line:%d\n",num[i],i);
+                 nbwarn++;
-               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-               agev[m][i]=-1;
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+                 agev[m][i]=-1;
                }
              }
-           }
+         }
-           else if(s[m][i] !=9){ /* Should no more exist */
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+                                  years but with the precision of a
-             if(mint[m][i]==99 || anint[m][i]==9999)
+                                  month */
-               agev[m][i]=1;
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-             else if(agev[m][i] <agemin){
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-               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 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 /*= 0 Unknown */
+         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=1; (m<= maxwav); m++){
+   }
-         if (s[m][i] > (nlstate+ndeath)) {
+   for (i=1; i<=imx; i++)  {
-           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);
+     for(m=firstpass; (m<=lastpass); m++){
-           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);
+       if (s[m][i] > (nlstate+ndeath)) {
-           goto end;
+         nberr++;
-         }
+         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);
- printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   free_vector(severity,1,maxwav);
-  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   free_imatrix(outcome,1,maxwav+1,1,n);
+   free_vector(moisnais,1,n);
-     free_vector(severity,1,maxwav);
+   free_vector(annais,1,n);
-     free_imatrix(outcome,1,maxwav+1,1,n);
+   /* free_matrix(mint,1,maxwav,1,n);
-     free_vector(moisnais,1,n);
+      free_matrix(anint,1,maxwav,1,n);*/
-     free_vector(annais,1,n);
+   free_vector(moisdc,1,n);
-     /* free_matrix(mint,1,maxwav,1,n);
+   free_vector(andc,1,n);
-        free_matrix(anint,1,maxwav,1,n);*/
-     free_vector(moisdc,1,n);
-     free_vector(andc,1,n);
-     wav=ivector(1,imx);
+   wav=ivector(1,imx);
-     dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-     mw=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 */
+   /* Concatenates waves */
-       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   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);
+   Tcode=ivector(1,100);
-       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-       ncodemax[1]=1;
+   ncodemax[1]=1;
-       if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
-    codtab=imatrix(1,100,1,10);
+   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
-    h=0;
+                                  the estimations*/
-    m=pow(2,cptcoveff);
+   h=0;
+   m=pow(2,cptcoveff);
-    for(k=1;k<=cptcoveff; k++){
+   for(k=1;k<=cptcoveff; k++){
-      for(i=1; i <=(m/pow(2,k));i++){
+     for(i=1; i <=(m/pow(2,k));i++){
-        for(j=1; j <= ncodemax[k]; j++){
+       for(j=1; j <= ncodemax[k]; j++){
-          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
-            h++;
+           h++;
-            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+           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("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);*/
+     }
+   }
+   /* 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);*/
-    /* Calculates basic frequencies. Computes observed prevalence at single age
+   /*------------ gnuplot -------------*/
-        and prints on file fileres'p'. */
+   strcpy(optionfilegnuplot,optionfilefiname);
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+   else{
+     fprintf(ficgp,"\n# %s\n", version);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     fprintf(ficgp,"set missing 'NaNq'\n");
+   }
+   /*  fclose(ficgp);*/
+   /*--------- index.htm --------*/
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   strcat(optionfilehtm,".htm");
-     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm), exit(0);
+   }
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   strcat(optionfilehtmcov,"-cov.htm");
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   }
+   else{
+   fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+ \n\
+ <hr  size=\"2\" color=\"#EC5E5E\">\
+  <ul><li><h4>Parameter files</h4>\n\
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+  - Date and time at start: %s</ul>\n",\
+           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           fileres,fileres,\
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+   fflush(fichtm);
+   strcpy(pathr,path);
+   strcat(pathr,optionfilefiname);
+   chdir(optionfilefiname); /* Move to directory named optionfile */
+   /* Calculates basic frequencies. Computes observed prevalence at single age
+      and prints on file fileres'p'. */
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
+   fprintf(fichtm,"\n");
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+           imx,agemin,agemax,jmin,jmax,jmean);
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-     /* For Powell, parameters are in a vector p[] starting at p[1]
-        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+   /* For Powell, parameters are in a vector p[] starting at p[1]
-     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+      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) */
-     if(mle==1){
+   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 --------------*/
+   /*--------- 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);
+   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");
-    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   printf("# 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");
-    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   for(i=1,jk=1; i <=nlstate; i++){
-    for(i=1,jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
-      for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
-        if (k != i)
+         printf("%d%d ",i,k);
-          {
+         fprintf(ficlog,"%d%d ",i,k);
-            printf("%d%d ",i,k);
+         fprintf(ficres,"%1d%1d ",i,k);
-            fprintf(ficlog,"%d%d ",i,k);
+         for(j=1; j <=ncovmodel; j++){
-            fprintf(ficres,"%1d%1d ",i,k);
+           printf("%f ",p[jk]);
-            for(j=1; j <=ncovmodel; j++){
+           fprintf(ficlog,"%f ",p[jk]);
-              printf("%f ",p[jk]);
+           fprintf(ficres,"%f ",p[jk]);
-              fprintf(ficlog,"%f ",p[jk]);
+           jk++;
-              fprintf(ficres,"%f ",p[jk]);
+         }
-              jk++;
+         printf("\n");
-            }
+         fprintf(ficlog,"\n");
-            printf("\n");
+         fprintf(ficres,"\n");
-            fprintf(ficlog,"\n");
+       }
-            fprintf(ficres,"\n");
+     }
-          }
+   }
-      }
+   if(mle!=0){
-    }
+     /* Computing hessian and covariance matrix */
-    if(mle==1){
+     ftolhess=ftol; /* Usually correct */
-      /* Computing hessian and covariance matrix */
+     hesscov(matcov, p, npar, delti, ftolhess, func);
-      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(ficres,"# Scales (for hessian or gradient estimation)\n");
+   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-    printf("# Scales (for hessian or gradient estimation)\n");
+   for(i=1,jk=1; i <=nlstate; i++){
-    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(j=1; j <=nlstate+ndeath; j++){
-    for(i=1,jk=1; i <=nlstate; i++){
+       if (j!=i) {
-      for(j=1; j <=nlstate+ndeath; j++){
+         fprintf(ficres,"%1d%1d",i,j);
-        if (j!=i) {
+         printf("%1d%1d",i,j);
-          fprintf(ficres,"%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i,j);
-          printf("%1d%1d",i,j);
+         for(k=1; k<=ncovmodel;k++){
-          fprintf(ficlog,"%1d%1d",i,j);
+           printf(" %.5e",delti[jk]);
-          for(k=1; k<=ncovmodel;k++){
+           fprintf(ficlog," %.5e",delti[jk]);
-            printf(" %.5e",delti[jk]);
+           fprintf(ficres," %.5e",delti[jk]);
-            fprintf(ficlog," %.5e",delti[jk]);
+           jk++;
-            fprintf(ficres," %.5e",delti[jk]);
+         }
-            jk++;
+         printf("\n");
-          }
+         fprintf(ficlog,"\n");
-          printf("\n");
+         fprintf(ficres,"\n");
-          fprintf(ficlog,"\n");
+       }
-          fprintf(ficres,"\n");
+     }
-        }
+   }
-      }
-    }
-    k=1;
-    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-    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;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){
+   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");
-      ungetc(c,ficpar);
+   if(mle>=1)
-      fgets(line, MAXLINE, ficpar);
+     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");
-      puts(line);
+   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");
-      fputs(line,ficparo);
+ /* # 121 Var(a12)\n\ */
-    }
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-    ungetc(c,ficpar);
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-    estepm=0;
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-    if (estepm==0 || estepm < stepm) estepm=stepm;
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-    if (fage <= 2) {
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-      bage = ageminpar;
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-      fage = agemaxpar;
-    }
+ /* Just to have a covariance matrix which will be more understandable
+    even is we still don't want to manage dictionary of variables
+ */
+   for(itimes=1;itimes<=2;itimes++){
+     jj=0;
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j==i) continue;
+         for(k=1; k<=ncovmodel;k++){
+           jj++;
+           ca[0]= k+'a'-1;ca[1]='\0';
+           if(itimes==1){
+             if(mle>=1)
+               printf("#%1d%1d%d",i,j,k);
+             fprintf(ficlog,"#%1d%1d%d",i,j,k);
+             fprintf(ficres,"#%1d%1d%d",i,j,k);
+           }else{
+             if(mle>=1)
+               printf("%1d%1d%d",i,j,k);
+             fprintf(ficlog,"%1d%1d%d",i,j,k);
+             fprintf(ficres,"%1d%1d%d",i,j,k);
+           }
+           ll=0;
+           for(li=1;li <=nlstate; li++){
+             for(lj=1;lj <=nlstate+ndeath; lj++){
+               if(lj==li) continue;
+               for(lk=1;lk<=ncovmodel;lk++){
+                 ll++;
+                 if(ll<=jj){
+                   cb[0]= lk +'a'-1;cb[1]='\0';
+                   if(ll<jj){
+                     if(itimes==1){
+                       if(mle>=1)
+                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                     }else{
+                       if(mle>=1)
+                         printf(" %.5e",matcov[jj][ll]);
+                       fprintf(ficlog," %.5e",matcov[jj][ll]);
+                       fprintf(ficres," %.5e",matcov[jj][ll]);
+                     }
+                   }else{
+                     if(itimes==1){
+                       if(mle>=1)
+                         printf(" Var(%s%1d%1d)",ca,i,j);
+                       fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                       fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                     }else{
+                       if(mle>=1)
+                         printf(" %.5e",matcov[jj][ll]);
+                       fprintf(ficlog," %.5e",matcov[jj][ll]);
+                       fprintf(ficres," %.5e",matcov[jj][ll]);
+                     }
+                   }
+                 }
+               } /* end lk */
+             } /* end lj */
+           } /* end li */
+           if(mle>=1)
+             printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+           numlinepar++;
+         } /* end k*/
+       } /*end j */
+     } /* end i */
+   } /* end itimes */
+   fflush(ficlog);
+   fflush(ficres);
+   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 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(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);
+   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-    while((c=getc(ficpar))=='#' && c!= EOF){
+   while((c=getc(ficpar))=='#' && c!= EOF){
-      ungetc(c,ficpar);
+     ungetc(c,ficpar);
-      fgets(line, MAXLINE, ficpar);
+     fgets(line, MAXLINE, ficpar);
-      puts(line);
+     puts(line);
-      fputs(line,ficparo);
+     fputs(line,ficparo);
-    }
+   }
-    ungetc(c,ficpar);
+   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);
+   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(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);
+   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){
+   while((c=getc(ficpar))=='#' && c!= EOF){
-      ungetc(c,ficpar);
+     ungetc(c,ficpar);
-      fgets(line, MAXLINE, ficpar);
+     fgets(line, MAXLINE, ficpar);
-      puts(line);
+     puts(line);
-      fputs(line,ficparo);
+     fputs(line,ficparo);
-    }
+   }
-    ungetc(c,ficpar);
+   ungetc(c,ficpar);
-    dateprev1=anprev1+mprev1/12.+jprev1/365.;
+   dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-    dateprev2=anprev2+mprev2/12.+jprev2/365.;
+   dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
    fscanf(ficpar,"pop_based=%d\n",&popbased);
    fprintf(ficparo,"pop_based=%d\n",popbased);
- Line 3760  printf("Total number of individuals= %d,
+ Line 4821  printf("Total number of individuals= %d,
    }
    ungetc(c,ficpar);
-   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
+   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,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
+   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);
- fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
+   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){
+   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
      puts(line);
- Line 3777  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4840  while((c=getc(ficpar))=='#' && c!= EOF){
    fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
    fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+   /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
- /*------------ gnuplot -------------*/
+   /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-  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);
-  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
- /*--------- index.htm --------*/
-   strcpy(optionfilehtm,optionfile);
+   replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
-   strcat(optionfilehtm,".htm");
+   printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-     printf("Problem with %s \n",optionfilehtm), exit(0);
-   }
-   fprintf(fichtm,"<body> <font size=\"2\">%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
- Total number of observations=%d <br>\n
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\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></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
-   fclose(fichtm);
-  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
- /*------------ free_vector  -------------*/
+   /*------------ free_vector  -------------*/
-  chdir(path);
+   /*  chdir(path); */
-  free_ivector(wav,1,imx);
+   free_ivector(wav,1,imx);
-  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+   free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+   free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
-  free_ivector(num,1,n);
+   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-  free_vector(agedc,1,n);
+   free_lvector(num,1,n);
-  /*free_matrix(covar,1,NCOVMAX,1,n);*/
+   free_vector(agedc,1,n);
-  fclose(ficparo);
+   /*free_matrix(covar,0,NCOVMAX,1,n);*/
-  fclose(ficres);
+   /*free_matrix(covar,1,NCOVMAX,1,n);*/
+   fclose(ficparo);
+   fclose(ficres);
    /*--------------- Prevalence limit  (stable prevalence) --------------*/
- Line 3842  Interval (in months) between two waves:
+ Line 4881  Interval (in months) between two waves:
    fprintf(ficrespl,"\n");
    prlim=matrix(1,nlstate,1,nlstate);
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-   k=0;
    agebase=ageminpar;
    agelim=agemaxpar;
    ftolpl=1.e-10;
    i1=cptcoveff;
    if (cptcovn < 1){i1=1;}
-   for(cptcov=1;cptcov<=i1;cptcov++){
+   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
+       k=k+1;
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
-         fprintf(ficrespl,"\n#******");
+       fprintf(ficrespl,"\n#******");
-         printf("\n#******");
+       printf("\n#******");
-         fprintf(ficlog,"\n#******");
+       fprintf(ficlog,"\n#******");
-         for(j=1;j<=cptcoveff;j++) {
+       for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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]]);
+         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(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         }
+       }
-         fprintf(ficrespl,"******\n");
+       fprintf(ficrespl,"******\n");
-         printf("******\n");
+       printf("******\n");
-         fprintf(ficlog,"******\n");
+       fprintf(ficlog,"******\n");
-         for (age=agebase; age<=agelim; age++){
+       for (age=agebase; age<=agelim; age++){
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-           fprintf(ficrespl,"%.0f",age );
+         fprintf(ficrespl,"%.0f ",age );
-           for(i=1; i<=nlstate;i++)
+         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");
+         fprintf(ficrespl,"\n");
-         }
        }
      }
+   }
    fclose(ficrespl);
    /*------------- h Pij x at various ages ------------*/
- Line 3900  Interval (in months) between two waves:
+ Line 4936  Interval (in months) between two waves:
    /* hstepm=1;   aff par mois*/
-   k=0;
+   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-   for(cptcov=1;cptcov<=i1;cptcov++){
+   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        k=k+1;
-         fprintf(ficrespij,"\n#****** ");
+       fprintf(ficrespij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+       for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficrespij,"******\n");
+       fprintf(ficrespij,"******\n");
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+       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=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
+         oldm=oldms;savm=savms;
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-           fprintf(ficrespij,"# Age");
+         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," %1d-%1d",i,j);
+               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-           fprintf(ficrespij,"\n");
-            for (h=0; h<=nhstepm; h++){
-             fprintf(ficrespij,"%d %f %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");
          }
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficrespij,"\n");
+       }
      }
    }
-   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
+   varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
    fclose(ficrespij);
+   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   for(i=1;i<=AGESUP;i++)
+     for(j=1;j<=NCOVMAX;j++)
+       for(k=1;k<=NCOVMAX;k++)
+         probs[i][j][k]=0.;
    /*---------- Forecasting ------------------*/
-   if((stepm == 1) && (strcmp(model,".")==0)){
+   /*if((stepm == 1) && (strcmp(model,".")==0)){*/
-     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
+   if(prevfcast==1){
-     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
+     /*    if(stepm ==1){*/
-   }
+       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
-   else{
+       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
-     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);
+ /*      else{ */
-     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);
+ /*        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); */
+ /*      } */
    }
- Line 3982  Interval (in months) between two waves:
+ Line 5026  Interval (in months) between two waves:
    }
    printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
    fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-   calagedate=-1;
-   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+   /* 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){
- Line 3992  Interval (in months) between two waves:
+ Line 5041  Interval (in months) between two waves:
      }
    }
-   k=0;
+   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-   for(cptcov=1;cptcov<=i1;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        k=k+1;
        fprintf(ficrest,"\n#****** ");
- Line 4020  Interval (in months) between two waves:
+ Line 5068  Interval (in months) between two waves:
        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) ");
- Line 4058  Interval (in months) between two waves:
+ Line 5106  Interval (in months) between two waves:
          }
          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_matrix(mint,1,maxwav,1,n);
+   free_vector(weight,1,n);
-     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
+   free_imatrix(Tvard,1,15,1,2);
-     free_vector(weight,1,n);
+   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);
-   free_vector(epj,1,nlstate+1);
    /*------- Variance of stable prevalence------*/
- Line 4079  free_matrix(mint,1,maxwav,1,n);
+ Line 5133  free_matrix(mint,1,maxwav,1,n);
    }
    printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
-   k=0;
+   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-   for(cptcov=1;cptcov<=i1;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        k=k+1;
        fprintf(ficresvpl,"\n#****** ");
- Line 4090  free_matrix(mint,1,maxwav,1,n);
+ Line 5143  free_matrix(mint,1,maxwav,1,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);
+       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(varpl,1,nlstate,(int) bage, (int)fage);
-   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
    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_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);
-   fprintf(fichtm,"\n</body>");
+   free_ivector(ncodemax,1,8);
-   fclose(fichtm);
+   free_ivector(Tvar,1,15);
-   fclose(ficgp);
+   free_ivector(Tprod,1,15);
+   free_ivector(Tvaraff,1,15);
+   free_ivector(Tage,1,15);
-   if(erreur >0){
+   free_ivector(Tcode,1,100);
-     printf("End of Imach with error or warning %d\n",erreur);
-     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+   fflush(fichtm);
+   fflush(ficgp);
+   if((nberr >0) || (nbwarn>0)){
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
    }else{
-    printf("End of Imach\n");
+     printf("End of Imach\n");
-    fprintf(ficlog,"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);
-   /* 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);*/
+   tm = *localtime(&end_time.tv_sec);
-   /*printf("Total time was %d uSec.\n", total_usecs);*/
+   tmg = *gmtime(&end_time.tv_sec);
+   strcpy(strtend,asctime(&tm));
+   printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ /*   if(fileappend(fichtm,optionfilehtm)){ */
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
+   fclose(fichtm);
+   fclose(fichtmcov);
+   fclose(ficgp);
+   fclose(ficlog);
    /*------ End -----------*/
+   chdir(path);
-  end:
+   strcpy(plotcmd,GNUPLOTPROGRAM);
- #ifdef windows
+   strcat(plotcmd," ");
-   /* chdir(pathcd);*/
+   strcat(plotcmd,optionfilegnuplot);
- #endif
+   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
-  /*system("wgnuplot graph.plt");*/
+   if((outcmd=system(plotcmd)) != 0){
-  /*system("../gp37mgw/wgnuplot graph.plt");*/
+     printf(" Problem with gnuplot\n");
-  /*system("cd ../gp37mgw");*/
+   }
-  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
+   printf(" Wait...");
-  strcpy(plotcmd,GNUPLOTPROGRAM);
-  strcat(plotcmd," ");
-  strcat(plotcmd,optionfilegnuplot);
-  printf("Starting: %s\n",plotcmd);fflush(stdout);
-  system(plotcmd);
-  /*#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: ");
+     printf("\nType e to edit output files, g to graph again and q for exiting: ");
      scanf("%s",z);
-     if (z[0] == 'c') system("./imach");
+ /*     if (z[0] == 'c') system("./imach"); */
-     else if (z[0] == 'e') system(optionfilehtm);
+     if (z[0] == 'e') system(optionfilehtm);
      else if (z[0] == 'g') system(plotcmd);
      else if (z[0] == 'q') exit(0);
    }
-   /*#endif */
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: ");
+     scanf("%s",z);
+   }
  }

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