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Diff for /imach/src/imach.c between versions 1.94 and 1.120

-version 1.94, 2003/06/27 13:00:02
+version 1.120, 2006/03/16 15:10:38
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.120  2006/03/16 15:10:38  lievre
+   (Module): refinements in the computation of lli if
+   status=-2 in order to have more reliable computation if stepm is
+   not 1 month. Version 0.98f
+   Revision 1.119  2006/03/15 17:42:26  brouard
+   (Module): Bug if status = -2, the loglikelihood was
+   computed as likelihood omitting the logarithm. Version O.98e
+   Revision 1.118  2006/03/14 18:20:07  brouard
+   (Module): varevsij Comments added explaining the second
+   table of variances if popbased=1 .
+   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+   (Module): Function pstamp added
+   (Module): Version 0.98d
+   Revision 1.117  2006/03/14 17:16:22  brouard
+   (Module): varevsij Comments added explaining the second
+   table of variances if popbased=1 .
+   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+   (Module): Function pstamp added
+   (Module): Version 0.98d
+   Revision 1.116  2006/03/06 10:29:27  brouard
+   (Module): Variance-covariance wrong links and
+   varian-covariance of ej. is needed (Saito).
+   Revision 1.115  2006/02/27 12:17:45  brouard
+   (Module): One freematrix added in mlikeli! 0.98c
+   Revision 1.114  2006/02/26 12:57:58  brouard
+   (Module): Some improvements in processing parameter
+   filename with strsep.
+   Revision 1.113  2006/02/24 14:20:24  brouard
+   (Module): Memory leaks checks with valgrind and:
+   datafile was not closed, some imatrix were not freed and on matrix
+   allocation too.
+   Revision 1.112  2006/01/30 09:55:26  brouard
+   (Module): Back to gnuplot.exe instead of wgnuplot.exe
+   Revision 1.111  2006/01/25 20:38:18  brouard
+   (Module): Lots of cleaning and bugs added (Gompertz)
+   (Module): Comments can be added in data file. Missing date values
+   can be a simple dot '.'.
+   Revision 1.110  2006/01/25 00:51:50  brouard
+   (Module): Lots of cleaning and bugs added (Gompertz)
+   Revision 1.109  2006/01/24 19:37:15  brouard
+   (Module): Comments (lines starting with a #) are allowed in data.
+   Revision 1.108  2006/01/19 18:05:42  lievre
+   Gnuplot problem appeared...
+   To be fixed
+   Revision 1.107  2006/01/19 16:20:37  brouard
+   Test existence of gnuplot in imach path
+   Revision 1.106  2006/01/19 13:24:36  brouard
+   Some cleaning and links added in html output
+   Revision 1.105  2006/01/05 20:23:19  lievre
+   *** empty log message ***
+   Revision 1.104  2005/09/30 16:11:43  lievre
+   (Module): sump fixed, loop imx fixed, and simplifications.
+   (Module): If the status is missing at the last wave but we know
+   that the person is alive, then we can code his/her status as -2
+   (instead of missing=-1 in earlier versions) and his/her
+   contributions to the likelihood is 1 - Prob of dying from last
+   health status (= 1-p13= p11+p12 in the easiest case of somebody in
+   the healthy state at last known wave). Version is 0.98
+   Revision 1.103  2005/09/30 15:54:49  lievre
+   (Module): sump fixed, loop imx fixed, and simplifications.
+   Revision 1.102  2004/09/15 17:31:30  brouard
+   Add the possibility to read data file including tab characters.
+   Revision 1.101  2004/09/15 10:38:38  brouard
+   Fix on curr_time
+   Revision 1.100  2004/07/12 18:29:06  brouard
+   Add version for Mac OS X. Just define UNIX in Makefile
+   Revision 1.99  2004/06/05 08:57:40  brouard
+   *** empty log message ***
+   Revision 1.98  2004/05/16 15:05:56  brouard
+   New version 0.97 . First attempt to estimate force of mortality
+   directly from the data i.e. without the need of knowing the health
+   state at each age, but using a Gompertz model: log u =a + b*age .
+   This is the basic analysis of mortality and should be done before any
+   other analysis, in order to test if the mortality estimated from the
+   cross-longitudinal survey is different from the mortality estimated
+   from other sources like vital statistic data.
+   The same imach parameter file can be used but the option for mle should be -3.
+   Agnès, who wrote this part of the code, tried to keep most of the
+   former routines in order to include the new code within the former code.
+   The output is very simple: only an estimate of the intercept and of
+   the slope with 95% confident intervals.
+   Current limitations:
+   A) Even if you enter covariates, i.e. with the
+   model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
+   B) There is no computation of Life Expectancy nor Life Table.
+   Revision 1.97  2004/02/20 13:25:42  lievre
+   Version 0.96d. Population forecasting command line is (temporarily)
+   suppressed.
+   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
- Line 108
+ Line 233
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
-   of the life expectancies. It also computes the stable prevalence.
+   of the life expectancies. It also computes the period (stable) prevalence.
    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
             Institut national d'études démographiques, Paris.
- Line 137
+ Line 262
        begin-prev-date,...
    open gnuplot file
    open html file
-   stable prevalence
+   period (stable) prevalence
     for age prevalim()
    h Pij x
    variance of p varprob
- Line 149
+ Line 274
    varevsij()
    if popbased==1 varevsij(,popbased)
    total life expectancies
-   Variance of stable prevalence
+   Variance of period (stable) prevalence
   end
  */
- Line 159
+ Line 284
  #include <math.h>
  #include <stdio.h>
  #include <stdlib.h>
+ #include <string.h>
  #include <unistd.h>
- #include <sys/time.h>
+ #include <limits.h>
+ #include <sys/types.h>
+ #include <sys/stat.h>
+ #include <errno.h>
+ extern int errno;
+ /* #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 132
- /*#define DEBUG*/
- /*#define windows*/
  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- Line 185
+ Line 320
  #define YEARM 12. /* Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
- #ifdef unix
+ #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ #ifdef UNIX
  #define DIRSEPARATOR '/'
+ #define CHARSEPARATOR "/"
  #define ODIRSEPARATOR '\\'
  #else
  #define DIRSEPARATOR '\\'
+ #define CHARSEPARATOR "\\"
  #define ODIRSEPARATOR '/'
  #endif
  /* $Id$ */
  /* $State$ */
- char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
+ char version[]="Imach version 0.98f, March 2006, INED-EUROREVES-Institut de longevite ";
  char fullversion[]="$Revision$ $Date$";
+ char strstart[80];
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
  int nvar;
  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
- Line 210  int popbased=0;
+ Line 350  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 ijmin, ijmax; /* Individuals having jmin and jmax */
  int gipmx, gsw; /* Global variables on the number of contributions
                     to the likelihood and the sum of weights (done by funcone)*/
  int mle, weightopt;
- Line 220  int **bh; /* bh[mi][i] is the bias (+ or
+ Line 361  int **bh; /* bh[mi][i] is the bias (+ or
  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 *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
  FILE *ficlog, *ficrespow;
  int globpr; /* Global variable for printing or not */
  double fretone; /* Only one call to likelihood */
  long ipmx; /* Number of contributions */
  double sw; /* Sum of weights */
+ char filerespow[FILENAMELENGTH];
  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
  FILE *ficresilk;
  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- Line 233  FILE *ficresprobmorprev;
+ Line 375  FILE *ficresprobmorprev;
  FILE *fichtm, *fichtmcov; /* Html File */
  FILE *ficreseij;
  char filerese[FILENAMELENGTH];
+ FILE *ficresstdeij;
+ char fileresstde[FILENAMELENGTH];
+ FILE *ficrescveij;
+ char filerescve[FILENAMELENGTH];
  FILE  *ficresvij;
  char fileresv[FILENAMELENGTH];
  FILE  *ficresvpl;
  char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- char tmpout[FILENAMELENGTH];
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
  char command[FILENAMELENGTH];
  int  outcmd=0;
- Line 261  long time_value;
+ Line 407  long time_value;
  extern long time();
  char strcurr[80], strfor[80];
+ char *endptr;
+ long lval;
  #define NR_END 1
  #define FREE_ARG char*
  #define FTOL 1.0e-10
- Line 288  static double maxarg1,maxarg2;
+ Line 437  static double maxarg1,maxarg2;
  static double sqrarg;
  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ int agegomp= AGEGOMP;
  int imx;
- int stepm;
+ int stepm=1;
  /* Stepm, step in month: minimum step interpolation*/
  int estepm;
- Line 298  int estepm;
+ Line 448  int estepm;
  int m,nb;
  long *num;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  double **pmmij, ***probs;
+ double *ageexmed,*agecens;
  double dateintmean=0;
  double *weight;
  int **s; /* Status */
  double *agedc, **covar, idx;
  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double *lsurv, *lpop, *tpop;
  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
  double ftolhess; /* Tolerance for computing hessian */
- Line 314  double ftolhess; /* Tolerance for comput
+ Line 466  double ftolhess; /* Tolerance for comput
  /**************** split *************************/
  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
  {
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+   */
    char  *ss;                            /* pointer */
    int   l1, l2;                         /* length counters */
    l1 = strlen(path );                   /* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   if ( ss == NULL ) {                   /* no directory, so use current */
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+     strcpy( name, path );               /* we got the fullname name because no directory */
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      /* get current working directory */
- Line 328  static int split( char *path, char *dirc
+ Line 484  static int split( char *path, char *dirc
      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
        return( GLOCK_ERROR_GETCWD );
      }
-     strcpy( name, path );               /* we've got it */
+     /* got dirc from getcwd*/
+     printf(" DIRC = %s \n",dirc);
    } else {                              /* strip direcotry from path */
      ss++;                               /* after this, the filename */
      l2 = strlen( ss );                  /* length of filename */
- Line 336  static int split( char *path, char *dirc
+ Line 493  static int split( char *path, char *dirc
      strcpy( name, ss );         /* save file name */
      strncpy( dirc, path, l1 - l2 );     /* now the directory */
      dirc[l1-l2] = 0;                    /* add zero */
+     printf(" DIRC2 = %s \n",dirc);
    }
+   /* We add a separator at the end of dirc if not exists */
    l1 = strlen( dirc );                  /* length of directory */
-   /*#ifdef windows
+   if( dirc[l1-1] != DIRSEPARATOR ){
-   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
+     dirc[l1] =  DIRSEPARATOR;
- #else
+     dirc[l1+1] = 0;
-   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
+     printf(" DIRC3 = %s \n",dirc);
- #endif
+   }
-   */
    ss = strrchr( name, '.' );            /* find last / */
-   ss++;
+   if (ss >0){
-   strcpy(ext,ss);                       /* save extension */
+     ss++;
-   l1= strlen( name);
+     strcpy(ext,ss);                     /* save extension */
-   l2= strlen(ss)+1;
+     l1= strlen( name);
-   strncpy( finame, name, l1-l2);
+     l2= strlen(ss)+1;
-   finame[l1-l2]= 0;
+     strncpy( finame, name, l1-l2);
+     finame[l1-l2]= 0;
+   }
    return( 0 );                          /* we're done */
  }
- Line 383  int nbocc(char *s, char occ)
+ Line 544  int nbocc(char *s, char occ)
  void cutv(char *u,char *v, char*t, char occ)
  {
-   /* cuts string t into u and v where u is ended by char occ excluding it
+   /* cuts string t into u and v where u ends before first occurence of char 'occ'
-      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
+      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       gives u="abcedf" and v="ghi2j" */
    int i,lg,j,p=0;
    i=0;
- Line 813  void powell(double p[], double **xi, int
+ Line 974  void powell(double p[], double **xi, int
      last_time=curr_time;
      (void) gettimeofday(&curr_time,&tzp);
      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(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++) {
+     */
+    for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12lf",i, p[i]);
        fprintf(ficrespow," %.12lf", p[i]);
- Line 825  void powell(double p[], double **xi, int
+ Line 987  void powell(double p[], double **xi, int
      fprintf(ficrespow,"\n");fflush(ficrespow);
      if(*iter <=3){
        tm = *localtime(&curr_time.tv_sec);
-       strcpy(strcurr,asctime(&tmf));
+       strcpy(strcurr,asctime(&tm));
  /*       asctime_r(&tm,strcurr); */
        forecast_time=curr_time;
        itmp = strlen(strcurr);
-       if(strcurr[itmp-1]=='\n')
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
          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);
- Line 841  void powell(double p[], double **xi, int
+ Line 1003  void powell(double p[], double **xi, int
          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);
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\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);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\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++) {
- Line 936  void powell(double p[], double **xi, int
+ Line 1098  void powell(double p[], double **xi, int
    }
  }
- /**** Prevalence limit (stable prevalence)  ****************/
+ /**** Prevalence limit (stable or period prevalence)  ****************/
  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
  {
- Line 1007  double **pmij(double **ps, double *cov,
+ Line 1169  double **pmij(double **ps, double *cov,
    int i,j,j1, nc, ii, jj;
      for(i=1; i<= nlstate; i++){
-     for(j=1; j<i;j++){
+       for(j=1; j<i;j++){
-       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-         /*s2 += param[i][j][nc]*cov[nc];*/
+           /*s2 += param[i][j][nc]*cov[nc];*/
-         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
+ /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
-       }
+         }
-       ps[i][j]=s2;
+         ps[i][j]=s2;
-       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
+ /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
-     }
+       }
-     for(j=i+1; j<=nlstate+ndeath;j++){
+       for(j=i+1; j<=nlstate+ndeath;j++){
-       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
+ /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+         }
+         ps[i][j]=s2;
        }
-       ps[i][j]=s2;
      }
-   }
      /*ps[3][2]=1;*/
-   for(i=1; i<= nlstate; i++){
+     for(i=1; i<= nlstate; i++){
-      s1=0;
+       s1=0;
-     for(j=1; j<i; j++)
+       for(j=1; j<i; j++)
-       s1+=exp(ps[i][j]);
+         s1+=exp(ps[i][j]);
-     for(j=i+1; j<=nlstate+ndeath; j++)
+       for(j=i+1; j<=nlstate+ndeath; j++)
-       s1+=exp(ps[i][j]);
+         s1+=exp(ps[i][j]);
-     ps[i][i]=1./(s1+1.);
+       ps[i][i]=1./(s1+1.);
-     for(j=1; j<i; j++)
+       for(j=1; j<i; j++)
-       ps[i][j]= exp(ps[i][j])*ps[i][i];
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-     for(j=i+1; j<=nlstate+ndeath; j++)
+       for(j=i+1; j<=nlstate+ndeath; j++)
-       ps[i][j]= exp(ps[i][j])*ps[i][i];
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-   } /* end i */
+     } /* end i */
-   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-     for(jj=1; jj<= nlstate+ndeath; jj++){
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-       ps[ii][jj]=0;
+         ps[ii][jj]=0;
-       ps[ii][ii]=1;
+         ps[ii][ii]=1;
+       }
      }
-   }
-   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
+ /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
-     for(jj=1; jj<= nlstate+ndeath; jj++){
+ /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
-      printf("%lf ",ps[ii][jj]);
+ /*         printf("ddd %lf ",ps[ii][jj]); */
-    }
+ /*       } */
-     printf("\n ");
+ /*       printf("\n "); */
-     }
+ /*        } */
-     printf("\n ");printf("%lf ",cov[2]);*/
+ /*        printf("\n ");printf("%lf ",cov[2]); */
- /*
+        /*
-   for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-   goto end;*/
+       goto end;*/
      return ps;
  }
- Line 1181  double func( double *x)
+ Line 1343  double func( double *x)
          } /* 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.
+         /* But now since version 0.9 we anticipate for bias at 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
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then 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
+          * from savm to out if bh is negative 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.
- Line 1196  double func( double *x)
+ Line 1358  double func( double *x)
          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
+         /* bias bh 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
+           /* i.e. if s2 is a death state and if the date of death is known
-              to the likelihood is the probability to die between last step unit time and current
+              then the contribution to the likelihood is the probability to
-              step unit time, which is also the differences between probability to die before dh
+              die between last step unit time and current  step unit time,
-              and probability to die before dh-stepm .
+              which is also equal to probability to die before dh
+              minus 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
- Line 1224  double func( double *x)
+ Line 1387  double func( double *x)
          lower mortality.
            */
            lli=log(out[s1][s2] - savm[s1][s2]);
-         }else{
+         } else if  (s2==-2) {
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           /*survp += out[s1][j]; */
+           lli= log(survp);
+         }
+         else if  (s2==-4) {
+           for (j=3,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           lli= log(survp);
+         }
+         else if  (s2==-5) {
+           for (j=1,survp=0. ; j<=2; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           lli= log(survp);
+         }
+         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 */
          }
- Line 1418  double funcone( double *x)
+ Line 1602  double funcone( double *x)
         */
        if( s2 > nlstate && (mle <5) ){  /* Jackson */
          lli=log(out[s1][s2] - savm[s1][s2]);
-       } else if (mle==1){
+       } else if  (s2==-2) {
+         for (j=1,survp=0. ; j<=nlstate; j++)
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         lli= log(survp);
+       }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 */
- Line 1434  double funcone( double *x)
+ Line 1622  double funcone( double *x)
        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\
+         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-  %10.6f %10.6f %10.6f ", \
+  %11.6f %11.6f %11.6f ", \
                  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++){
- Line 1500  void mlikeli(FILE *ficres,double p[], in
+ Line 1688  void mlikeli(FILE *ficres,double p[], in
    double **xi;
    double fret;
    double fretone; /* Only one call to likelihood */
-   char filerespow[FILENAMELENGTH];
+   /*  char filerespow[FILENAMELENGTH];*/
    xi=matrix(1,npar,1,npar);
    for (i=1;i<=npar;i++)
      for (j=1;j<=npar;j++)
- Line 1520  void mlikeli(FILE *ficres,double p[], in
+ Line 1708  void mlikeli(FILE *ficres,double p[], in
    powell(p,xi,npar,ftol,&iter,&fret,func);
+   free_matrix(xi,1,npar,1,npar);
    fclose(ficrespow);
    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));
- Line 1535  void hesscov(double **matcov, double p[]
+ Line 1724  void hesscov(double **matcov, double p[]
    int i, j,jk;
    int *indx;
-   double hessii(double p[], double delta, int theta, double delti[]);
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-   double hessij(double p[], double delti[], int i, int j);
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
    void lubksb(double **a, int npar, int *indx, double b[]) ;
    void ludcmp(double **a, int npar, int *indx, double *d) ;
+   double gompertz(double p[]);
    hess=matrix(1,npar,1,npar);
    printf("\nCalculation of the hessian matrix. Wait...\n");
- Line 1547  void hesscov(double **matcov, double p[]
+ Line 1736  void hesscov(double **matcov, double p[]
    for (i=1;i<=npar;i++){
      printf("%d",i);fflush(stdout);
      fprintf(ficlog,"%d",i);fflush(ficlog);
-     hess[i][i]=hessii(p,ftolhess,i,delti);
-     /*printf(" %f ",p[i]);*/
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-     /*printf(" %lf ",hess[i][i]);*/
+     /*  printf(" %f ",p[i]);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
    }
    for (i=1;i<=npar;i++) {
- Line 1557  void hesscov(double **matcov, double p[]
+ Line 1748  void hesscov(double **matcov, double p[]
        if (j>i) {
          printf(".%d%d",i,j);fflush(stdout);
          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-         hess[i][j]=hessij(p,delti,i,j);
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
          hess[j][i]=hess[i][j];
          /*printf(" %lf ",hess[i][j]);*/
        }
- Line 1628  void hesscov(double **matcov, double p[]
+ Line 1820  void hesscov(double **matcov, double p[]
  }
  /*************** hessian matrix ****************/
- double hessii( double x[], double delta, int theta, double delti[])
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
  {
    int i;
    int l=1, lmax=20;
    double k1,k2;
    double p2[NPARMAX+1];
    double res;
-   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
    double fx;
    int k=0,kmax=10;
    double l1;
- Line 1675  double hessii( double x[], double delta,
+ Line 1867  double hessii( double x[], double delta,
  }
- double hessij( double x[], double delti[], int thetai,int thetaj)
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
  {
    int i;
    int l=1, l1, lmax=20;
- Line 1784  void lubksb(double **a, int n, int *indx
+ Line 1976  void lubksb(double **a, int n, int *indx
    }
  }
+ void pstamp(FILE *fichier)
+ {
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+ }
  /************ Frequencies ********************/
- 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)
+ 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, char strstart[])
  {  /* Some frequencies */
    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
- Line 1793  void  freqsummary(char fileres[], int ia
+ Line 1990  void  freqsummary(char fileres[], int ia
    double ***freq; /* Frequencies */
    double *pp, **prop;
    double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   FILE *ficresp;
    char fileresp[FILENAMELENGTH];
    pp=vector(1,nlstate);
- Line 1805  void  freqsummary(char fileres[], int ia
+ Line 2001  void  freqsummary(char fileres[], int ia
      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      exit(0);
    }
-   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
    j1=0;
    j=cptcoveff;
- Line 1818  void  freqsummary(char fileres[], int ia
+ Line 2014  void  freqsummary(char fileres[], int ia
        j1++;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
          scanf("%d", i);*/
-       for (i=-1; i<=nlstate+ndeath; i++)
+       for (i=-5; i<=nlstate+ndeath; i++)
-         for (jk=-1; jk<=nlstate+ndeath; jk++)
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
            for(m=iagemin; m <= iagemax+3; m++)
              freq[i][jk][m]=0;
- Line 1858  void  freqsummary(char fileres[], int ia
+ Line 2054  void  freqsummary(char fileres[], int ia
        }
        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+       pstamp(ficresp);
        if  (cptcovn>0) {
          fprintf(ficresp, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- Line 1944  void  freqsummary(char fileres[], int ia
+ Line 2140  void  freqsummary(char fileres[], int ia
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
-   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
    free_vector(pp,1,nlstate);
    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
    /* End of Freq */
- Line 2053  void  concatwav(int wav[], int **dh, int
+ Line 2249  void  concatwav(int wav[], int **dh, int
      mi=0;
      m=firstpass;
      while(s[m][i] <= nlstate){
-       if(s[m][i]>=1)
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
          mw[++mi][i]=m;
        if(m >=lastpass)
          break;
- Line 2071  void  concatwav(int wav[], int **dh, int
+ Line 2267  void  concatwav(int wav[], int **dh, int
      if(mi==0){
        nbwarn++;
        if(first==0){
-         printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
          first=1;
        }
        if(first==1){
-         fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
        }
      } /* end mi==0 */
    } /* End individuals */
- Line 2093  void  concatwav(int wav[], int **dh, int
+ Line 2289  void  concatwav(int wav[], int **dh, int
                nberr++;
                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                j=1; /* Temporary Dangerous patch */
-               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
+               printf("   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. 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);
+               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. You MUST fix the contradiction between dates.\n",stepm);
              }
              k=k+1;
-             if (j >= jmax) jmax=j;
+             if (j >= jmax){
-             if (j <= jmin) jmin=j;
+               jmax=j;
+               ijmax=i;
+             }
+             if (j <= jmin){
+               jmin=j;
+               ijmin=i;
+             }
              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);*/
- Line 2107  void  concatwav(int wav[], int **dh, int
+ Line 2309  void  concatwav(int wav[], int **dh, int
          }
          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);*/
+ /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
            k=k+1;
-           if (j >= jmax) jmax=j;
+           if (j >= jmax) {
-           else if (j <= jmin)jmin=j;
+             jmax=j;
+             ijmax=i;
+           }
+           else if (j <= jmin){
+             jmin=j;
+             ijmin=i;
+           }
            /*        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){
- Line 2153  void  concatwav(int wav[], int **dh, int
+ Line 2362  void  concatwav(int wav[], int **dh, int
      } /* end wave */
    }
    jmean=sum/k;
-   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   }
  /*********** Tricode ****************************/
- Line 2200  void tricode(int *Tvar, int **nbcode, in
+ Line 2409  void tricode(int *Tvar, int **nbcode, in
   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.*/
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     ij=Tvar[i];
     Ndum[ij]++;
   }
- Line 2218  void tricode(int *Tvar, int **nbcode, in
+ Line 2427  void tricode(int *Tvar, int **nbcode, in
  /*********** Health Expectancies ****************/
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
+ void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+ {
+   /* Health expectancies, no variances */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+   double age, agelim, hf;
+   double ***p3mat;
+   double eip;
+   pstamp(ficreseij);
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+   fprintf(ficreseij,"# Age");
+   for(i=1; i<=nlstate;i++){
+     for(j=1; j<=nlstate;j++){
+       fprintf(ficreseij," e%1d%1d ",i,j);
+     }
+     fprintf(ficreseij," e%1d. ",i);
+   }
+   fprintf(ficreseij,"\n");
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else  hstepm=estepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * 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 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
+    * hypothesis. A more precise result, taking into account a more precise
+    * curvature will be obtained if estepm is as small as stepm. */
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like estepm months */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed only each two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+      results. So we changed our mind and took the option of the best precision.
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   agelim=AGESUP;
+   /* nhstepm age range expressed in number of stepm */
+   nstepm=(int) rint((agelim-age)*YEARM/stepm);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   /* if (stepm >= YEARM) hstepm=1;*/
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     printf("%d|",(int)age);fflush(stdout);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+     /* Computing expectancies */
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++)
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+         }
+     fprintf(ficreseij,"%3.0f",age );
+     for(i=1; i<=nlstate;i++){
+       eip=0;
+       for(j=1; j<=nlstate;j++){
+         eip +=eij[i][j][(int)age];
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       }
+       fprintf(ficreseij,"%9.4f", eip );
+     }
+     fprintf(ficreseij,"\n");
+   }
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   printf("\n");
+   fprintf(ficlog,"\n");
+ }
+ void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
  {
-   /* Health expectancies */
+   /* Covariances of health expectancies eij and of total life expectancies according
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
+    to initial status i, ei. .
+   */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
    double age, agelim, hf;
-   double ***p3mat,***varhe;
+   double ***p3matp, ***p3matm, ***varhe;
    double **dnewm,**doldm;
-   double *xp;
+   double *xp, *xm;
    double **gp, **gm;
    double ***gradg, ***trgradg;
    int theta;
+   double eip, vip;
    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
    xp=vector(1,npar);
+   xm=vector(1,npar);
    dnewm=matrix(1,nlstate*nlstate,1,npar);
    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-   fprintf(ficreseij,"# Health expectancies\n");
+   pstamp(ficresstdeij);
-   fprintf(ficreseij,"# Age");
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-   for(i=1; i<=nlstate;i++)
+   fprintf(ficresstdeij,"# Age");
+   for(i=1; i<=nlstate;i++){
      for(j=1; j<=nlstate;j++)
-       fprintf(ficreseij," %1d-%1d (SE)",i,j);
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-   fprintf(ficreseij,"\n");
+     fprintf(ficresstdeij," e%1d. ",i);
+   }
+   fprintf(ficresstdeij,"\n");
+   pstamp(ficrescveij);
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   fprintf(ficrescveij,"# Age");
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++){
+       cptj= (j-1)*nlstate+i;
+       for(i2=1; i2<=nlstate;i2++)
+         for(j2=1; j2<=nlstate;j2++){
+           cptj2= (j2-1)*nlstate+i2;
+           if(cptj2 <= cptj)
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+         }
+     }
+   fprintf(ficrescveij,"\n");
    if(estepm < stepm){
      printf ("Problem %d lower than %d\n",estepm, stepm);
    }
- Line 2272  void evsij(char fileres[], double ***eij
+ Line 2601  void evsij(char fileres[], double ***eij
    */
    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   /* If stepm=6 months */
+   /* nhstepm age range expressed in number of stepm */
    agelim=AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   nstepm=(int) rint((agelim-age)*YEARM/stepm);
-     /* nhstepm age range expressed in number of stepm */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm);
+   /* if (stepm >= YEARM) hstepm=1;*/
-     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     /* if (stepm >= YEARM) hstepm=1;*/
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-     gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-     gm=matrix(0,nhstepm,1,nlstate*nlstate);
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+   for (age=bage; age<=fage; age ++){
      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     /* Computing Variances of health expectancies */
+     /* Computing  Variances of health expectancies */
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-      for(theta=1; theta <=npar; theta++){
+        decrease memory allocation */
+     for(theta=1; theta <=npar; theta++){
        for(i=1; i<=npar; i++){
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-       cptj=0;
        for(j=1; j<= nlstate; j++){
          for(i=1; i<=nlstate; i++){
-           cptj=cptj+1;
+           for(h=0; h<=nhstepm-1; h++){
-           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
            }
          }
        }
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-       for(i=1; i<=npar; i++)
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       cptj=0;
-       for(j=1; j<= nlstate; j++){
-         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*nlstate; j++)
          for(h=0; h<=nhstepm-1; h++){
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
          }
-      }
+     }/* End theta */
- /* End theta */
+     for(h=0; h<=nhstepm-1; h++)
-      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-      for(h=0; h<=nhstepm-1; h++)
        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*nlstate;i++)
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-       for(j=1;j<=nlstate*nlstate;j++)
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-         varhe[i][j][(int)age] =0.;
+         varhe[ij][ji][(int)age] =0.;
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
- Line 2350  void evsij(char fileres[], double ***eij
+ Line 2666  void evsij(char fileres[], double ***eij
        for(k=0;k<=nhstepm-1;k++){
          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-         for(i=1;i<=nlstate*nlstate;i++)
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-           for(j=1;j<=nlstate*nlstate;j++)
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
        }
      }
      /* Computing expectancies */
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
- /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
          }
-     fprintf(ficreseij,"%3.0f",age );
+     fprintf(ficresstdeij,"%3.0f",age );
-     cptj=0;
+     for(i=1; i<=nlstate;i++){
+       eip=0.;
+       vip=0.;
+       for(j=1; j<=nlstate;j++){
+         eip += eij[i][j][(int)age];
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+       }
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+     }
+     fprintf(ficresstdeij,"\n");
+     fprintf(ficrescveij,"%3.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
-         cptj++;
+         cptj= (j-1)*nlstate+i;
-         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
+         for(i2=1; i2<=nlstate;i2++)
+           for(j2=1; j2<=nlstate;j2++){
+             cptj2= (j2-1)*nlstate+i2;
+             if(cptj2 <= cptj)
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+           }
        }
-     fprintf(ficreseij,"\n");
+     fprintf(ficrescveij,"\n");
-     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    printf("\n");
    fprintf(ficlog,"\n");
+   free_vector(xm,1,npar);
    free_vector(xp,1,npar);
    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
- Line 2390  void evsij(char fileres[], double ***eij
+ Line 2727  void evsij(char fileres[], double ***eij
  }
  /************ Variance ******************/
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
+ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
  {
    /* Variance of health expectancies */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
- Line 2441  void varevsij(char optionfilefiname[], d
+ Line 2778  void varevsij(char optionfilefiname[], d
      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
    }
    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);
+   pstamp(ficresprobmorprev);
    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++){
- Line 2451  void varevsij(char optionfilefiname[], d
+ Line 2790  void varevsij(char optionfilefiname[], d
    }
    fprintf(ficresprobmorprev,"\n");
    fprintf(ficgp,"\n# Routine varevsij");
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
    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(fichtm,"\n<br>%s  <br>\n",digitp);
  /*   } */
    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   pstamp(ficresvij);
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+   if(popbased==1)
+     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+   else
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
    fprintf(ficresvij,"# Age");
    for(i=1; i<=nlstate;i++)
      for(j=1; j<=nlstate;j++)
-       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
    fprintf(ficresvij,"\n");
    xp=vector(1,npar);
- Line 2688  void varevsij(char optionfilefiname[], d
+ Line 3032  void varevsij(char optionfilefiname[], d
  }  /* 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)
+ 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, char strstart[])
  {
    /* Variance of prevalence limit */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
- Line 2701  void varprevlim(char fileres[], double *
+ Line 3045  void varprevlim(char fileres[], double *
    double **gradg, **trgradg;
    double age,agelim;
    int theta;
-   fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
+   pstamp(ficresvpl);
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
    fprintf(ficresvpl,"# Age");
    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %1d-%1d",i,i);
- Line 2771  void varprevlim(char fileres[], double *
+ Line 3116  void varprevlim(char fileres[], double *
  }
  /************ Variance of one-step probabilities  ******************/
- void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
  {
    int i, j=0,  i1, k1, l1, t, tj;
    int k2, l2, j1,  z1;
- Line 2816  void varprob(char optionfilefiname[], do
+ Line 3161  void varprob(char optionfilefiname[], do
    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   pstamp(ficresprob);
    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
    fprintf(ficresprob,"# Age");
+   pstamp(ficresprobcov);
    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
    fprintf(ficresprobcov,"# Age");
+   pstamp(ficresprobcor);
    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-   fprintf(ficresprobcov,"# Age");
+   fprintf(ficresprobcor,"# Age");
    for(i=1; i<=nlstate;i++)
- Line 2845  void varprob(char optionfilefiname[], do
+ Line 3192  void varprob(char optionfilefiname[], do
    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
    fprintf(fichtm,"\n");
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
    file %s<br>\n",optionfilehtmcov);
    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
  and drawn. It helps understanding how is the covariance between two incidences.\
- Line 2879  To be simple, these graphs help to under
+ Line 3226  To be simple, these graphs help to under
          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]]);
- Line 3073  To be simple, these graphs help to under
+ Line 3420  To be simple, these graphs help to under
    }
    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_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
    free_vector(xp,1,npar);
    fclose(ficresprob);
    fclose(ficresprobcov);
- Line 3090  void printinghtml(char fileres[], char t
+ Line 3439  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><a href='#firstorder'>Result files (first order: no variance)</a>\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 \
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
+ </ul>");
-  - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-  - Life expectancies by age and initial health status (estepm=%2d months): \
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-    <a href=\"%s\">%s</a> <br>\n</li>", \
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
+    fprintf(fichtm,"\
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+    fprintf(fichtm,"\
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+    fprintf(fichtm,"\
+  - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij (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>");
   m=cptcoveff;
- Line 3123  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3474  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: %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: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
       /* Quasi-incidences */
       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-        /* Stable prevalence in each health state */
+        /* Period (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>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+ <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,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): %s%d%d.png <br> \
+         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,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): %s%d.png<br>\
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),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> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-  - Variance of one-step probabilities: <a href=\"%s\">%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=\"%s\">%s</a> <br>\n\
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%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=\"%s\">%s</a><br>\n\
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-  - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
+  fprintf(fichtm,"\
-  - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          rfileres,rfileres,\
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
+  fprintf(fichtm,"\
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+  fprintf(fichtm,"\
+  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+  fprintf(fichtm,"\
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+  fprintf(fichtm,"\
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
- Line 3168  health expectancies in states (1) and (2
+ Line 3531  health expectancies in states (1) and (2
  /*      <br>",fileres,fileres,fileres,fileres); */
  /*  else  */
  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
- fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+  fflush(fichtm);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   m=cptcoveff;
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- Line 3184  fprintf(fichtm," <ul><li><b>Graphs</b></
+ Line 3548  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 period prevalence (with confident\
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- interval) in state (%d): %s%d%d.png <br>\
+ prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
  <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>");
- Line 3227  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 3594  plot [%.f:%.f] \"%s\" every :::%d::%d u
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }
-      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);
+      fprintf(ficgp,"\" t\"Period (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)");
- Line 3275  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 3642  plot [%.f:%.f] \"%s\" every :::%d::%d u
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<= nlstate ; cpt ++) {
-       k=2+nlstate*(2*cpt-2);
+       /*       k=2+nlstate*(2*cpt-2); */
+       k=2+(nlstate+1)*(cpt-1);
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
        fprintf(ficgp,"set ter png small\n\
  set size 0.65,0.65\n\
- Line 3289  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 3657  plot [%.f:%.f] \"%s\" every :::%d::%d u
        */
        for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+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);*/
        }
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
      }
    }
- Line 3842  void prwizard(int ncovmodel, int nlstate
+ Line 4212  void prwizard(int ncovmodel, int nlstate
          } /* end k*/
        } /*end j */
      } /* end i */
-   }
+   } /* end itimes */
  } /* end of prwizard */
+ /******************* Gompertz Likelihood ******************************/
+ double gompertz(double x[])
+ {
+   double A,B,L=0.0,sump=0.,num=0.;
+   int i,n=0; /* n is the size of the sample */
+   for (i=0;i<=imx-1 ; i++) {
+     sump=sump+weight[i];
+     /*    sump=sump+1;*/
+     num=num+1;
+   }
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+   for (i=1;i<=imx ; i++)
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+       if (cens[i] == 0 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
+         L=L+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+       }
+     }
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   return -2*L*num/sump;
+ }
+ /******************* Printing html file ***********/
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   int imx,  double p[],double **matcov,double agemortsup){
+   int i,k;
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   for (i=1;i<=2;i++)
+     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+   fprintf(fichtm,"</ul>");
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+  for (k=agegomp;k<(agemortsup-2);k++)
+    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+   fflush(fichtm);
+ }
+ /******************* Gnuplot file **************/
+ void printinggnuplotmort(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;
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     /*#endif */
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+   fprintf(ficgp, "set ter png small\n set log y\n");
+   fprintf(ficgp, "set size 0.65,0.65\n");
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+ }
  /***********************************************/
- Line 3855  int main(int argc, char *argv[])
+ Line 4311  int main(int argc, char *argv[])
  {
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-   int jj, imk;
+   int linei, month, year,iout;
+   int jj, ll, li, lj, lk, imk;
    int numlinepar=0; /* Current linenumber of parameter file */
+   int itimes;
+   int NDIM=2;
+   char ca[32], cb[32], cc[32];
+   char dummy[]="                         ";
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
+   struct stat info;
    double agedeb, agefin,hf;
    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
- Line 3871  int main(int argc, char *argv[])
+ Line 4334  int main(int argc, char *argv[])
    int *indx;
    char line[MAXLINE], linepar[MAXLINE];
    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-   char pathr[MAXLINE];
+   char pathr[MAXLINE], pathimach[MAXLINE];
+   char **bp, *tok, *val; /* pathtot */
    int firstobs=1, lastobs=10;
    int sdeb, sfin; /* Status at beginning and end */
    int c,  h , cpt,l;
- Line 3881  int main(int argc, char *argv[])
+ Line 4345  int main(int argc, char *argv[])
    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
    int mobilav=0,popforecast=0;
    int hstepm, nhstepm;
+   int agemortsup;
+   float  sumlpop=0.;
    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;
- Line 3898  int main(int argc, char *argv[])
+ Line 4364  int main(int argc, char *argv[])
    double *epj, vepp;
    double kk1, kk2;
    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double **ximort;
    char *alph[]={"a","a","b","c","d","e"}, str[4];
+   int *dcwave;
    char z[1]="c", occ;
    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
-   char strstart[80], *strt, strtend[80];
+   char  *strt, strtend[80];
    char *stratrunc;
    int lstra;
    long total_usecs;
+ /*   setlocale (LC_ALL, ""); */
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
    (void) gettimeofday(&start_time,&tzp);
    curr_time=start_time;
- Line 3941  int main(int argc, char *argv[])
+ Line 4413  int main(int argc, char *argv[])
    printf("\n%s\n%s",version,fullversion);
    if(argc <=1){
      printf("\nEnter the parameter file name: ");
-     scanf("%s",pathtot);
+     fgets(pathr,FILENAMELENGTH,stdin);
+     i=strlen(pathr);
+     if(pathr[i-1]=='\n')
+       pathr[i-1]='\0';
+    for (tok = pathr; tok != NULL; ){
+       printf("Pathr |%s|\n",pathr);
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+       printf("val= |%s| pathr=%s\n",val,pathr);
+       strcpy (pathtot, val);
+       if(pathr[0] == '\0') break; /* Dirty */
+     }
    }
    else{
      strcpy(pathtot,argv[1]);
- Line 3951  int main(int argc, char *argv[])
+ Line 4433  int main(int argc, char *argv[])
      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
    /* cutv(path,optionfile,pathtot,'\\');*/
+   /* Split argv[0], imach program to get pathimach */
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+  /*   strcpy(pathimach,argv[0]); */
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-   chdir(path);
+   chdir(path); /* Can be a relative path */
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+     printf("Current directory %s!\n",pathcd);
    strcpy(command,"mkdir ");
    strcat(command,optionfilefiname);
    if((outcmd=system(command)) != 0){
- Line 3977  int main(int argc, char *argv[])
+ Line 4467  int main(int argc, char *argv[])
    }
    fprintf(ficlog,"Log filename:%s\n",filelog);
    fprintf(ficlog,"\n%s\n%s",version,fullversion);
-   fprintf(ficlog,"\nEnter the parameter file name: ");
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-   fprintf(ficlog,"pathtot=%s\n\
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
   path=%s \n\
   optionfile=%s\n\
   optionfilext=%s\n\
-  optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
    printf("Local time (at start):%s",strstart);
    fprintf(ficlog,"Local time (at start): %s",strstart);
- Line 4050  int main(int argc, char *argv[])
+ Line 4540  int main(int argc, char *argv[])
    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   delti=delti3[1][1];
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
    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);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
      fclose (ficparo);
      fclose (ficlog);
      exit(0);
    }
-   /* Read guess parameters */
+   else if(mle==-3) {
-   /* Reads comments: lines beginning with '#' */
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     matcov=matrix(1,npar,1,npar);
+   }
+   else{
+     /* 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);
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     puts(line);
+     for(i=1; i <=nlstate; i++){
-     fputs(line,ficparo);
+       j=0;
-     fputs(line,ficlog);
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-   }
+         if(jj==i) continue;
-   ungetc(c,ficpar);
+         j++;
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+         if ((i1 != i) && (j1 != j)){
-   for(i=1; i <=nlstate; i++){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-     j=0;
+           exit(1);
-     for(jj=1; jj <=nlstate+ndeath; jj++){
+         }
-       if(jj==i) continue;
+         fprintf(ficparo,"%1d%1d",i1,j1);
-       j++;
+         if(mle==1)
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
+           printf("%1d%1d",i,j);
-       if ((i1 != i) && (j1 != j)){
+         fprintf(ficlog,"%1d%1d",i,j);
-         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+         for(k=1; k<=ncovmodel;k++){
-         exit(1);
+           fscanf(ficpar," %lf",&param[i][j][k]);
-       }
+           if(mle==1){
-       fprintf(ficparo,"%1d%1d",i1,j1);
+             printf(" %lf",param[i][j][k]);
-       if(mle==1)
+             fprintf(ficlog," %lf",param[i][j][k]);
-         printf("%1d%1d",i,j);
+           }
-       fprintf(ficlog,"%1d%1d",i,j);
+           else
-       for(k=1; k<=ncovmodel;k++){
+             fprintf(ficlog," %lf",param[i][j][k]);
-         fscanf(ficpar," %lf",&param[i][j][k]);
+           fprintf(ficparo," %lf",param[i][j][k]);
-         if(mle==1){
+         }
-           printf(" %lf",param[i][j][k]);
+         fscanf(ficpar,"\n");
-           fprintf(ficlog," %lf",param[i][j][k]);
+         numlinepar++;
-         }
+         if(mle==1)
-         else
+           printf("\n");
-           fprintf(ficlog," %lf",param[i][j][k]);
+         fprintf(ficlog,"\n");
-         fprintf(ficparo," %lf",param[i][j][k]);
+         fprintf(ficparo,"\n");
        }
-       fscanf(ficpar,"\n");
+     }
+     fflush(ficlog);
+     p=param[1][1];
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
        numlinepar++;
-       if(mle==1)
+       puts(line);
-         printf("\n");
+       fputs(line,ficparo);
-       fprintf(ficlog,"\n");
+       fputs(line,ficlog);
-       fprintf(ficparo,"\n");
      }
-   }
-   fflush(ficlog);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-   p=param[1][1];
-   /* Reads comments: lines beginning with '#' */
-   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
-     puts(line);
-     fputs(line,ficparo);
-     fputs(line,ficlog);
-   }
-   ungetc(c,ficpar);
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     for(i=1; i <=nlstate; i++){
-   /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
+       for(j=1; j <=nlstate+ndeath-1; j++){
-   for(i=1; i <=nlstate; i++){
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     for(j=1; j <=nlstate+ndeath-1; j++){
+         if ((i1-i)*(j1-j)!=0){
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-       if ((i1-i)*(j1-j)!=0){
+           exit(1);
-         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);
-       printf("%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i1,j1);
-       fprintf(ficparo,"%1d%1d",i1,j1);
+         for(k=1; k<=ncovmodel;k++){
-       fprintf(ficlog,"%1d%1d",i1,j1);
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-       for(k=1; k<=ncovmodel;k++){
+           printf(" %le",delti3[i][j][k]);
-         fscanf(ficpar,"%le",&delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
-         printf(" %le",delti3[i][j][k]);
+           fprintf(ficlog," %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");
        }
-       fscanf(ficpar,"\n");
-       numlinepar++;
-       printf("\n");
-       fprintf(ficparo,"\n");
-       fprintf(ficlog,"\n");
      }
-   }
+     fflush(ficlog);
-   fflush(ficlog);
-   delti=delti3[1][1];
+     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 */
+     /* 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 '#' */
+     /* Reads comments: lines beginning with '#' */
-   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);
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
-     puts(line);
-     fputs(line,ficparo);
-     fputs(line,ficlog);
-   }
-   ungetc(c,ficpar);
-   matcov=matrix(1,npar,1,npar);
+     matcov=matrix(1,npar,1,npar);
-   for(i=1; i <=npar; i++){
+     for(i=1; i <=npar; i++){
-     fscanf(ficpar,"%s",&str);
+       fscanf(ficpar,"%s",&str);
-     if(mle==1)
+       if(mle==1)
-       printf("%s",str);
+         printf("%s",str);
-     fprintf(ficlog,"%s",str);
+       fprintf(ficlog,"%s",str);
-     fprintf(ficparo,"%s",str);
+       fprintf(ficparo,"%s",str);
-     for(j=1; j <=i; j++){
+       for(j=1; j <=i; j++){
-       fscanf(ficpar," %le",&matcov[i][j]);
+         fscanf(ficpar," %le",&matcov[i][j]);
-       if(mle==1){
+         if(mle==1){
-         printf(" %.5le",matcov[i][j]);
+           printf(" %.5le",matcov[i][j]);
+         }
+         fprintf(ficlog," %.5le",matcov[i][j]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
        }
-       fprintf(ficlog," %.5le",matcov[i][j]);
+       fscanf(ficpar,"\n");
-       fprintf(ficparo," %.5le",matcov[i][j]);
+       numlinepar++;
+       if(mle==1)
+         printf("\n");
+       fprintf(ficlog,"\n");
+       fprintf(ficparo,"\n");
      }
-     fscanf(ficpar,"\n");
+     for(i=1; i <=npar; i++)
-     numlinepar++;
+       for(j=i+1;j<=npar;j++)
+         matcov[i][j]=matcov[j][i];
      if(mle==1)
        printf("\n");
      fprintf(ficlog,"\n");
-     fprintf(ficparo,"\n");
-   }
-   for(i=1; i <=npar; i++)
-     for(j=i+1;j<=npar;j++)
-       matcov[i][j]=matcov[j][i];
-   if(mle==1)
-     printf("\n");
-   fprintf(ficlog,"\n");
-   fflush(ficlog);
-   /*-------- Rewriting paramater file ----------*/
-   strcpy(rfileres,"r");    /* "Rparameterfile */
-   strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-   strcat(rfileres,".");    /* */
-   strcat(rfileres,optionfilext);    /* Other files have txt extension */
-   if((ficres =fopen(rfileres,"w"))==NULL) {
-     printf("Problem writing new parameter file: %s\n", fileres);goto end;
-     fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-   }
-   fprintf(ficres,"#%s\n",version);
+     fflush(ficlog);
+     /*-------- Rewriting parameter file ----------*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     strcat(rfileres,".");    /* */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     if((ficres =fopen(rfileres,"w"))==NULL) {
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+     }
+     fprintf(ficres,"#%s\n",version);
+   }    /* End of mle != -3 */
    /*-------- data file ----------*/
    if((fic=fopen(datafile,"r"))==NULL)    {
-     printf("Problem with datafile: %s\n", datafile);goto end;
+     printf("Problem while opening datafile: %s\n", datafile);goto end;
-     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
    }
    n= lastobs;
- Line 4232  int main(int argc, char *argv[])
+ Line 4732  int main(int argc, char *argv[])
    ncodemax=ivector(1,8);
    i=1;
-   while (fgets(line, MAXLINE, fic) != NULL)    {
+   linei=0;
-     if ((i >= firstobs) && (i <=lastobs)) {
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+     linei=linei+1;
-       for (j=maxwav;j>=1;j--){
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-         cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
+       if(line[j] == '\t')
-         strcpy(line,stra);
+         line[j] = ' ';
-         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);
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+       ;
+     };
+     line[j+1]=0;  /* Trims blanks at end of line */
+     if(line[0]=='#'){
+       fprintf(ficlog,"Comment line\n%s\n",line);
+       printf("Comment line\n%s\n",line);
+       continue;
+     }
+     for (j=maxwav;j>=1;j--){
+       cutv(stra, strb,line,' ');
+       errno=0;
+       lval=strtol(strb,&endptr,10);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+       if( strb[0]=='\0' || (*endptr != '\0')){
+         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+         exit(1);
        }
+       s[j][i]=lval;
-       cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
+       strcpy(line,stra);
+       cutv(stra, strb,line,' ');
-       cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-       cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
+       }
+       else  if(iout=sscanf(strb,"%s.") != 0){
-       cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
+         month=99;
-       for (j=ncovcol;j>=1;j--){
+         year=9999;
-         cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+       }else{
-       }
+         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-       lstra=strlen(stra);
+         exit(1);
-       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
+       anint[j][i]= (double) year;
-         num[i]=atol(stra);
+       mint[j][i]= (double)month;
+       strcpy(line,stra);
-       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+     } /* ENd Waves */
-         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;}*/
+     cutv(stra, strb,line,' ');
-       i=i+1;
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
      }
-   }
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+       exit(1);
+     }
+     andc[i]=(double) year;
+     moisdc[i]=(double) month;
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
+     else  if(iout=sscanf(strb,"%s.") != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
+       exit(1);
+     }
+     annais[i]=(double)(year);
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     errno=0;
+     lval=strtol(strb,&endptr,10);
+     if( strb[0]=='\0' || (*endptr != '\0')){
+       printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
+       exit(1);
+     }
+     weight[i]=(double)(lval);
+     strcpy(line,stra);
+     for (j=ncovcol;j>=1;j--){
+       cutv(stra, strb,line,' ');
+       errno=0;
+       lval=strtol(strb,&endptr,10);
+       if( strb[0]=='\0' || (*endptr != '\0')){
+         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
+         exit(1);
+       }
+       if(lval <-1 || lval >1){
+         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
+         exit(1);
+       }
+       covar[j][i]=(double)(lval);
+       strcpy(line,stra);
+     }
+     lstra=strlen(stra);
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       stratrunc = &(stra[lstra-9]);
+       num[i]=atol(stratrunc);
+     }
+     else
+       num[i]=atol(stra);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+     i=i+1;
+   } /* End loop reading  data */
+   fclose(fic);
    /* printf("ii=%d", ij);
       scanf("%d",i);*/
    imx=i-1; /* Number of individuals */
- Line 4279  int main(int argc, char *argv[])
+ Line 4856  int main(int argc, char *argv[])
       if (s[4][i]==9)  s[4][i]=-1;
       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
-  for (i=1; i<=imx; i++)
+   /* 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*/
+   /* Calculation of the number of parameters from char model */
    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
    Tprod=ivector(1,15);
    Tvaraff=ivector(1,15);
- Line 4363  int main(int argc, char *argv[])
+ Line 4940  int main(int argc, char *argv[])
    printf("cptcovprod=%d ", cptcovprod);
    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-   scanf("%d ",i);
+   scanf("%d ",i);*/
-   fclose(fic);*/
      /*  if(mle==1){*/
    if (weightopt != 1) { /* Maximisation without weights*/
- Line 4397  int main(int argc, char *argv[])
+ Line 4973  int main(int argc, char *argv[])
    for (i=1; i<=imx; i++)  {
      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
      for(m=firstpass; (m<= lastpass); m++){
-       if(s[m][i] >0){
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
          if (s[m][i] >= nlstate+1) {
            if(agedc[i]>0)
              if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
- Line 4413  int main(int argc, char *argv[])
+ Line 4989  int main(int argc, char *argv[])
              }
          }
          else if(s[m][i] !=9){ /* Standard case, age in fractional
-                                  years but with the precision of a
+                                  years but with the precision of a month */
-                                  month */
            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
            if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
              agev[m][i]=1;
- Line 4457  int main(int argc, char *argv[])
+ Line 5032  int main(int argc, char *argv[])
  }*/
    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);
+   agegomp=(int)agemin;
    free_vector(severity,1,maxwav);
    free_imatrix(outcome,1,maxwav+1,1,n);
    free_vector(moisnais,1,n);
- Line 4513  int main(int argc, char *argv[])
+ Line 5090  int main(int argc, char *argv[])
    /*------------ gnuplot -------------*/
    strcpy(optionfilegnuplot,optionfilefiname);
+   if(mle==-3)
+     strcat(optionfilegnuplot,"-mort");
    strcat(optionfilegnuplot,".gp");
    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
      printf("Problem with file %s",optionfilegnuplot);
    }
- Line 4526  int main(int argc, char *argv[])
+ Line 5106  int main(int argc, char *argv[])
    /*--------- index.htm --------*/
    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   if(mle==-3)
+     strcat(optionfilehtm,"-mort");
    strcat(optionfilehtm,".htm");
    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
      printf("Problem with %s \n",optionfilehtm), exit(0);
- Line 4549  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5131  Title=%s <br>Datafile=%s Firstpass=%d La
  \n\
  <hr  size=\"2\" color=\"#EC5E5E\">\
   <ul><li><h4>Parameter files</h4>\n\
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\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,\
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
            fileres,fileres,\
            filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
    fflush(fichtm);
- Line 4564  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5148  Title=%s <br>Datafile=%s Firstpass=%d La
    /* 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);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
    fprintf(fichtm,"\n");
    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
- Line 4583  Interval (in months) between two waves:
+ Line 5167  Interval (in months) between two waves:
    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-   likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
-   printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+   if (mle==-3){
-   for (k=1; k<=npar;k++)
+     ximort=matrix(1,NDIM,1,NDIM);
-     printf(" %d %8.5f",k,p[k]);
+     cens=ivector(1,n);
-   printf("\n");
+     ageexmed=vector(1,n);
-   globpr=1; /* to print the contributions */
+     agecens=vector(1,n);
-   likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     dcwave=ivector(1,n);
-   printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-   for (k=1; k<=npar;k++)
+     for (i=1; i<=imx; i++){
-     printf(" %d %8.5f",k,p[k]);
+       dcwave[i]=-1;
-   printf("\n");
+       for (m=firstpass; m<=lastpass; m++)
-   if(mle>=1){ /* Could be 1 or 2 */
+         if (s[m][i]>nlstate) {
-     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+           dcwave[i]=m;
-   }
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+           break;
+         }
+     }
+     for (i=1; i<=imx; i++) {
+       if (wav[i]>0){
+         ageexmed[i]=agev[mw[1][i]][i];
+         j=wav[i];
+         agecens[i]=1.;
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
+           cens[i]= 1;
+         }else if (ageexmed[i]< 1)
+           cens[i]= -1;
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+           cens[i]=0 ;
+       }
+       else cens[i]=-1;
+     }
-   /*--------- results files --------------*/
+     for (i=1;i<=NDIM;i++) {
-   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);
+       for (j=1;j<=NDIM;j++)
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     }
+     p[1]=0.0268; p[NDIM]=0.083;
+     /*printf("%lf %lf", p[1], p[2]);*/
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+     strcpy(filerespow,"pow-mort");
+     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,ximort,NDIM,ftol,&iter,&fret,gompertz);
+     fclose(ficrespow);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
-   jk=1;
+     for(i=1; i <=NDIM; i++)
-   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       for(j=i+1;j<=NDIM;j++)
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+         matcov[i][j]=matcov[j][i];
-   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   for(i=1,jk=1; i <=nlstate; i++){
+     printf("\nCovariance matrix\n ");
-     for(k=1; k <=(nlstate+ndeath); k++){
+     for(i=1; i <=NDIM; i++) {
-       if (k != i)
+       for(j=1;j<=NDIM;j++){
-         {
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\n ");
+     }
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     for (i=1;i<=NDIM;i++)
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     lsurv=vector(1,AGESUP);
+     lpop=vector(1,AGESUP);
+     tpop=vector(1,AGESUP);
+     lsurv[agegomp]=100000;
+     for (k=agegomp;k<=AGESUP;k++) {
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
+     }
+     tpop[agegomp]=sumlpop;
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+                      stepm, weightopt,\
+                      model,imx,p,matcov,agemortsup);
+     free_vector(lsurv,1,AGESUP);
+     free_vector(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+   } /* Endof if mle==-3 */
+   else{ /* For mle >=1 */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     globpr=1; /* to print the contributions */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     if(mle>=1){ /* Could be 1 or 2 */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     /*--------- results files --------------*/
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
            printf("%d%d ",i,k);
            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);
- Line 4623  Interval (in months) between two waves:
+ Line 5328  Interval (in months) between two waves:
            fprintf(ficlog,"\n");
            fprintf(ficres,"\n");
          }
+       }
      }
-   }
+     if(mle!=0){
-   if(mle!=0){
+       /* Computing hessian and covariance matrix */
-     /* Computing hessian and covariance matrix */
+       ftolhess=ftol; /* Usually correct */
-     ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, p, npar, delti, ftolhess, func);
-     hesscov(matcov, p, npar, delti, ftolhess, func);
+     }
-   }
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
-   fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
-   printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
-   for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
-     for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
-       if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
-         fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
-         printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
-         fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
-         for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
-           printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
-           fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
-           fprintf(ficres," %.5e",delti[jk]);
+             jk++;
-           jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
          }
-         printf("\n");
-         fprintf(ficlog,"\n");
-         fprintf(ficres,"\n");
        }
      }
-   }
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-   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)
-   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");
-     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");
-   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");
+     /* # 121 Var(a12)\n\ */
-   for(i=1,k=1;i<=npar;i++){
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     /*  if (k>nlstate) k=1;
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-         i1=(i-1)/(ncovmodel*nlstate)+1;
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-         fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-         printf("%s%d%d",alph[k],i1,tab[i]);
+     /* # 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" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
      */
-     fprintf(ficres,"%3d",i);
+     for(itimes=1;itimes<=2;itimes++){
-     if(mle==1)
+       jj=0;
-       printf("%3d",i);
+       for(i=1; i <=nlstate; i++){
-     fprintf(ficlog,"%3d",i);
+         for(j=1; j <=nlstate+ndeath; j++){
-     for(j=1; j<=i;j++){
+           if(j==i) continue;
-       fprintf(ficres," %.5e",matcov[i][j]);
+           for(k=1; k<=ncovmodel;k++){
-       if(mle==1)
+             jj++;
-         printf(" %.5e",matcov[i][j]);
+             ca[0]= k+'a'-1;ca[1]='\0';
-       fprintf(ficlog," %.5e",matcov[i][j]);
+             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);
      }
-     fprintf(ficres,"\n");
-     if(mle==1)
-       printf("\n");
-     fprintf(ficlog,"\n");
-     k++;
-   }
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   estepm=0;
-   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
-   if (estepm==0 || estepm < stepm) estepm=stepm;
-   if (fage <= 2) {
-     bage = ageminpar;
-     fage = agemaxpar;
-   }
-   fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-   fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
+     estepm=0;
-     fputs(line,ficparo);
+     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;
-   ungetc(c,ficpar);
+     if (fage <= 2) {
+       bage = ageminpar;
-   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);
+       fage = agemaxpar;
-   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     }
-   fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-   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);
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       puts(line);
+       fputs(line,ficparo);
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
+     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);
-     fputs(line,ficparo);
+     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);
-   ungetc(c,ficpar);
+     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);
-   dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-   fscanf(ficpar,"pop_based=%d\n",&popbased);
+       puts(line);
-   fprintf(ficparo,"pop_based=%d\n",popbased);
+       fputs(line,ficparo);
-   fprintf(ficres,"pop_based=%d\n",popbased);
+     }
-   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-   }
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-   ungetc(c,ficpar);
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
-   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,"pop_based=%d\n",popbased);
-   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,"pop_based=%d\n",popbased);
-   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);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   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);
+       ungetc(c,ficpar);
-   /* day and month of proj2 are not used but only year anproj2.*/
+       fgets(line, MAXLINE, ficpar);
+       puts(line);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       fputs(line,ficparo);
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
+     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);
-     fputs(line,ficparo);
+     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   }
+     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   ungetc(c,ficpar);
+     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);
-   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
+     /* day and month of proj2 are not used but only year anproj2.*/
-   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-   /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
-   /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-   replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-   printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
-                model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
-                jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+                  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(bh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
-   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-   free_lvector(num,1,n);
+     free_lvector(num,1,n);
-   free_vector(agedc,1,n);
+     free_vector(agedc,1,n);
-   /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
-   /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
-   fclose(ficparo);
+     fclose(ficparo);
-   fclose(ficres);
+     fclose(ficres);
-   /*--------------- Prevalence limit  (stable prevalence) --------------*/
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-   strcpy(filerespl,"pl");
+     strcpy(filerespl,"pl");
-   strcat(filerespl,fileres);
+     strcat(filerespl,fileres);
-   if((ficrespl=fopen(filerespl,"w"))==NULL) {
+     if((ficrespl=fopen(filerespl,"w"))==NULL) {
-     printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
+       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-     fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
+       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-   }
+     }
-   printf("Computing stable prevalence: result on file '%s' \n", filerespl);
+     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
+     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficrespl,"#Stable prevalence \n");
+     pstamp(ficrespl);
-   fprintf(ficrespl,"#Age ");
+     fprintf(ficrespl,"# Period (stable) prevalence \n");
-   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     fprintf(ficrespl,"#Age ");
-   fprintf(ficrespl,"\n");
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     fprintf(ficrespl,"\n");
-   prlim=matrix(1,nlstate,1,nlstate);
+     prlim=matrix(1,nlstate,1,nlstate);
-   agebase=ageminpar;
-   agelim=agemaxpar;
+     agebase=ageminpar;
-   ftolpl=1.e-10;
+     agelim=agemaxpar;
-   i1=cptcoveff;
+     ftolpl=1.e-10;
-   if (cptcovn < 1){i1=1;}
+     i1=cptcoveff;
+     if (cptcovn < 1){i1=1;}
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       k=k+1;
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+         k=k+1;
-       fprintf(ficrespl,"\n#******");
+         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
-       printf("\n#******");
+         fprintf(ficrespl,"\n#******");
-       fprintf(ficlog,"\n#******");
+         printf("\n#******");
-       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficlog,"\n#******");
-         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         for(j=1;j<=cptcoveff;j++) {
-         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       }
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficrespl,"******\n");
+         }
-       printf("******\n");
+         fprintf(ficrespl,"******\n");
-       fprintf(ficlog,"******\n");
+         printf("******\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(j=1;j<=cptcoveff;j++)
+           for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         for(i=1; i<=nlstate;i++)
+           for(i=1; i<=nlstate;i++)
-           fprintf(ficrespl," %.5f", prlim[i][i]);
+             fprintf(ficrespl," %.5f", prlim[i][i]);
-         fprintf(ficrespl,"\n");
+           fprintf(ficrespl,"\n");
+         }
        }
      }
-   }
+     fclose(ficrespl);
-   fclose(ficrespl);
-   /*------------- h Pij x at various ages ------------*/
+     /*------------- h Pij x at various ages ------------*/
-   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-   if((ficrespij=fopen(filerespij,"w"))==NULL) {
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
-     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-   }
+     }
-   printf("Computing pij: result on file '%s' \n", filerespij);
+     printf("Computing pij: result on file '%s' \n", filerespij);
-   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
-   /*if (stepm<=24) stepsize=2;*/
+     /*if (stepm<=24) stepsize=2;*/
-   agelim=AGESUP;
+     agelim=AGESUP;
-   hstepm=stepsize*YEARM; /* Every year of age */
+     hstepm=stepsize*YEARM; /* Every year of age */
-   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-   /* hstepm=1;   aff par mois*/
-   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     /* hstepm=1;   aff par mois*/
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     pstamp(ficrespij);
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-       k=k+1;
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       fprintf(ficrespij,"\n#****** ");
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-       for(j=1;j<=cptcoveff;j++)
+         k=k+1;
-         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrespij,"\n#****** ");
-       fprintf(ficrespij,"******\n");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrespij,"******\n");
-       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+         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,"# Cov Agex agex+h hpijx with i,j=");
+           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-         for(i=1; i<=nlstate;i++)
-           for(j=1; j<=nlstate+ndeath;j++)
-             fprintf(ficrespij," %1d-%1d",i,j);
-         fprintf(ficrespij,"\n");
-         for (h=0; h<=nhstepm; h++){
-           fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
            for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate+ndeath;j++)
-               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+               fprintf(ficrespij," %1d-%1d",i,j);
+           fprintf(ficrespij,"\n");
+           for (h=0; h<=nhstepm; h++){
+             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+             for(i=1; i<=nlstate;i++)
+               for(j=1; j<=nlstate+ndeath;j++)
+                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+             fprintf(ficrespij,"\n");
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            fprintf(ficrespij,"\n");
          }
-         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         fprintf(ficrespij,"\n");
        }
      }
-   }
-   varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
-   fclose(ficrespij);
+     fclose(ficrespij);
-   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(i=1;i<=AGESUP;i++)
-   /*---------- Forecasting ------------------*/
+       for(j=1;j<=NCOVMAX;j++)
-   /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+         for(k=1;k<=NCOVMAX;k++)
-   if(prevfcast==1){
+           probs[i][j][k]=0.;
-     /*    if(stepm ==1){*/
+     /*---------- Forecasting ------------------*/
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
        prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
        /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
- /*      }  */
+       /*      }  */
- /*      else{ */
+       /*      else{ */
- /*        erreur=108; */
+       /*        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); */
+       /*        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); */
+       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
- /*      } */
+       /*      } */
-   }
+     }
-   /*---------- Health expectancies and variances ------------*/
+     /*---------- Health expectancies and variances ------------*/
-   strcpy(filerest,"t");
+     strcpy(filerest,"t");
-   strcat(filerest,fileres);
+     strcat(filerest,fileres);
-   if((ficrest=fopen(filerest,"w"))==NULL) {
+     if((ficrest=fopen(filerest,"w"))==NULL) {
-     printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
-     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
-   }
+     }
-   printf("Computing Total LEs with variances: file '%s' \n", filerest);
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
-   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
-   strcpy(filerese,"e");
+     strcpy(filerese,"e");
-   strcat(filerese,fileres);
+     strcat(filerese,fileres);
-   if((ficreseij=fopen(filerese,"w"))==NULL) {
+     if((ficreseij=fopen(filerese,"w"))==NULL) {
-     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
-     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
-   }
+     }
-   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
-   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
-   strcpy(fileresv,"v");
+     strcpy(fileresstde,"stde");
-   strcat(fileresv,fileres);
+     strcat(fileresstde,fileres);
-   if((ficresvij=fopen(fileresv,"w"))==NULL) {
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
-     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
-     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
-   }
+     }
-   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
-   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
-   /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     strcpy(filerescve,"cve");
-   prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     strcat(filerescve,fileres);
-   /*  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",\
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
- ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
-   */
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     strcpy(fileresv,"v");
+     strcat(fileresv,fileres);
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     }
+     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+     */
-   if (mobilav!=0) {
+     if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
      }
-   }
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-       k=k+1;
+         k=k+1;
-       fprintf(ficrest,"\n#****** ");
+         fprintf(ficrest,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
+         for(j=1;j<=cptcoveff;j++)
-         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficrest,"******\n");
+         fprintf(ficrest,"******\n");
-       fprintf(ficreseij,"\n#****** ");
+         fprintf(ficreseij,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficresstdeij,"\n#****** ");
-         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrescveij,"\n#****** ");
-       fprintf(ficreseij,"******\n");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficresvij,"\n#****** ");
+           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
-       fprintf(ficresvij,"******\n");
+         fprintf(ficreseij,"******\n");
+         fprintf(ficresstdeij,"******\n");
-       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         fprintf(ficrescveij,"******\n");
-       oldm=oldms;savm=savms;
-       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
+         fprintf(ficresvij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
-       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       oldm=oldms;savm=savms;
+         fprintf(ficresvij,"******\n");
-       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);
-       }
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
-       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         oldm=oldms;savm=savms;
-       fprintf(ficrest,"\n");
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+         if(popbased==1){
-       epj=vector(1,nlstate+1);
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
-       for(age=bage; age <=fage ;age++){
-         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-         if (popbased==1) {
-           if(mobilav ==0){
-             for(i=1; i<=nlstate;i++)
-               prlim[i][i]=probs[(int)age][i][k];
-           }else{ /* mobilav */
-             for(i=1; i<=nlstate;i++)
-               prlim[i][i]=mobaverage[(int)age][i][k];
-           }
-         }
-         fprintf(ficrest," %4.0f",age);
-         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-           for(i=1, epj[j]=0.;i <=nlstate;i++) {
-             epj[j] += prlim[i][i]*eij[i][j][(int)age];
-             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
-           }
-           epj[nlstate+1] +=epj[j];
          }
-         for(i=1, vepp=0.;i <=nlstate;i++)
+         pstamp(ficrest);
-           for(j=1;j <=nlstate;j++)
+         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
-             vepp += vareij[i][j][(int)age];
+         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
-         for(j=1;j <=nlstate;j++){
-           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
-         }
          fprintf(ficrest,"\n");
-       }
-       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-       free_vector(epj,1,nlstate+1);
-     }
-   }
-   free_vector(weight,1,n);
-   free_imatrix(Tvard,1,15,1,2);
-   free_imatrix(s,1,maxwav+1,1,n);
-   free_matrix(anint,1,maxwav,1,n);
-   free_matrix(mint,1,maxwav,1,n);
-   free_ivector(cod,1,n);
-   free_ivector(tab,1,NCOVMAX);
-   fclose(ficreseij);
-   fclose(ficresvij);
-   fclose(ficrest);
-   fclose(ficpar);
-   /*------- Variance of stable prevalence------*/
-   strcpy(fileresvpl,"vpl");
-   strcat(fileresvpl,fileres);
-   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-     printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
-     exit(0);
-   }
-   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+         epj=vector(1,nlstate+1);
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         for(age=bage; age <=fage ;age++){
-       k=k+1;
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-       fprintf(ficresvpl,"\n#****** ");
+           if (popbased==1) {
-       for(j=1;j<=cptcoveff;j++)
+             if(mobilav ==0){
-         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+               for(i=1; i<=nlstate;i++)
-       fprintf(ficresvpl,"******\n");
+                 prlim[i][i]=probs[(int)age][i][k];
+             }else{ /* mobilav */
+               for(i=1; i<=nlstate;i++)
+                 prlim[i][i]=mobaverage[(int)age][i][k];
+             }
+           }
+           fprintf(ficrest," %4.0f",age);
+           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+             }
+             epj[nlstate+1] +=epj[j];
+           }
+           for(i=1, vepp=0.;i <=nlstate;i++)
+             for(j=1;j <=nlstate;j++)
+               vepp += vareij[i][j][(int)age];
+           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+           for(j=1;j <=nlstate;j++){
+             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+           }
+           fprintf(ficrest,"\n");
+         }
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_vector(epj,1,nlstate+1);
+       }
+     }
+     free_vector(weight,1,n);
+     free_imatrix(Tvard,1,15,1,2);
+     free_imatrix(s,1,maxwav+1,1,n);
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficreseij);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
+     /*------- Variance of period (stable) prevalence------*/
+     strcpy(fileresvpl,"vpl");
+     strcat(fileresvpl,fileres);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
+         fprintf(ficresvpl,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvpl,"******\n");
-       varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         varpl=matrix(1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
+         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,strstart);
-       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       }
      }
-   }
-   fclose(ficresvpl);
+     fclose(ficresvpl);
-   /*---------- End : free ----------------*/
-   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(covar,0,NCOVMAX,1,n);
-   free_matrix(matcov,1,npar,1,npar);
-   /*free_vector(delti,1,npar);*/
-   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-   free_matrix(agev,1,maxwav,1,imx);
-   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ivector(ncodemax,1,8);
+     /*---------- End : free ----------------*/
-   free_ivector(Tvar,1,15);
+     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ivector(Tprod,1,15);
+     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ivector(Tvaraff,1,15);
-   free_ivector(Tage,1,15);
+   }  /* mle==-3 arrives here for freeing */
-   free_ivector(Tcode,1,100);
+   free_matrix(prlim,1,nlstate,1,nlstate);
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(covar,0,NCOVMAX,1,n);
+     free_matrix(matcov,1,npar,1,npar);
+     /*free_vector(delti,1,npar);*/
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_ivector(ncodemax,1,8);
+     free_ivector(Tvar,1,15);
+     free_ivector(Tprod,1,15);
+     free_ivector(Tvaraff,1,15);
+     free_ivector(Tage,1,15);
+     free_ivector(Tcode,1,100);
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     free_imatrix(codtab,1,100,1,10);
    fflush(fichtm);
    fflush(ficgp);
    if((nberr >0) || (nbwarn>0)){
-     printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+     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");
- Line 5101  ageminpar, agemax, s[lastpass][imx], age
+ Line 5892  ageminpar, agemax, s[lastpass][imx], age
    tm = *localtime(&end_time.tv_sec);
    tmg = *gmtime(&end_time.tv_sec);
    strcpy(strtend,asctime(&tm));
-   printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend);
+   printf("Local time at start %s\nLocal time 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));
- Line 5117  ageminpar, agemax, s[lastpass][imx], age
+ Line 5908  ageminpar, agemax, s[lastpass][imx], age
    fclose(ficlog);
    /*------ End -----------*/
-   chdir(path);
-   strcpy(plotcmd,GNUPLOTPROGRAM);
+    printf("Before Current directory %s!\n",pathcd);
-   strcat(plotcmd," ");
+    if(chdir(pathcd) != 0)
-   strcat(plotcmd,optionfilegnuplot);
+     printf("Can't move to directory %s!\n",path);
-   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
+   if(getcwd(pathcd,MAXLINE) > 0)
+     printf("Current directory %s!\n",pathcd);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
+   sprintf(plotcmd,"gnuplot");
+ #ifndef UNIX
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef UNIX
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
    if((outcmd=system(plotcmd)) != 0){
-     printf(" Problem with gnuplot\n");
+     printf("\n Problem with gnuplot\n");
    }
    printf(" Wait...");
    while (z[0] != 'q') {
- Line 5131  ageminpar, agemax, s[lastpass][imx], age
+ Line 5947  ageminpar, agemax, s[lastpass][imx], age
      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] == 'e') system(optionfilehtm);
+     if (z[0] == 'e') {
+       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+       system(optionfilehtm);
+     }
      else if (z[0] == 'g') system(plotcmd);
      else if (z[0] == 'q') exit(0);
    }

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

Removed from v.1.94
changed lines
	Added in v.1.120