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Diff for /imach/src/imach.c between versions 1.105 and 1.138

-version 1.105, 2006/01/05 20:23:19
+version 1.138, 2010/04/30 18:19:40
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.138  2010/04/30 18:19:40  brouard
+   *** empty log message ***
+   Revision 1.137  2010/04/29 18:11:38  brouard
+   (Module): Checking covariates for more complex models
+   than V1+V2. A lot of change to be done. Unstable.
+   Revision 1.136  2010/04/26 20:30:53  brouard
+   (Module): merging some libgsl code. Fixing computation
+   of likelione (using inter/intrapolation if mle = 0) in order to
+   get same likelihood as if mle=1.
+   Some cleaning of code and comments added.
+   Revision 1.135  2009/10/29 15:33:14  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.134  2009/10/29 13:18:53  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.133  2009/07/06 10:21:25  brouard
+   just nforces
+   Revision 1.132  2009/07/06 08:22:05  brouard
+   Many tings
+   Revision 1.131  2009/06/20 16:22:47  brouard
+   Some dimensions resccaled
+   Revision 1.130  2009/05/26 06:44:34  brouard
+   (Module): Max Covariate is now set to 20 instead of 8. A
+   lot of cleaning with variables initialized to 0. Trying to make
+   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
+   Revision 1.129  2007/08/31 13:49:27  lievre
+   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
+   Revision 1.128  2006/06/30 13:02:05  brouard
+   (Module): Clarifications on computing e.j
+   Revision 1.127  2006/04/28 18:11:50  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   (Module): In order to speed up (in case of numerous covariates) we
+   compute health expectancies (without variances) in a first step
+   and then all the health expectancies with variances or standard
+   deviation (needs data from the Hessian matrices) which slows the
+   computation.
+   In the future we should be able to stop the program is only health
+   expectancies and graph are needed without standard deviations.
+   Revision 1.126  2006/04/28 17:23:28  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   Version 0.98h
+   Revision 1.125  2006/04/04 15:20:31  lievre
+   Errors in calculation of health expectancies. Age was not initialized.
+   Forecasting file added.
+   Revision 1.124  2006/03/22 17:13:53  lievre
+   Parameters are printed with %lf instead of %f (more numbers after the comma).
+   The log-likelihood is printed in the log file
+   Revision 1.123  2006/03/20 10:52:43  brouard
+   * imach.c (Module): <title> changed, corresponds to .htm file
+   name. <head> headers where missing.
+   * imach.c (Module): Weights can have a decimal point as for
+   English (a comma might work with a correct LC_NUMERIC environment,
+   otherwise the weight is truncated).
+   Modification of warning when the covariates values are not 0 or
+.
+   Version 0.98g
+   Revision 1.122  2006/03/20 09:45:41  brouard
+   (Module): Weights can have a decimal point as for
+   English (a comma might work with a correct LC_NUMERIC environment,
+   otherwise the weight is truncated).
+   Modification of warning when the covariates values are not 0 or
+.
+   Version 0.98g
+   Revision 1.121  2006/03/16 17:45:01  lievre
+   * imach.c (Module): Comments concerning covariates added
+   * imach.c (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 1.120  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 ***
- Line 39
+ Line 193
    The same imach parameter file can be used but the option for mle should be -3.
-   Agn�s, who wrote this part of the code, tried to keep most of the
+   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
- Line 170
+ Line 324
    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 Agn�s Li�vre (lievre@ined.fr).
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
-            Institut national d'�tudes d�mographiques, Paris.
+            Institut national d'études démographiques, Paris.
    This software have been partly granted by Euro-REVES, a concerted action
    from the European Union.
    It is copyrighted identically to a GNU software product, ie programme and
- Line 199
+ Line 353
        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 211
+ Line 365
    varevsij()
    if popbased==1 varevsij(,popbased)
    total life expectancies
-   Variance of stable prevalence
+   Variance of period (stable) prevalence
   end
  */
- Line 221
+ Line 375
  #include <math.h>
  #include <stdio.h>
  #include <stdlib.h>
+ #include <string.h>
  #include <unistd.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"
+ #ifdef GSL
+ #include <gsl/gsl_errno.h>
+ #include <gsl/gsl_multimin.h>
+ #endif
  /* #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 */
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+ #define MAXPARM 128 /* Maximum number of parameters for the optimization */
  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
  #define NINTERVMAX 8
  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
- #define NCOVMAX 8 /* Maximum number of covariates */
+ #define NCOVMAX 20 /* Maximum number of covariates */
  #define MAXN 20000
  #define YEARM 12. /* Number of months per year */
  #define AGESUP 130
- Line 253
+ Line 419
  #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 0.98, September 2005, INED-EUROREVES ";
+ char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
  char fullversion[]="$Revision$ $Date$";
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ char strstart[80];
- int nvar;
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
+ int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
  int npar=NPARMAX;
  int nlstate=2; /* Number of live states */
  int ndeath=1; /* Number of dead states */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
- int maxwav; /* Maxim number of waves */
+ int maxwav=0; /* Maxim number of waves */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- int gipmx, gsw; /* Global variables on the number of contributions
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
                     to the likelihood and the sum of weights (done by funcone)*/
- int mle, weightopt;
+ int mle=1, weightopt=0;
  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
             * wave mi and wave mi+1 is not an exact multiple of stepm. */
- double jmean; /* Mean space between 2 waves */
+ double jmean=1; /* 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 ; */ /* Used in readdata only */
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
  FILE *ficlog, *ficrespow;
- int globpr; /* Global variable for printing or not */
+ int globpr=0; /* Global variable for printing or not */
  double fretone; /* Only one call to likelihood */
- long ipmx; /* Number of contributions */
+ long ipmx=0; /* Number of contributions */
  double sw; /* Sum of weights */
  char filerespow[FILENAMELENGTH];
  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- Line 300  FILE *ficresprobmorprev;
+ Line 472  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],  tmpout2[FILENAMELENGTH];
  char command[FILENAMELENGTH];
  int  outcmd=0;
- Line 328  long time_value;
+ Line 504  long time_value;
  extern long time();
  char strcurr[80], strfor[80];
+ char *endptr;
+ long lval;
+ double dval;
  #define NR_END 1
  #define FREE_ARG char*
  #define FTOL 1.0e-10
- Line 375  double dateintmean=0;
+ Line 555  double dateintmean=0;
  double *weight;
  int **s; /* Status */
  double *agedc, **covar, idx;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
  double *lsurv, *lpop, *tpop;
  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
- Line 384  double ftolhess; /* Tolerance for comput
+ Line 564  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)
+   /* 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 */
- Line 393  static int split( char *path, char *dirc
+ Line 573  static int split( char *path, char *dirc
    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 401  static int split( char *path, char *dirc
+ Line 582  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 409  static int split( char *path, char *dirc
+ Line 591  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 / */
    if (ss >0){
      ss++;
- Line 426  static int split( char *path, char *dirc
+ Line 609  static int split( char *path, char *dirc
      strncpy( finame, name, l1-l2);
      finame[l1-l2]= 0;
    }
    return( 0 );                          /* we're done */
  }
- Line 444  void replace_back_to_slash(char *s, char
+ Line 628  void replace_back_to_slash(char *s, char
    }
  }
+ char *trimbb(char *out, char *in)
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
+   char *s;
+   s=out;
+   while (*in != '\0'){
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
+       in++;
+     }
+     *out++ = *in++;
+   }
+   *out='\0';
+   return s;
+ }
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
+ {
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+      gives blocc="abcdef2ghi" and alocc="j".
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
+   */
+   char *s, *t;
+   t=in;s=in;
+   while (*in != '\0'){
+     while( *in == occ){
+       *blocc++ = *in++;
+       s=in;
+     }
+     *blocc++ = *in++;
+   }
+   if (s == t) /* occ not found */
+     *(blocc-(in-s))='\0';
+   else
+     *(blocc-(in-s)-1)='\0';
+   in=s;
+   while ( *in != '\0'){
+     *alocc++ = *in++;
+   }
+   *alocc='\0';
+   return s;
+ }
  int nbocc(char *s, char occ)
  {
    int i,j=0;
- Line 456  int nbocc(char *s, char occ)
+ Line 683  int nbocc(char *s, char occ)
    return j;
  }
- void cutv(char *u,char *v, char*t, char occ)
+ /* void cutv(char *u,char *v, char*t, char occ) */
- {
+ /* { */
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-      gives u="abcedf" and v="ghi2j" */
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   int i,lg,j,p=0;
+ /*   int i,lg,j,p=0; */
-   i=0;
+ /*   i=0; */
-   for(j=0; j<=strlen(t)-1; j++) {
+ /*   lg=strlen(t); */
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+ /*   for(j=0; j<=lg-1; j++) { */
-   }
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
+ /*   } */
-   lg=strlen(t);
+ /*   for(j=0; j<p; j++) { */
-   for(j=0; j<p; j++) {
+ /*     (u[j] = t[j]); */
-     (u[j] = t[j]);
+ /*   } */
-   }
+ /*      u[p]='\0'; */
-      u[p]='\0';
-    for(j=0; j<= lg; j++) {
+ /*    for(j=0; j<= lg; j++) { */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   }
+ /*   } */
- }
+ /* } */
  /********************** nrerror ********************/
- Line 888  void powell(double p[], double **xi, int
+ Line 1115  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); fflush(ficlog);
-     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
-     */
     for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12lf",i, p[i]);
- Line 1012  void powell(double p[], double **xi, int
+ Line 1238  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 1022  double **prevalim(double **prlim, int nl
+ Line 1248  double **prevalim(double **prlim, int nl
    int i, ii,j,k;
    double min, max, maxmin, maxmax,sumnew=0.;
    double **matprod2();
-   double **out, cov[NCOVMAX], **pmij();
+   double **out, cov[NCOVMAX+1], **pmij();
    double **newm;
    double agefin, delaymax=50 ; /* Max number of years to converge */
- Line 1037  double **prevalim(double **prlim, int nl
+ Line 1263  double **prevalim(double **prlim, int nl
    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
      newm=savm;
      /* Covariates have to be included here again */
-      cov[2]=agefin;
+     cov[2]=agefin;
-       for (k=1; k<=cptcovn;k++) {
+     for (k=1; k<=cptcovn;k++) {
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+       /*        printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
-       }
+     }
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+     for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       for (k=1; k<=cptcovprod;k++)
+     for (k=1; k<=cptcovprod;k++)
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
      savm=oldm;
      oldm=newm;
      maxmax=0.;
- Line 1078  double **prevalim(double **prlim, int nl
+ Line 1304  double **prevalim(double **prlim, int nl
  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
  {
-   double s1, s2;
+   /* According to parameters values stored in x and the covariate's values stored in cov,
+      computes the probability to be observed in state j being in state i by appying the
+      model to the ncovmodel covariates (including constant and age).
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+      ncth covariate in the global vector x is given by the formula:
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+      Outputs ps[i][j] the probability to be observed in j being in j according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
+   double s1, lnpijopii;
    /*double t34;*/
    int i,j,j1, nc, ii, jj;
      for(i=1; i<= nlstate; i++){
        for(j=1; j<i;j++){
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           /*s2 += param[i][j][nc]*cov[nc];*/
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
          }
-         ps[i][j]=s2;
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
        }
        for(j=i+1; j<=nlstate+ndeath;j++){
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           /*lnpijopii += 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); */
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
          }
-         ps[i][j]=s2;
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
        }
      }
-     /*ps[3][2]=1;*/
      for(i=1; i<= nlstate; i++){
        s1=0;
-       for(j=1; j<i; j++)
+       for(j=1; j<i; j++){
-         s1+=exp(ps[i][j]);
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-       for(j=i+1; j<=nlstate+ndeath; j++)
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         s1+=exp(ps[i][j]);
+       }
+       for(j=i+1; j<=nlstate+ndeath; j++){
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       }
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
        ps[i][i]=1./(s1+1.);
+       /* Computing other pijs */
        for(j=1; j<i; j++)
          ps[i][j]= exp(ps[i][j])*ps[i][i];
        for(j=i+1; j<=nlstate+ndeath; j++)
- Line 1173  double ***hpxij(double ***po, int nhstep
+ Line 1418  double ***hpxij(double ***po, int nhstep
       */
    int i, j, d, h, k;
-   double **out, cov[NCOVMAX];
+   double **out, cov[NCOVMAX+1];
    double **newm;
    /* Hstepm could be zero and should return the unit matrix */
- Line 1189  double ***hpxij(double ***po, int nhstep
+ Line 1434  double ***hpxij(double ***po, int nhstep
        /* Covariates have to be included here again */
        cov[1]=1.;
        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       for (k=1; k<=cptcovn;k++)
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        for (k=1; k<=cptcovage;k++)
          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        for (k=1; k<=cptcovprod;k++)
- Line 1206  double ***hpxij(double ***po, int nhstep
+ Line 1452  double ***hpxij(double ***po, int nhstep
      for(i=1; i<=nlstate+ndeath; i++)
        for(j=1;j<=nlstate+ndeath;j++) {
          po[i][j][h]=newm[i][j];
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-          */
        }
+     /*printf("h=%d ",h);*/
    } /* end h */
+ /*     printf("\n H=%d \n",h); */
    return po;
  }
- Line 1218  double ***hpxij(double ***po, int nhstep
+ Line 1465  double ***hpxij(double ***po, int nhstep
  double func( double *x)
  {
    int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double sw; /* Sum of weights */
    double lli; /* Individual log likelihood */
- Line 1237  double func( double *x)
+ Line 1484  double func( double *x)
    if(mle==1){
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       /* Computes the values of the ncovmodel covariates of the model
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
+          to be observed in j being in i according to the model.
+        */
        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
+          has been calculated etc */
        for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 1248  double func( double *x)
+ Line 1503  double func( double *x)
            newm=savm;
            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 1305  double func( double *x)
+ Line 1560  double func( double *x)
          } else if  (s2==-2) {
            for (j=1,survp=0. ; j<=nlstate; j++)
-             survp += out[s1][j];
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-           lli= survp;
+           /*survp += out[s1][j]; */
-         }
+           lli= log(survp);
-         else if  (s2==-4) {
-           for (j=3,survp=0. ; j<=nlstate; j++)
-             survp += out[s1][j];
-           lli= survp;
          }
-         else if  (s2==-5) {
+         else if  (s2==-4) {
-           for (j=1,survp=0. ; j<=2; j++)
+           for (j=3,survp=0. ; j<=nlstate; j++)
-             survp += out[s1][j];
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-           lli= survp;
+           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 1472  double funcone( double *x)
+ Line 1727  double funcone( double *x)
  {
    /* Same as likeli but slower because of a lot of printf and if */
    int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double lli; /* Individual log likelihood */
    double llt;
- Line 1516  double funcone( double *x)
+ Line 1771  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 1524  double funcone( double *x)
+ Line 1783  double funcone( double *x)
          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
        } else if (mle==4){  /* mle=4 no inter-extrapolation */
          lli=log(out[s1][s2]); /* Original formula */
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+       } else{  /* mle=0 back to 1 */
-         lli=log(out[s1][s2]); /* Original formula */
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         /*lli=log(out[s1][s2]); */ /* Original formula */
        } /* End of if */
        ipmx +=1;
        sw += weight[i];
        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       /*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 1618  void mlikeli(FILE *ficres,double p[], in
+ Line 1878  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 1734  double hessii(double x[], double delta,
+ Line 1995  double hessii(double x[], double delta,
    int i;
    int l=1, lmax=20;
    double k1,k2;
-   double p2[NPARMAX+1];
+   double p2[MAXPARM+1]; /* identical to x */
    double res;
    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
    double fx;
- Line 1755  double hessii(double x[], double delta,
+ Line 2016  double hessii(double x[], double delta,
        /*res= (k1-2.0*fx+k2)/delt/delt; */
        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
- #ifdef DEBUG
+ #ifdef DEBUGHESS
        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
  #endif
- Line 1781  double hessij( double x[], double delti[
+ Line 2042  double hessij( double x[], double delti[
    int i;
    int l=1, l1, lmax=20;
    double k1,k2,k3,k4,res,fx;
-   double p2[NPARMAX+1];
+   double p2[MAXPARM+1];
    int k;
    fx=func(x);
- Line 1885  void lubksb(double **a, int n, int *indx
+ Line 2146  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, char strstart[])
  {  /* Some frequencies */
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   int i, m, jk, k1,i1, j1, bool, z1,j;
    int first;
    double ***freq; /* Frequencies */
    double *pp, **prop;
    double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   FILE *ficresp;
    char fileresp[FILENAMELENGTH];
    pp=vector(1,nlstate);
- Line 1959  void  freqsummary(char fileres[], int ia
+ Line 2224  void  freqsummary(char fileres[], int ia
        }
        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
- fprintf(ficresp, "#Local time at start: %s", strstart);
+       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 1988  fprintf(ficresp, "#Local time at start:
+ Line 2253  fprintf(ficresp, "#Local time at start:
              pos += freq[jk][m][i];
            if(pp[jk]>=1.e-10){
              if(first==1){
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              }
              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
            }else{
- Line 2059  void prevalence(double ***probs, double
+ Line 2324  void prevalence(double ***probs, double
       We still use firstpass and lastpass as another selection.
    */
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+   int i, m, jk, k1, i1, j1, bool, z1,j;
    double ***freq; /* Frequencies */
    double *pp, **prop;
    double pos,posprop;
- Line 2117  void prevalence(double ***probs, double
+ Line 2382  void prevalence(double ***probs, double
            if( i <=  iagemax){
              if(posprop>=1.e-5){
                probs[i][jk][j1]= prop[jk][i]/posprop;
-             }
+             } else
+               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
            }
          }/* end jk */
        }/* end i */
- Line 2172  void  concatwav(int wav[], int **dh, int
+ Line 2438  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 2199  void  concatwav(int wav[], int **dh, int
+ Line 2465  void  concatwav(int wav[], int **dh, int
                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 2211  void  concatwav(int wav[], int **dh, int
+ Line 2483  void  concatwav(int wav[], int **dh, int
  /*        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 2230  void  concatwav(int wav[], int **dh, int
+ Line 2508  void  concatwav(int wav[], int **dh, int
              dh[mi][i]=jk;
              bh[mi][i]=0;
            }else{ /* We want a negative bias in order to only have interpolation ie
-                   * at the price of an extra matrix product in likelihood */
+                   * to avoid the price of an extra matrix product in likelihood */
              dh[mi][i]=jk+1;
              bh[mi][i]=ju;
            }
- Line 2255  void  concatwav(int wav[], int **dh, int
+ Line 2533  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 ****************************/
  void tricode(int *Tvar, int **nbcode, int imx)
  {
+   /* Uses cptcovn+2*cptcovprod as the number of covariates */
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+   /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
-   int cptcode=0;
+   int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+   int modmaxcovj=0; /* Modality max of covariates j */
    cptcoveff=0;
    for (k=0; k<maxncov; k++) Ndum[k]=0;
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+   for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+   for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
-                                modality*/
+                                modality of this covariate Vj*/
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
-       Ndum[ij]++; /*store the modality */
+                                       modality of the nth covariate of individual i. */
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+       if (ij > modmaxcovj) modmaxcovj=ij;
-                                        Tvar[j]. If V=sex and male is 0 and
+       /* getting the maximum value of the modality of the covariate
-                                        female is 1, then  cptcode=1.*/
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-     }
+          female is 1, then modmaxcovj=1.*/
+     }
-     for (i=0; i<=cptcode; i++) {
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+     for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
-     }
+       if( Ndum[i] != 0 )
+         ncodemax[j]++;
+       /* Number of modalities of the j th covariate. In fact
+          ncodemax[j]=2 (dichotom. variables only) but it could be more for
+          historical reasons */
+     } /* Ndum[-1] number of undefined modalities */
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
      ij=1;
-     for (i=1; i<=ncodemax[j]; i++) {
+     for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
-       for (k=0; k<= maxncov; k++) {
+       for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
-         if (Ndum[k] != 0) {
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-           nbcode[Tvar[j]][ij]=k;
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+                                      k is a modality. If we have model=V1+V1*sex
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
            ij++;
          }
          if (ij > ncodemax[j]) break;
-       }
+       }  /* end of loop on */
-     }
+     } /* end of loop on modality */
-   }
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+   for (k=0; k< maxncov; k++) Ndum[k]=0;
-  for (i=1; i<=ncovmodel-2; i++) {
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
     /* 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];
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
     Ndum[ij]++;
   }
   ij=1;
-  for (i=1; i<= maxncov; i++) {
+  for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     if((Ndum[i]!=0) && (i<=ncovcol)){
       Tvaraff[ij]=i; /*For printing */
       ij++;
     }
   }
+  ij--;
-  cptcoveff=ij-1; /*Number of simple covariates*/
+  cptcoveff=ij; /*Number of simple covariates*/
  }
  /*********** 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,char strstart[] )
+ void evsij(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;
+   int nhstepma, nstepma; /* Decreasing with age */
+   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;
+   /* 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 */
+ /* nhstepm age range expressed in number of stepm */
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+   /* 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 ++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     /* if (stepm >= YEARM) hstepm=1;*/
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
+     /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
+     hpxij(p3mat,nhstepma,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(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;
+   int nhstepma, nstepma; /* Decreasing with age */
    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,"# Local time at start: %s", strstart);
+   pstamp(ficresstdeij);
-   fprintf(ficreseij,"# Health expectancies\n");
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-   fprintf(ficreseij,"# Age");
+   fprintf(ficresstdeij,"# Age");
-   for(i=1; i<=nlstate;i++)
+   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 2375  void evsij(char fileres[], double ***eij
+ Line 2793  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-bage)*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;*/
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3matp=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);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+   for (age=bage; age<=fage; age ++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      /* 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 */
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-     gp=matrix(0,nhstepm,1,nlstate*nlstate);
-     gm=matrix(0,nhstepm,1,nlstate*nlstate);
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
+     /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      /* 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 2453  void evsij(char fileres[], double ***eij
+ Line 2863  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 2546  void varevsij(char optionfilefiname[], d
+ Line 2978  void varevsij(char optionfilefiname[], d
    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
+   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 2556  void varevsij(char optionfilefiname[], d
+ Line 2988  void varevsij(char optionfilefiname[], d
    }
    fprintf(ficresprobmorprev,"\n");
    fprintf(ficgp,"\n# Routine varevsij");
-  fprintf(fichtm, "#Local time at start: %s", strstart);
+   /* 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);
-  fprintf(ficresvij, "#Local time at start: %s", strstart);
+   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 (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
+   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 2588  void varevsij(char optionfilefiname[], d
+ Line 3024  void varevsij(char optionfilefiname[], d
    /* 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
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-      and note for a fixed period like k years */
    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       survival function given by stepm (the optimization length). Unfortunately it
       means that if the survival funtion is printed every two years of age and if
- Line 2655  void varevsij(char optionfilefiname[], d
+ Line 3090  void varevsij(char optionfilefiname[], d
          }
        }
-       for(j=1; j<= nlstate; j++){
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
          for(h=0; h<=nhstepm; h++){
            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
- Line 2765  void varevsij(char optionfilefiname[], d
+ Line 3200  void varevsij(char optionfilefiname[], d
    free_vector(gmp,nlstate+1,nlstate+ndeath);
    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
- Line 2807  void varprevlim(char fileres[], double *
+ Line 3242  void varprevlim(char fileres[], double *
    double **gradg, **trgradg;
    double age,agelim;
    int theta;
-   fprintf(ficresvpl, "#Local time at start: %s", strstart);
-   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 2922  void varprob(char optionfilefiname[], do
+ Line 3358  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);
-   fprintf(ficresprob, "#Local time at start: %s", strstart);
+   pstamp(ficresprob);
    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
    fprintf(ficresprob,"# Age");
-   fprintf(ficresprobcov, "#Local time at start: %s", strstart);
+   pstamp(ficresprobcov);
    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
    fprintf(ficresprobcov,"# Age");
-   fprintf(ficresprobcor, "#Local time at start: %s", strstart);
+   pstamp(ficresprobcor);
    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-   fprintf(ficresprobcov,"# Age");
+   fprintf(ficresprobcor,"# Age");
    for(i=1; i<=nlstate;i++)
- Line 2943  void varprob(char optionfilefiname[], do
+ Line 3379  void varprob(char optionfilefiname[], do
    fprintf(ficresprobcov,"\n");
    fprintf(ficresprobcor,"\n");
   */
-  xp=vector(1,npar);
+   xp=vector(1,npar);
    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
- Line 3096  To be simple, these graphs help to under
+ Line 3532  To be simple, these graphs help to under
        /* Confidence intervalle of pij  */
        /*
-         fprintf(ficgp,"\nset noparametric;unset label");
+         fprintf(ficgp,"\nunset parametric;unset label");
          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
- Line 3127  To be simple, these graphs help to under
+ Line 3563  To be simple, these graphs help to under
                    /* Computing eigen value of matrix of covariance */
                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                   if ((lc2 <0) || (lc1 <0) ){
+                     printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+                     fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
+                     lc1=fabs(lc1);
+                     lc2=fabs(lc2);
+                   }
                    /* Eigen vectors */
                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                    /*v21=sqrt(1.-v11*v11); *//* error */
- Line 3181  To be simple, these graphs help to under
+ Line 3624  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 3199  void printinghtml(char fileres[], char t
+ Line 3644  void printinghtml(char fileres[], char t
                    double jprev2, double mprev2,double anprev2){
    int jj1, k1, i1, cpt;
-    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 \
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+ </ul>");
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\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 ",
             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
     fprintf(fichtm,"\
   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
     fprintf(fichtm,"\
-  - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
     fprintf(fichtm,"\
-  - Life expectancies by age and initial health status (estepm=%2d months): \
+  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
-    <a href=\"%s\">%s</a> <br>\n</li>",
+    <a href=\"%s\">%s</a> <br>\n",
             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+    fprintf(fichtm,"\
+  - Population projections by age and states: \
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
- Line 3229  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3680  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);
       }
     } /* end i1 */
   }/* End k1 */
- Line 3250  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3701  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   fprintf(fichtm,"\
- \n<br><li><h4> Result files (second order: variances)</h4>\n\
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
- Line 3263  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3714  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
   fprintf(fichtm,"\
-  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+  - 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), e<sup>ij</sup> 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,"\
-  - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (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",
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   fprintf(fichtm,"\
-  - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
+  - 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 3300  prevalence (with 95%% confidence interva
+ Line 3759  prevalence (with 95%% confidence interva
  <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>\
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+ true period expectancies (those weighted with period prevalences are also\
+  drawn in addition to the population based expectancies computed using\
+  observed and cahotic prevalences: %s%d.png<br>\
  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     } /* end i1 */
   }/* End k1 */
- Line 3312  health expectancies in states (1) and (2
+ Line 3774  health expectancies in states (1) and (2
  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-   int ng;
+   int ng=0;
  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
- Line 3339  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 3801  plot [%.f:%.f] \"%s\" every :::%d::%d u
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-        else 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 3389  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 3851  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 3403  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 3866  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 3964  double gompertz(double x[])
+ Line 4429  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;*/
- Line 3976  double gompertz(double x[])
+ Line 4442  double gompertz(double x[])
    for (i=1;i<=imx ; i++)
      {
-       if (cens[i]==1 & wav[i]>1)
+       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)
+       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 && 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]);*/
        }
- Line 3994  double gompertz(double x[])
+ Line 4461  double gompertz(double x[])
    return -2*L*num/sump;
  }
+ #ifdef GSL
+ /******************* Gompertz_f Likelihood ******************************/
+ double gompertz_f(const gsl_vector *v, void *params)
+ {
+   double A,B,LL=0.0,sump=0.,num=0.;
+   double *x= (double *) v->data;
+   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]);*/
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
+   for (i=1;i<=imx ; i++)
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
+       if (cens[i] == 0 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
+         LL=LL+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);*/
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
+   return -2*LL*num/sump;
+ }
+ #endif
  /******************* Printing html file ***********/
  void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
- Line 4009  void printinghtmlmort(char fileres[], ch
+ Line 4517  void printinghtmlmort(char fileres[], ch
  fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-  fprintf(fichtm,"\nAge   lx     qx    dx    Lx     Tx     e(x)<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]);
- Line 4041  void printinggnuplotmort(char fileres[],
+ Line 4549  void printinggnuplotmort(char fileres[],
  }
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
+ {
+   /*-------- data file ----------*/
+   FILE *fic;
+   char dummy[]="                         ";
+   int i, j, n;
+   int linei, month, year,iout;
+   char line[MAXLINE], linetmp[MAXLINE];
+   char stra[80], strb[80];
+   char *stratrunc;
+   int lstra;
- /***********************************************/
+   if((fic=fopen(datafile,"r"))==NULL)    {
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+   }
+   i=1;
+   linei=0;
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+     linei=linei+1;
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+       if(line[j] == '\t')
+         line[j] = ' ';
+     }
+     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;
+     }
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
+     for (j=0; line[j]!='\0';j++){
+       line[j]=linetmp[j];
+     }
+     for (j=maxwav;j>=1;j--){
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
+       }else{
+         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 '%s' at line number %ld 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);
+           fprintf(ficlog,"Error reading data around '%s' at line number %ld 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);fflush(ficlog);
+           return 1;
+         }
+       }
+       s[j][i]=lval;
+       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 for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+         fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
+         return 1;
+       }
+       anint[j][i]= (double) year;
+       mint[j][i]= (double)month;
+       strcpy(line,stra);
+     } /* ENd Waves */
+     cutv(stra, strb,line,' ');
+     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 for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+         fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 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 for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     if (year==9999) {
+       printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     annais[i]=(double)(year);
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     errno=0;
+     dval=strtod(strb,&endptr);
+     if( strb[0]=='\0' || (*endptr != '\0')){
+       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fflush(ficlog);
+       return 1;
+     }
+     weight[i]=dval;
+     strcpy(line,stra);
+     for (j=ncovcol;j>=1;j--){
+       cutv(stra, strb,line,' ');
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
+       }else{
+         errno=0;
+         lval=strtol(strb,&endptr,10);
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
+           fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
+           return 1;
+         }
+       }
+       if(lval <-1 || lval >1){
+         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n \
+  Exiting.\n",lval,linei, i,line,j);
+         fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n \
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
+         return 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 */
+   *imax=i-1; /* Number of individuals */
+   fclose(fic);
+   return (0);
+   endread:
+     printf("Exiting readdata: ");
+     fclose(fic);
+     return (1);
+ }
+ int decodemodel ( char model[], int lastobs)
+ {
+   int i, j, k;
+   int i1, j1, k1, k2;
+   char modelsav[80];
+    char stra[80], strb[80], strc[80], strd[80],stre[80];
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
+     j=0, j1=0, k1=1, k2=1;
+     j=nbocc(model,'+'); /* j=Number of '+' */
+     j1=nbocc(model,'*'); /* j1=Number of '*' */
+     cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
+                   but the covariates which are product must be computed and stored. */
+     cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
+     strcpy(modelsav,model);
+     if (strstr(model,"AGE") !=0){
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
+       return 1;
+     }
+     /* This loop fills the array Tvar from the string 'model'.*/
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
+     /*  k=1 Tvar[1]=2 (from V2) */
+     /*  k=5 Tvar[5] */
+     /* for (k=1; k<=cptcovn;k++) { */
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+     /*  } */
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+     for(k=cptcovn; k>=1;k--){
+       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4
+                                     */
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+       /*scanf("%d",i);*/
+       if (strchr(strb,'*')) {  /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
+         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+         if (strcmp(strc,"age")==0) { /* Vn*age */
+           cptcovprod--;
+           cutv(strb,stre,strd,'V'); /* stre="V3" */
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
+           cptcovage++; /* Sums the number of covariates which include age as a product */
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
+           /*printf("stre=%s ", stre);*/
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+           cptcovprod--;
+           cutv(strb,stre,strc,'V');
+           Tvar[k]=atoi(stre);
+           cptcovage++;
+           Tage[cptcovage]=k;
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+           Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
+                                   because this model-covariate is a construction we invent a new column
+                                   ncovcol + k1
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+           Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
+           Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
+           Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
+           Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
+           for (i=1; i<=lastobs;i++){
+             /* Computes the new covariate which is a product of
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+           }
+           k1++;
+           k2=k2+2;
+         } /* End age is not in the model */
+       } /* End if model includes a product */
+       else { /* no more sum */
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+        /*  scanf("%d",i);*/
+         cutv(strd,strc,strb,'V');
+         Tvar[k]=atoi(strc);
+       }
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+         scanf("%d",i);*/
+     } /* end of loop + */
+   } /* end model */
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   printf("cptcovprod=%d ", cptcovprod);
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   scanf("%d ",i);*/
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
+   endread:
+     printf("Exiting decodemodel: ");
+     return (1);
+ }
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+ {
+   int i, m;
+   for (i=1; i<=imx; i++) {
+     for(m=2; (m<= maxwav); m++) {
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+         anint[m][i]=9999;
+         s[m][i]=-1;
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+         *nberr++;
+         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+         s[m][i]=-1;
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+         *nberr++;
+         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+       }
+     }
+   }
+   for (i=1; i<=imx; i++)  {
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     for(m=firstpass; (m<= lastpass); m++){
+       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)
+               agev[m][i]=agedc[i];
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+             else {
+               if ((int)andc[i]!=9999){
+                 nbwarn++;
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+                 agev[m][i]=-1;
+               }
+             }
+         }
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
+                                  years but with the precision of a month */
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+             agev[m][i]=1;
+           else if(agev[m][i] < *agemin){
+             *agemin=agev[m][i];
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
+           }
+           else if(agev[m][i] >*agemax){
+             *agemax=agev[m][i];
+             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+           }
+           /*agev[m][i]=anint[m][i]-annais[i];*/
+           /*     agev[m][i] = age[i]+2*m;*/
+         }
+         else { /* =9 */
+           agev[m][i]=1;
+           s[m][i]=-1;
+         }
+       }
+       else /*= 0 Unknown */
+         agev[m][i]=1;
+     }
+   }
+   for (i=1; i<=imx; i++)  {
+     for(m=firstpass; (m<=lastpass); m++){
+       if (s[m][i] > (nlstate+ndeath)) {
+         *nberr++;
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         return 1;
+       }
+     }
+   }
+   /*for (i=1; i<=imx; i++){
+   for (m=firstpass; (m<lastpass); m++){
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+ }
+ }*/
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   return (0);
+   endread:
+     printf("Exiting calandcheckages: ");
+     return (1);
+ }
+ /***********************************************/
  /**************** Main Program *****************/
  /***********************************************/
  int main(int argc, char *argv[])
  {
+ #ifdef GSL
+   const gsl_multimin_fminimizer_type *T;
+   size_t iteri = 0, it;
+   int rval = GSL_CONTINUE;
+   int status = GSL_SUCCESS;
+   double ssval;
+ #endif
    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 linei, month, year,iout;
    int jj, ll, li, lj, lk, imk;
    int numlinepar=0; /* Current linenumber of parameter file */
    int itimes;
    int NDIM=2;
+   int vpopbased=0;
    char ca[32], cb[32], cc[32];
    /*  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 4073  int main(int argc, char *argv[])
+ Line 4980  int main(int argc, char *argv[])
    char line[MAXLINE], linepar[MAXLINE];
    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[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;
    int ju,jl, mi;
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   int i1,j1, jk,aa,bb, stepsize, ij;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
    int mobilav=0,popforecast=0;
    int hstepm, nhstepm;
- Line 4090  int main(int argc, char *argv[])
+ Line 4998  int main(int argc, char *argv[])
    double bage, fage, age, agelim, agebase;
    double ftolpl=FTOL;
    double **prlim;
-   double *severity;
    double ***param; /* Matrix of parameters */
    double  *p;
    double **matcov; /* Matrix of covariance */
- Line 4107  int main(int argc, char *argv[])
+ Line 5014  int main(int argc, char *argv[])
    char z[1]="c", occ;
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+   /*char  *strt;*/
-   char strstart[80], *strt, strtend[80];
+   char strtend[80];
-   char *stratrunc;
-   int lstra;
    long total_usecs;
- Line 4150  int main(int argc, char *argv[])
+ Line 5055  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 4160  int main(int argc, char *argv[])
+ Line 5075  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("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,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 4256  int main(int argc, char *argv[])
+ Line 5177  int main(int argc, char *argv[])
    covar=matrix(0,NCOVMAX,1,n);
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
+      v1+v2*age+v2*v3 makes cptcovn = 3
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+   */
+   if (strlen(model)>1)
+     cptcovn=nbocc(model,'+')+1;
+   /* ncovprod */
+   ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
+     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fflush(stdout);
+     fclose (ficlog);
+     goto end;
+   }
    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)*/
- Line 4273  int main(int argc, char *argv[])
+ Line 5205  int main(int argc, char *argv[])
      free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
      fclose (ficparo);
      fclose (ficlog);
+     goto end;
      exit(0);
    }
    else if(mle==-3) {
- Line 4303  int main(int argc, char *argv[])
+ Line 5236  int main(int argc, char *argv[])
          j++;
          fscanf(ficpar,"%1d%1d",&i1,&j1);
          if ((i1 != i) && (j1 != j)){
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+ It might be a problem of design; if ncovcol and the model are correct\n \
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
            exit(1);
          }
          fprintf(ficparo,"%1d%1d",i1,j1);
- Line 4330  int main(int argc, char *argv[])
+ Line 5265  int main(int argc, char *argv[])
      }
      fflush(ficlog);
      p=param[1][1];
      /* Reads comments: lines beginning with '#' */
- Line 4386  int main(int argc, char *argv[])
+ Line 5320  int main(int argc, char *argv[])
      ungetc(c,ficpar);
      matcov=matrix(1,npar,1,npar);
+     for(i=1; i <=npar; i++)
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
      for(i=1; i <=npar; i++){
        fscanf(ficpar,"%s",&str);
        if(mle==1)
- Line 4429  int main(int argc, char *argv[])
+ Line 5366  int main(int argc, char *argv[])
      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;
-     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
-   }
    n= lastobs;
-   severity = vector(1,maxwav);
-   outcome=imatrix(1,maxwav+1,1,n);
    num=lvector(1,n);
    moisnais=vector(1,n);
    annais=vector(1,n);
- Line 4449  int main(int argc, char *argv[])
+ Line 5379  int main(int argc, char *argv[])
    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
    mint=matrix(1,maxwav,1,n);
    anint=matrix(1,maxwav,1,n);
-   s=imatrix(1,maxwav+1,1,n);
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
    tab=ivector(1,NCOVMAX);
-   ncodemax=ivector(1,8);
+   ncodemax=ivector(1,8); /* hard coded ? */
-   i=1;
-   while (fgets(line, MAXLINE, fic) != NULL)    {
-     if ((i >= firstobs) && (i <=lastobs)) {
-       for(j=0; line[j] != '\n';j++){  /* Untabifies line */
-         if(line[j] == '\t')
-           line[j] = ' ';
-       }
-       for (j=maxwav;j>=1;j--){
-         cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
-         strcpy(line,stra);
-         cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
-         cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
-       }
-       cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
-       for (j=ncovcol;j>=1;j--){
-         cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
-       }
-       lstra=strlen(stra);
-       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-         stratrunc = &(stra[lstra-9]);
-         num[i]=atol(stratrunc);
-       }
-       else
-         num[i]=atol(stra);
-       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
-       i=i+1;
-     }
-   }
-   /* printf("ii=%d", ij);
-      scanf("%d",i);*/
-   imx=i-1; /* Number of individuals */
-   /* for (i=1; i<=imx; i++){
+   /* Reads data from file datafile */
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+     goto end;
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
-     }*/
-    /*  for (i=1; i<=imx; i++){
-      if (s[4][i]==9)  s[4][i]=-1;
-      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
-  for (i=1; i<=imx; i++)
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
-      else weight[i]=1;*/
-   /* Calculation of the number of parameter from char model*/
+   /* 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 */
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
+         k=3 V4 Tvar[k=3]= 4 (from V4)
+         k=2 V1 Tvar[k=2]= 1 (from V1)
+         k=1 Tvar[1]=2 (from V2)
+     */
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+   */
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
+     Tvar[3=V1*V4]=4+1 etc */
    Tprod=ivector(1,15);
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+   */
    Tvaraff=ivector(1,15);
-   Tvard=imatrix(1,15,1,2);
+   Tvard=imatrix(1,15,1,2); /* For V3*V2 Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-   Tage=ivector(1,15);
+   Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+covariates (3 plus signs)
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
-     j=0, j1=0, k1=1, k2=1;
+                       */
-     j=nbocc(model,'+'); /* j=Number of '+' */
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
-     cptcovn=j+1;
-     cptcovprod=j1; /*Number of products */
-     strcpy(modelsav,model);
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
-       printf("Error. Non available option model=%s ",model);
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
-       goto end;
-     }
-     /* This loop fills the array Tvar from the string 'model'.*/
-     for(i=(j+1); i>=1;i--){
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-       /*scanf("%d",i);*/
-       if (strchr(strb,'*')) {  /* Model includes a product */
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
-         if (strcmp(strc,"age")==0) { /* Vn*age */
-           cptcovprod--;
-           cutv(strb,stre,strd,'V');
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
-           cptcovage++;
-             Tage[cptcovage]=i;
-             /*printf("stre=%s ", stre);*/
-         }
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
-           cptcovprod--;
-           cutv(strb,stre,strc,'V');
-           Tvar[i]=atoi(stre);
-           cptcovage++;
-           Tage[cptcovage]=i;
-         }
-         else {  /* Age is not in the model */
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
-           Tvar[i]=ncovcol+k1;
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
-           Tprod[k1]=i;
-           Tvard[k1][1]=atoi(strc); /* m*/
-           Tvard[k1][2]=atoi(stre); /* n */
-           Tvar[cptcovn+k2]=Tvard[k1][1];
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
-           for (k=1; k<=lastobs;k++)
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
-           k1++;
-           k2=k2+2;
-         }
-       }
-       else { /* no more sum */
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-        /*  scanf("%d",i);*/
-       cutv(strd,strc,strb,'V');
-       Tvar[i]=atoi(strc);
-       }
-       strcpy(modelsav,stra);
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-         scanf("%d",i);*/
-     } /* end of loop + */
-   } /* end model */
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-   printf("cptcovprod=%d ", cptcovprod);
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-   scanf("%d ",i);
+   if(decodemodel(model, lastobs) == 1)
-   fclose(fic);*/
+     goto end;
+   if((double)(lastobs-imx)/(double)imx > 1.10){
+     nbwarn++;
+     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+   }
      /*  if(mle==1){*/
-   if (weightopt != 1) { /* Maximisation without weights*/
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
-     for(i=1;i<=n;i++) weight[i]=1.0;
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
    }
      /*-calculation of age at interview from date of interview and age at death -*/
    agev=matrix(1,maxwav,1,imx);
-   for (i=1; i<=imx; i++) {
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
-     for(m=2; (m<= maxwav); m++) {
+     goto end;
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-         anint[m][i]=9999;
-         s[m][i]=-1;
-       }
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         nberr++;
-         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-         s[m][i]=-1;
-       }
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-         nberr++;
-         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-       }
-     }
-   }
-   for (i=1; i<=imx; i++)  {
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-     for(m=firstpass; (m<= lastpass); m++){
-       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)
-               agev[m][i]=agedc[i];
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-             else {
-               if ((int)andc[i]!=9999){
-                 nbwarn++;
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-                 agev[m][i]=-1;
-               }
-             }
-         }
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
-                                  years but with the precision of a
-                                  month */
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-             agev[m][i]=1;
-           else if(agev[m][i] <agemin){
-             agemin=agev[m][i];
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
-           }
-           else if(agev[m][i] >agemax){
-             agemax=agev[m][i];
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
-           }
-           /*agev[m][i]=anint[m][i]-annais[i];*/
-           /*     agev[m][i] = age[i]+2*m;*/
-         }
-         else { /* =9 */
-           agev[m][i]=1;
-           s[m][i]=-1;
-         }
-       }
-       else /*= 0 Unknown */
-         agev[m][i]=1;
-     }
-   }
-   for (i=1; i<=imx; i++)  {
-     for(m=firstpass; (m<=lastpass); m++){
-       if (s[m][i] > (nlstate+ndeath)) {
-         nberr++;
-         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-         goto end;
-       }
-     }
-   }
-   /*for (i=1; i<=imx; i++){
-   for (m=firstpass; (m<lastpass); m++){
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
- }
- }*/
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
    agegomp=(int)agemin;
-   free_vector(severity,1,maxwav);
-   free_imatrix(outcome,1,maxwav+1,1,n);
    free_vector(moisnais,1,n);
    free_vector(annais,1,n);
    /* free_matrix(mint,1,maxwav,1,n);
- Line 4707  int main(int argc, char *argv[])
+ Line 5454  int main(int argc, char *argv[])
    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-   Tcode=ivector(1,100);
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
    ncodemax[1]=1;
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);
- Line 4717  int main(int argc, char *argv[])
+ Line 5463  int main(int argc, char *argv[])
    h=0;
    m=pow(2,cptcoveff);
-   for(k=1;k<=cptcoveff; k++){
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-     for(i=1; i <=(m/pow(2,k));i++){
+     for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
-       for(j=1; j <= ncodemax[k]; j++){
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
            h++;
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+           if (h>m) {
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+             h=1;
+             codtab[h][k]=j;
+             codtab[h][Tvar[k]]=j;
+           }
+           printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
          }
        }
      }
- Line 4732  int main(int argc, char *argv[])
+ Line 5482  int main(int argc, char *argv[])
       codtab[1][2]=1;codtab[2][2]=2; */
    /* for(i=1; i <=m ;i++){
       for(k=1; k <=cptcovn; k++){
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
       }
       printf("\n");
       }
- Line 4760  int main(int argc, char *argv[])
+ Line 5510  int main(int argc, char *argv[])
      strcat(optionfilehtm,"-mort");
    strcat(optionfilehtm,".htm");
    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+     printf("Problem with %s \n",optionfilehtm);
+     exit(0);
    }
    strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
- Line 4769  int main(int argc, char *argv[])
+ Line 5520  int main(int argc, char *argv[])
      printf("Problem with %s \n",optionfilehtmcov), exit(0);
    }
    else{
-   fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
-           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
  \n\
  <hr  size=\"2\" color=\"#EC5E5E\">\
   <ul><li><h4>Parameter files</h4>\n\
+  - 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,\
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
            fileres,fileres,\
            filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
    fflush(fichtm);
- Line 4815  Interval (in months) between two waves:
+ Line 5568  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*/
    if (mle==-3){
      ximort=matrix(1,NDIM,1,NDIM);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
      cens=ivector(1,n);
      ageexmed=vector(1,n);
      agecens=vector(1,n);
- Line 4824  Interval (in months) between two waves:
+ Line 5579  Interval (in months) between two waves:
      for (i=1; i<=imx; i++){
        dcwave[i]=-1;
-       for (j=1; j<=lastpass; j++)
+       for (m=firstpass; m<=lastpass; m++)
-         if (s[j][i]>nlstate) {
+         if (s[m][i]>nlstate) {
-           dcwave[i]=j;
+           dcwave[i]=m;
            /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
            break;
          }
- Line 4835  Interval (in months) between two waves:
+ Line 5590  Interval (in months) between two waves:
      for (i=1; i<=imx; i++) {
        if (wav[i]>0){
          ageexmed[i]=agev[mw[1][i]][i];
-         j=wav[i];agecens[i]=1.;
+         j=wav[i];
-         if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
+         agecens[i]=1.;
-         cens[i]=1;
+         if (ageexmed[i]> 1 && wav[i] > 0){
-         if (ageexmed[i]<1) cens[i]=-1;
+           agecens[i]=agev[mw[j][i]][i];
-         if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
+           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;
      }
- Line 4849  Interval (in months) between two waves:
+ Line 5608  Interval (in months) between two waves:
        for (j=1;j<=NDIM;j++)
          ximort[i][j]=(i == j ? 1.0 : 0.0);
      }
-     p[1]=0.1; p[2]=0.1;
+     p[1]=0.0268; p[NDIM]=0.083;
      /*printf("%lf %lf", p[1], p[2]);*/
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ #ifdef GSL
-   strcpy(filerespow,"pow-mort");
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
-   strcat(filerespow,fileres);
+ #elsedef
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-     printf("Problem with resultfile: %s\n", filerespow);
+ #endif
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+     strcpy(filerespow,"pow-mort");
-   }
+     strcat(filerespow,fileres);
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   /*  for (i=1;i<=nlstate;i++)
+       printf("Problem with resultfile: %s\n", filerespow);
-     for(j=1;j<=nlstate+ndeath;j++)
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     }
-   */
+ #ifdef GSL
-   fprintf(ficrespow,"\n");
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+ #elsedef
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
+     /*  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");
+ #ifdef GSL
+     /* gsl starts here */
+     T = gsl_multimin_fminimizer_nmsimplex;
+     gsl_multimin_fminimizer *sfm = NULL;
+     gsl_vector *ss, *x;
+     gsl_multimin_function minex_func;
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+     /* Initial vertex size vector */
+     ss = gsl_vector_alloc (NDIM);
+     if (ss == NULL){
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+     }
+     /* Set all step sizes to 1 */
+     gsl_vector_set_all (ss, 0.001);
+     /* Starting point */
+     x = gsl_vector_alloc (NDIM);
+     if (x == NULL){
+       gsl_vector_free(ss);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+     }
+     /* Initialize method and iterate */
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
+ /*     gsl_vector_set(x, 0, 0.0268); */
+ /*     gsl_vector_set(x, 1, 0.083); */
+     gsl_vector_set(x, 0, p[1]);
+     gsl_vector_set(x, 1, p[2]);
+     minex_func.f = &gompertz_f;
+     minex_func.n = NDIM;
+     minex_func.params = (void *)&p; /* ??? */
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+     printf("Iterations beginning .....\n\n");
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
+     iteri=0;
+     while (rval == GSL_CONTINUE){
+       iteri++;
+       status = gsl_multimin_fminimizer_iterate(sfm);
+       if (status) printf("error: %s\n", gsl_strerror (status));
+       fflush(0);
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+     gsl_vector_free(x); /* initial values */
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ #endif
      fclose(ficrespow);
-     hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
      for(i=1; i <=NDIM; i++)
        for(j=i+1;j<=NDIM;j++)
- Line 4889  Interval (in months) between two waves:
+ Line 5733  Interval (in months) between two waves:
      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);
+     lsurv=vector(1,AGESUP);
      lpop=vector(1,AGESUP);
      tpop=vector(1,AGESUP);
      lsurv[agegomp]=100000;
-      for (k=agegomp;k<=AGESUP;k++) {
+     for (k=agegomp;k<=AGESUP;k++) {
        agemortsup=k;
        if (p[1]*exp(p[2]*(k-agegomp))>1) break;
      }
-       for (k=agegomp;k<agemortsup;k++)
+     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;
+     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");
+     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,path); /* Even gnuplot wants a / */
+     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);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
    } /* Endof if mle==-3 */
-   else{ /* For mle >=1 */
+   else{ /* For mle >=1 */
+     globpr=0;/* debug */
      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++)
- Line 4962  lsurv=vector(1,AGESUP);
+ Line 5812  lsurv=vector(1,AGESUP);
            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);
            for(j=1; j <=ncovmodel; j++){
-             printf("%f ",p[jk]);
+             printf("%lf ",p[jk]);
-             fprintf(ficlog,"%f ",p[jk]);
+             fprintf(ficlog,"%lf ",p[jk]);
-             fprintf(ficres,"%f ",p[jk]);
+             fprintf(ficres,"%lf ",p[jk]);
              jk++;
            }
            printf("\n");
- Line 5156  lsurv=vector(1,AGESUP);
+ Line 6006  lsurv=vector(1,AGESUP);
      /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
      /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
      printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
      printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
- Line 5178  lsurv=vector(1,AGESUP);
+ Line 6028  lsurv=vector(1,AGESUP);
      fclose(ficres);
-     /*--------------- Prevalence limit  (stable prevalence) --------------*/
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
      strcpy(filerespl,"pl");
      strcat(filerespl,fileres);
      if((ficrespl=fopen(filerespl,"w"))==NULL) {
-       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
+       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, "#Local time at start: %s", strstart);
+     pstamp(ficrespl);
-     fprintf(ficrespl,"#Stable prevalence \n");
+     fprintf(ficrespl,"# Period (stable) prevalence \n");
      fprintf(ficrespl,"#Age ");
      for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
      fprintf(ficrespl,"\n");
- Line 5205  lsurv=vector(1,AGESUP);
+ Line 6055  lsurv=vector(1,AGESUP);
      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
          k=k+1;
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+         /* to clean */
+         printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
          fprintf(ficrespl,"\n#******");
          printf("\n#******");
          fprintf(ficlog,"\n#******");
- Line 5249  lsurv=vector(1,AGESUP);
+ Line 6100  lsurv=vector(1,AGESUP);
      hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
      /* hstepm=1;   aff par mois*/
-     fprintf(ficrespij, "#Local time at start: %s", strstart);
+     pstamp(ficrespij);
      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- Line 5311  lsurv=vector(1,AGESUP);
+ Line 6162  lsurv=vector(1,AGESUP);
      }
-     /*---------- Health expectancies and variances ------------*/
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
-     strcpy(filerest,"t");
+     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-     strcat(filerest,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((ficrest=fopen(filerest,"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 total LE resultfile: %s\n", filerest);goto end;
+     */
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     if (mobilav!=0) {
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
      }
-     printf("Computing Total LEs with variances: file '%s' \n", filerest);
-     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
+     /*---------- Health expectancies, no variances ------------*/
      strcpy(filerese,"e");
      strcat(filerese,fileres);
      if((ficreseij=fopen(filerese,"w"))==NULL) {
- Line 5331  lsurv=vector(1,AGESUP);
+ Line 6188  lsurv=vector(1,AGESUP);
      }
      printf("Computing Health Expectancies: result on file '%s' \n", filerese);
      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
+         fprintf(ficreseij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficreseij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       }
+     }
+     fclose(ficreseij);
+     /*---------- Health expectancies and variances ------------*/
+     strcpy(filerest,"t");
+     strcat(filerest,fileres);
+     if((ficrest=fopen(filerest,"w"))==NULL) {
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     }
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     strcpy(fileresstde,"stde");
+     strcat(fileresstde,fileres);
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     }
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"cve");
+     strcat(filerescve,fileres);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       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);
- Line 5341  lsurv=vector(1,AGESUP);
+ Line 6247  lsurv=vector(1,AGESUP);
      printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
      fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
-     */
-     if (mobilav!=0) {
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       }
-     }
      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
          k=k+1;
- Line 5363  lsurv=vector(1,AGESUP);
+ Line 6255  lsurv=vector(1,AGESUP);
            fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          fprintf(ficrest,"******\n");
-         fprintf(ficreseij,"\n#****** ");
+         fprintf(ficresstdeij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrescveij,"\n#****** ");
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficreseij,"******\n");
+           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficresstdeij,"******\n");
+         fprintf(ficrescveij,"******\n");
          fprintf(ficresvij,"\n#****** ");
          for(j=1;j<=cptcoveff;j++)
- Line 5375  lsurv=vector(1,AGESUP);
+ Line 6271  lsurv=vector(1,AGESUP);
          eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
          oldm=oldms;savm=savms;
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
          vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
+         pstamp(ficrest);
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-         if(popbased==1){
+           oldm=oldms;savm=savms;
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
-         }
+           if(vpopbased==1)
+             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
-         fprintf(ficrest, "#Local time at start: %s", strstart);
+           else
-         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           fprintf(ficrest,"# Age e.. (std) ");
-         fprintf(ficrest,"\n");
+           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           fprintf(ficrest,"\n");
-         epj=vector(1,nlstate+1);
+           epj=vector(1,nlstate+1);
-         for(age=bage; age <=fage ;age++){
+           for(age=bage; age <=fage ;age++){
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-           if (popbased==1) {
+             if (vpopbased==1) {
-             if(mobilav ==0){
+               if(mobilav ==0){
-               for(i=1; i<=nlstate;i++)
+                 for(i=1; i<=nlstate;i++)
-                 prlim[i][i]=probs[(int)age][i][k];
+                   prlim[i][i]=probs[(int)age][i][k];
-             }else{ /* mobilav */
+               }else{ /* mobilav */
-               for(i=1; i<=nlstate;i++)
+                 for(i=1; i<=nlstate;i++)
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+                   prlim[i][i]=mobaverage[(int)age][i][k];
+               }
              }
-           }
-           fprintf(ficrest," %4.0f",age);
+             fprintf(ficrest," %4.0f",age);
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+               for(i=1, epj[j]=0.;i <=nlstate;i++) {
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               }
+               epj[nlstate+1] +=epj[j];
              }
-             epj[nlstate+1] +=epj[j];
-           }
-           for(i=1, vepp=0.;i <=nlstate;i++)
+             for(i=1, vepp=0.;i <=nlstate;i++)
-             for(j=1;j <=nlstate;j++)
+               for(j=1;j <=nlstate;j++)
-               vepp += vareij[i][j][(int)age];
+                 vepp += vareij[i][j][(int)age];
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
-           for(j=1;j <=nlstate;j++){
+             for(j=1;j <=nlstate;j++){
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             }
+             fprintf(ficrest,"\n");
            }
-           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);
- Line 5432  lsurv=vector(1,AGESUP);
+ Line 6330  lsurv=vector(1,AGESUP);
      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 stable prevalence------*/
+     /*------- Variance of period (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);
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
        exit(0);
      }
-     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
+     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++){
- Line 5469  lsurv=vector(1,AGESUP);
+ Line 6368  lsurv=vector(1,AGESUP);
      free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
    }  /* mle==-3 arrives here for freeing */
+  endfree:
+   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);*/
- Line 5486  lsurv=vector(1,AGESUP);
+ Line 6386  lsurv=vector(1,AGESUP);
      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);
- Line 5515  lsurv=vector(1,AGESUP);
+ Line 6415  lsurv=vector(1,AGESUP);
    fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
    /*  printf("Total time was %d uSec.\n", total_usecs);*/
  /*   if(fileappend(fichtm,optionfilehtm)){ */
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
    fclose(fichtm);
+   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
    fclose(fichtmcov);
    fclose(ficgp);
    fclose(ficlog);
    /*------ End -----------*/
-   chdir(path);
-   strcpy(plotcmd,"\"");
+    printf("Before Current directory %s!\n",pathcd);
-   strcat(plotcmd,pathimach);
+    if(chdir(pathcd) != 0)
-   strcat(plotcmd,GNUPLOTPROGRAM);
+     printf("Can't move to directory %s!\n",path);
-   strcat(plotcmd,"\"");
+   if(getcwd(pathcd,MAXLINE) > 0)
-   strcat(plotcmd," ");
+     printf("Current directory %s!\n",pathcd);
-   strcat(plotcmd,optionfilegnuplot);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
-   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
+   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') {

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	Added in v.1.138