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Diff for /imach/src/imach.c between versions 1.84 and 1.128

-version 1.84, 2003/06/13 21:44:43
+version 1.128, 2006/06/30 13:02:05
  Line 1
  /* $Id$
    $State$
    $Log$
+   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 ***
+   Revision 1.104  2005/09/30 16:11:43  lievre
+   (Module): sump fixed, loop imx fixed, and simplifications.
+   (Module): If the status is missing at the last wave but we know
+   that the person is alive, then we can code his/her status as -2
+   (instead of missing=-1 in earlier versions) and his/her
+   contributions to the likelihood is 1 - Prob of dying from last
+   health status (= 1-p13= p11+p12 in the easiest case of somebody in
+   the healthy state at last known wave). Version is 0.98
+   Revision 1.103  2005/09/30 15:54:49  lievre
+   (Module): sump fixed, loop imx fixed, and simplifications.
+   Revision 1.102  2004/09/15 17:31:30  brouard
+   Add the possibility to read data file including tab characters.
+   Revision 1.101  2004/09/15 10:38:38  brouard
+   Fix on curr_time
+   Revision 1.100  2004/07/12 18:29:06  brouard
+   Add version for Mac OS X. Just define UNIX in Makefile
+   Revision 1.99  2004/06/05 08:57:40  brouard
+   *** empty log message ***
+   Revision 1.98  2004/05/16 15:05:56  brouard
+   New version 0.97 . First attempt to estimate force of mortality
+   directly from the data i.e. without the need of knowing the health
+   state at each age, but using a Gompertz model: log u =a + b*age .
+   This is the basic analysis of mortality and should be done before any
+   other analysis, in order to test if the mortality estimated from the
+   cross-longitudinal survey is different from the mortality estimated
+   from other sources like vital statistic data.
+   The same imach parameter file can be used but the option for mle should be -3.
+   Agn�s, who wrote this part of the code, tried to keep most of the
+   former routines in order to include the new code within the former code.
+   The output is very simple: only an estimate of the intercept and of
+   the slope with 95% confident intervals.
+   Current limitations:
+   A) Even if you enter covariates, i.e. with the
+   model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
+   B) There is no computation of Life Expectancy nor Life Table.
+   Revision 1.97  2004/02/20 13:25:42  lievre
+   Version 0.96d. Population forecasting command line is (temporarily)
+   suppressed.
+   Revision 1.96  2003/07/15 15:38:55  brouard
+   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
+   rewritten within the same printf. Workaround: many printfs.
+   Revision 1.95  2003/07/08 07:54:34  brouard
+   * imach.c (Repository):
+   (Repository): Using imachwizard code to output a more meaningful covariance
+   matrix (cov(a12,c31) instead of numbers.
+   Revision 1.94  2003/06/27 13:00:02  brouard
+   Just cleaning
+   Revision 1.93  2003/06/25 16:33:55  brouard
+   (Module): On windows (cygwin) function asctime_r doesn't
+   exist so I changed back to asctime which exists.
+   (Module): Version 0.96b
+   Revision 1.92  2003/06/25 16:30:45  brouard
+   (Module): On windows (cygwin) function asctime_r doesn't
+   exist so I changed back to asctime which exists.
+   Revision 1.91  2003/06/25 15:30:29  brouard
+   * imach.c (Repository): Duplicated warning errors corrected.
+   (Repository): Elapsed time after each iteration is now output. It
+   helps to forecast when convergence will be reached. Elapsed time
+   is stamped in powell.  We created a new html file for the graphs
+   concerning matrix of covariance. It has extension -cov.htm.
+   Revision 1.90  2003/06/24 12:34:15  brouard
+   (Module): Some bugs corrected for windows. Also, when
+   mle=-1 a template is output in file "or"mypar.txt with the design
+   of the covariance matrix to be input.
+   Revision 1.89  2003/06/24 12:30:52  brouard
+   (Module): Some bugs corrected for windows. Also, when
+   mle=-1 a template is output in file "or"mypar.txt with the design
+   of the covariance matrix to be input.
+   Revision 1.88  2003/06/23 17:54:56  brouard
+   * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
+   Revision 1.87  2003/06/18 12:26:01  brouard
+   Version 0.96
+   Revision 1.86  2003/06/17 20:04:08  brouard
+   (Module): Change position of html and gnuplot routines and added
+   routine fileappend.
+   Revision 1.85  2003/06/17 13:12:43  brouard
+   * imach.c (Repository): Check when date of death was earlier that
+   current date of interview. It may happen when the death was just
+   prior to the death. In this case, dh was negative and likelihood
+   was wrong (infinity). We still send an "Error" but patch by
+   assuming that the date of death was just one stepm after the
+   interview.
+   (Repository): Because some people have very long ID (first column)
+   we changed int to long in num[] and we added a new lvector for
+   memory allocation. But we also truncated to 8 characters (left
+   truncation)
+   (Repository): No more line truncation errors.
    Revision 1.84  2003/06/13 21:44:43  brouard
    * imach.c (Repository): Replace "freqsummary" at a correct
    place. It differs from routine "prevalence" which may be called
    many times. Probs is memory consuming and must be used with
    parcimony.
-   Version 0.95a2 (should output exactly the same maximization than 0.8a2)
+   Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    Revision 1.83  2003/06/10 13:39:11  lievre
    *** empty log message ***
- Line 56
+ Line 288
    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).
             Institut national d'�tudes d�mographiques, Paris.
- Line 85
+ Line 317
        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 97
+ Line 329
    varevsij()
    if popbased==1 varevsij(,popbased)
    total life expectancies
-   Variance of stable prevalence
+   Variance of period (stable) prevalence
   end
  */
- Line 107
+ Line 339
  #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"
+ /* #include <libintl.h> */
+ /* #define _(String) gettext (String) */
  #define MAXLINE 256
  #define GNUPLOTPROGRAM "gnuplot"
  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- #define FILENAMELENGTH 80
+ #define FILENAMELENGTH 132
- /*#define DEBUG*/
- #define windows
  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- Line 129
+ Line 375
  #define YEARM 12. /* Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
- #ifdef windows
+ #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
- #define DIRSEPARATOR '\\'
+ #ifdef UNIX
- #define ODIRSEPARATOR '/'
- #else
  #define DIRSEPARATOR '/'
+ #define CHARSEPARATOR "/"
  #define ODIRSEPARATOR '\\'
+ #else
+ #define DIRSEPARATOR '\\'
+ #define CHARSEPARATOR "\\"
+ #define ODIRSEPARATOR '/'
  #endif
  /* $Id$ */
  /* $State$ */
- char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
+ char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
  char fullversion[]="$Revision$ $Date$";
- int erreur; /* Error number */
+ char strstart[80];
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
  int nvar;
  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
  int npar=NPARMAX;
- Line 154  int popbased=0;
+ Line 405  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
  int maxwav; /* Maxim number of waves */
  int jmin, jmax; /* min, max spacing between 2 waves */
+ int ijmin, ijmax; /* Individuals having jmin and jmax */
+ int gipmx, gsw; /* Global variables on the number of contributions
+                    to the likelihood and the sum of weights (done by funcone)*/
  int mle, weightopt;
  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 */
- Line 162  int **bh; /* bh[mi][i] is the bias (+ or
+ Line 416  int **bh; /* bh[mi][i] is the bias (+ or
  double jmean; /* Mean space between 2 waves */
  double **oldm, **newm, **savm; /* Working pointers to matrices */
  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
  FILE *ficlog, *ficrespow;
+ int globpr; /* Global variable for printing or not */
+ double fretone; /* Only one call to likelihood */
+ long ipmx; /* Number of contributions */
+ double sw; /* Sum of weights */
+ char filerespow[FILENAMELENGTH];
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ FILE *ficresilk;
  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
  FILE *ficresprobmorprev;
- FILE *fichtm; /* Html File */
+ 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;
  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
  char filelog[FILENAMELENGTH]; /* Log file */
  char filerest[FILENAMELENGTH];
  char fileregp[FILENAMELENGTH];
  char popfile[FILENAMELENGTH];
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ struct timezone tzp;
+ extern int gettimeofday();
+ struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ long time_value;
+ extern long time();
+ char strcurr[80], strfor[80];
+ char *endptr;
+ long lval;
+ double dval;
  #define NR_END 1
  #define FREE_ARG char*
- Line 212  static double maxarg1,maxarg2;
+ Line 493  static double maxarg1,maxarg2;
  static double sqrarg;
  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ int agegomp= AGEGOMP;
  int imx;
- int stepm;
+ int stepm=1;
  /* Stepm, step in month: minimum step interpolation*/
  int estepm;
  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
  int m,nb;
- int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
+ long *num;
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  double **pmmij, ***probs;
+ double *ageexmed,*agecens;
  double dateintmean=0;
  double *weight;
  int **s; /* Status */
  double *agedc, **covar, idx;
  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double *lsurv, *lpop, *tpop;
  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
  double ftolhess; /* Tolerance for computing hessian */
- Line 237  double ftolhess; /* Tolerance for comput
+ Line 522  double ftolhess; /* Tolerance for comput
  /**************** split *************************/
  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
  {
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+   */
    char  *ss;                            /* pointer */
    int   l1, l2;                         /* length counters */
    l1 = strlen(path );                   /* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   if ( ss == NULL ) {                   /* no directory, so use current */
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+     strcpy( name, path );               /* we got the fullname name because no directory */
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      /* get current working directory */
- Line 251  static int split( char *path, char *dirc
+ Line 540  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 259  static int split( char *path, char *dirc
+ Line 549  static int split( char *path, char *dirc
      strcpy( name, ss );         /* save file name */
      strncpy( dirc, path, l1 - l2 );     /* now the directory */
      dirc[l1-l2] = 0;                    /* add zero */
+     printf(" DIRC2 = %s \n",dirc);
    }
+   /* We add a separator at the end of dirc if not exists */
    l1 = strlen( dirc );                  /* length of directory */
- #ifdef windows
+   if( dirc[l1-1] != DIRSEPARATOR ){
-   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
+     dirc[l1] =  DIRSEPARATOR;
- #else
+     dirc[l1+1] = 0;
-   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
+     printf(" DIRC3 = %s \n",dirc);
- #endif
+   }
    ss = strrchr( name, '.' );            /* find last / */
-   ss++;
+   if (ss >0){
-   strcpy(ext,ss);                       /* save extension */
+     ss++;
-   l1= strlen( name);
+     strcpy(ext,ss);                     /* save extension */
-   l2= strlen(ss)+1;
+     l1= strlen( name);
-   strncpy( finame, name, l1-l2);
+     l2= strlen(ss)+1;
-   finame[l1-l2]= 0;
+     strncpy( finame, name, l1-l2);
+     finame[l1-l2]= 0;
+   }
    return( 0 );                          /* we're done */
  }
  /******************************************/
- void replace(char *s, char*t)
+ void replace_back_to_slash(char *s, char*t)
  {
    int i;
-   int lg=20;
+   int lg=0;
    i=0;
    lg=strlen(t);
    for(i=0; i<= lg; i++) {
- Line 305  int nbocc(char *s, char occ)
+ Line 600  int nbocc(char *s, char occ)
  void cutv(char *u,char *v, char*t, char occ)
  {
-   /* cuts string t into u and v where u is ended by char occ excluding it
+   /* cuts string t into u and v where u ends before first occurence of char 'occ'
-      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
+      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       gives u="abcedf" and v="ghi2j" */
    int i,lg,j,p=0;
    i=0;
- Line 349  void free_vector(double*v, int nl, int n
+ Line 644  void free_vector(double*v, int nl, int n
  }
  /************************ivector *******************************/
- char *cvector(long nl,long nh)
+ int *ivector(long nl,long nh)
  {
-   char *v;
+   int *v;
-   v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-   if (!v) nrerror("allocation failure in cvector");
+   if (!v) nrerror("allocation failure in ivector");
    return v-nl+NR_END;
  }
  /******************free ivector **************************/
- void free_cvector(char *v, long nl, long nh)
+ void free_ivector(int *v, long nl, long nh)
  {
    free((FREE_ARG)(v+nl-NR_END));
  }
- /************************ivector *******************************/
+ /************************lvector *******************************/
- int *ivector(long nl,long nh)
+ long *lvector(long nl,long nh)
  {
-   int *v;
+   long *v;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
    if (!v) nrerror("allocation failure in ivector");
    return v-nl+NR_END;
  }
- /******************free ivector **************************/
+ /******************free lvector **************************/
- void free_ivector(int *v, long nl, long nh)
+ void free_lvector(long *v, long nl, long nh)
  {
    free((FREE_ARG)(v+nl-NR_END));
  }
- Line 432  double **matrix(long nrl, long nrh, long
+ Line 727  double **matrix(long nrl, long nrh, long
    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    return m;
-   /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
     */
  }
- Line 487  void free_ma3x(double ***m, long nrl, lo
+ Line 782  void free_ma3x(double ***m, long nrl, lo
    free((FREE_ARG)(m+nrl-NR_END));
  }
+ /*************** function subdirf ***********/
+ char *subdirf(char fileres[])
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/"); /* Add to the right */
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
+ /*************** function subdirf2 ***********/
+ char *subdirf2(char fileres[], char *preop)
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
+ /*************** function subdirf3 ***********/
+ char *subdirf3(char fileres[], char *preop, char *preop2)
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
+   strcat(tmpout,preop2);
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
  /***************** f1dim *************************/
  extern int ncom;
  extern double *pcom,*xicom;
- Line 662  void linmin(double p[], double xi[], int
+ Line 992  void linmin(double p[], double xi[], int
    free_vector(pcom,1,n);
  }
+ char *asc_diff_time(long time_sec, char ascdiff[])
+ {
+   long sec_left, days, hours, minutes;
+   days = (time_sec) / (60*60*24);
+   sec_left = (time_sec) % (60*60*24);
+   hours = (sec_left) / (60*60) ;
+   sec_left = (sec_left) %(60*60);
+   minutes = (sec_left) /60;
+   sec_left = (sec_left) % (60);
+   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+   return ascdiff;
+ }
  /*************** powell ************************/
  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
              double (*func)(double []))
- Line 672  void powell(double p[], double **xi, int
+ Line 1015  void powell(double p[], double **xi, int
    double del,t,*pt,*ptt,*xit;
    double fp,fptt;
    double *xits;
+   int niterf, itmp;
    pt=vector(1,n);
    ptt=vector(1,n);
    xit=vector(1,n);
- Line 682  void powell(double p[], double **xi, int
+ Line 1027  void powell(double p[], double **xi, int
      fp=(*fret);
      ibig=0;
      del=0.0;
-     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+     last_time=curr_time;
-     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+     (void) gettimeofday(&curr_time,&tzp);
-     fprintf(ficrespow,"%d %.12f",*iter,*fret);
+     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);
-     for (i=1;i<=n;i++) {
+     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); */
+    for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12lf",i, p[i]);
        fprintf(ficrespow," %.12lf", p[i]);
      }
      printf("\n");
      fprintf(ficlog,"\n");
-     fprintf(ficrespow,"\n");
+     fprintf(ficrespow,"\n");fflush(ficrespow);
+     if(*iter <=3){
+       tm = *localtime(&curr_time.tv_sec);
+       strcpy(strcurr,asctime(&tm));
+ /*       asctime_r(&tm,strcurr); */
+       forecast_time=curr_time;
+       itmp = strlen(strcurr);
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+         strcurr[itmp-1]='\0';
+       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       for(niterf=10;niterf<=30;niterf+=10){
+         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+         tmf = *localtime(&forecast_time.tv_sec);
+ /*      asctime_r(&tmf,strfor); */
+         strcpy(strfor,asctime(&tmf));
+         itmp = strlen(strfor);
+         if(strfor[itmp-1]=='\n')
+         strfor[itmp-1]='\0';
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+       }
+     }
      for (i=1;i<=n;i++) {
        for (j=1;j<=n;j++) xit[j]=xi[j][i];
        fptt=(*fret);
- Line 784  void powell(double p[], double **xi, int
+ Line 1153  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 855  double **pmij(double **ps, double *cov,
+ Line 1224  double **pmij(double **ps, double *cov,
    int i,j,j1, nc, ii, jj;
      for(i=1; i<= nlstate; i++){
-     for(j=1; j<i;j++){
+       for(j=1; j<i;j++){
-       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-         /*s2 += param[i][j][nc]*cov[nc];*/
+           /*s2 += param[i][j][nc]*cov[nc];*/
-         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
+ /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
-       }
+         }
-       ps[i][j]=s2;
+         ps[i][j]=s2;
-       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
+ /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
-     }
+       }
-     for(j=i+1; j<=nlstate+ndeath;j++){
+       for(j=i+1; j<=nlstate+ndeath;j++){
-       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
+ /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+         }
+         ps[i][j]=s2;
        }
-       ps[i][j]=s2;
      }
-   }
      /*ps[3][2]=1;*/
-   for(i=1; i<= nlstate; i++){
+     for(i=1; i<= nlstate; i++){
-      s1=0;
+       s1=0;
-     for(j=1; j<i; j++)
+       for(j=1; j<i; j++)
-       s1+=exp(ps[i][j]);
+         s1+=exp(ps[i][j]);
-     for(j=i+1; j<=nlstate+ndeath; j++)
+       for(j=i+1; j<=nlstate+ndeath; j++)
-       s1+=exp(ps[i][j]);
+         s1+=exp(ps[i][j]);
-     ps[i][i]=1./(s1+1.);
+       ps[i][i]=1./(s1+1.);
-     for(j=1; j<i; j++)
+       for(j=1; j<i; j++)
-       ps[i][j]= exp(ps[i][j])*ps[i][i];
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-     for(j=i+1; j<=nlstate+ndeath; j++)
+       for(j=i+1; j<=nlstate+ndeath; j++)
-       ps[i][j]= exp(ps[i][j])*ps[i][i];
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-   } /* end i */
+     } /* end i */
-   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-     for(jj=1; jj<= nlstate+ndeath; jj++){
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-       ps[ii][jj]=0;
+         ps[ii][jj]=0;
-       ps[ii][ii]=1;
+         ps[ii][ii]=1;
+       }
      }
-   }
-   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
+ /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
-     for(jj=1; jj<= nlstate+ndeath; jj++){
+ /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
-      printf("%lf ",ps[ii][jj]);
+ /*         printf("ddd %lf ",ps[ii][jj]); */
-    }
+ /*       } */
-     printf("\n ");
+ /*       printf("\n "); */
-     }
+ /*        } */
-     printf("\n ");printf("%lf ",cov[2]);*/
+ /*        printf("\n ");printf("%lf ",cov[2]); */
- /*
+        /*
-   for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-   goto end;*/
+       goto end;*/
      return ps;
  }
- Line 978  double ***hpxij(double ***po, int nhstep
+ Line 1347  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 1029  double func( double *x)
+ Line 1399  double func( double *x)
          } /* end mult */
          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         /* But now since version 0.9 we anticipate for bias and large stepm.
+         /* But now since version 0.9 we anticipate for bias at large stepm.
           * If stepm is larger than one month (smallest stepm) and if the exact delay
           * (in months) between two waves is not a multiple of stepm, we rounded to
           * the nearest (and in case of equal distance, to the lowest) interval but now
           * we keep into memory the bias bh[mi][i] and also the previous matrix product
-          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           * -stepm/2 to stepm/2 .
           * For stepm=1 the results are the same as for previous versions of Imach.
           * For stepm > 1 the results are less biased than in previous versions.
- Line 1044  double func( double *x)
+ Line 1414  double func( double *x)
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
-         /* bias is positive if real duration
+         /* bias bh is positive if real duration
           * is higher than the multiple of stepm and negative otherwise.
           */
          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
          if( s2 > nlstate){
-           /* i.e. if s2 is a death state and if the date of death is known then the contribution
+           /* i.e. if s2 is a death state and if the date of death is known
-              to the likelihood is the probability to die between last step unit time and current
+              then the contribution to the likelihood is the probability to
-              step unit time, which is also the differences between probability to die before dh
+              die between last step unit time and current  step unit time,
-              and probability to die before dh-stepm .
+              which is also equal to probability to die before dh
+              minus probability to die before dh-stepm .
               In version up to 0.92 likelihood was computed
          as if date of death was unknown. Death was treated as any other
          health state: the date of the interview describes the actual state
- Line 1072  double func( double *x)
+ Line 1443  double func( double *x)
          lower mortality.
            */
            lli=log(out[s1][s2] - savm[s1][s2]);
-         }else{
+         } else if  (s2==-2) {
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           /*survp += out[s1][j]; */
+           lli= log(survp);
+         }
+         else if  (s2==-4) {
+           for (j=3,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           lli= log(survp);
+         }
+         else if  (s2==-5) {
+           for (j=1,survp=0. ; j<=2; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           lli= log(survp);
+         }
+         else{
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
          }
- Line 1105  double func( double *x)
+ Line 1497  double func( double *x)
            oldm=newm;
          } /* end mult */
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         /* But now since version 0.9 we anticipate for bias and large stepm.
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
-          * (in months) between two waves is not a multiple of stepm, we rounded to
-          * the nearest (and in case of equal distance, to the lowest) interval but now
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
-          * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
-          * For stepm=1 the results are the same as for previous versions of Imach.
-          * For stepm > 1 the results are less biased than in previous versions.
-          */
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
-         /* bias is positive if real duration
-          * is higher than the multiple of stepm and negative otherwise.
-          */
          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-         /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-         /*if(lli ==000.0)*/
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          ipmx +=1;
          sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- Line 1156  double func( double *x)
+ Line 1527  double func( double *x)
            oldm=newm;
          } /* end mult */
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         /* But now since version 0.9 we anticipate for bias and large stepm.
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
-          * (in months) between two waves is not a multiple of stepm, we rounded to
-          * the nearest (and in case of equal distance, to the lowest) interval but now
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
-          * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
-          * For stepm=1 the results are the same as for previous versions of Imach.
-          * For stepm > 1 the results are less biased than in previous versions.
-          */
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
-         /* bias is positive if real duration
-          * is higher than the multiple of stepm and negative otherwise.
-          */
-         /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-         /*if(lli ==000.0)*/
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          ipmx +=1;
          sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- Line 1217  double func( double *x)
+ Line 1568  double func( double *x)
          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]); */
        } /* end of wave */
      } /* end of individual */
    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
- Line 1255  double func( double *x)
+ Line 1606  double func( double *x)
    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   /*exit(0); */
    return -l;
  }
+ /*************** log-likelihood *************/
+ double funcone( double *x)
+ {
+   /* Same as likeli but slower because of a lot of printf and if */
+   int i, ii, j, k, mi, d, kk;
+   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   double **out;
+   double lli; /* Individual log likelihood */
+   double llt;
+   int s1, s2;
+   double bbh, survp;
+   /*extern weight */
+   /* We are differentiating ll according to initial status */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   /*for(i=1;i<imx;i++)
+     printf(" %d\n",s[4][i]);
+   */
+   cov[1]=1.;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     for(mi=1; mi<= wav[i]-1; mi++){
+       for (ii=1;ii<=nlstate+ndeath;ii++)
+         for (j=1;j<=nlstate+ndeath;j++){
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         }
+       for(d=0; d<dh[mi][i]; d++){
+         newm=savm;
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         for (kk=1; kk<=cptcovage;kk++) {
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         }
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         savm=oldm;
+         oldm=newm;
+       } /* end mult */
+       s1=s[mw[mi][i]][i];
+       s2=s[mw[mi+1][i]][i];
+       bbh=(double)bh[mi][i]/(double)stepm;
+       /* bias is positive if real duration
+        * is higher than the multiple of stepm and negative otherwise.
+        */
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         lli=log(out[s1][s2] - savm[s1][s2]);
+       } else if  (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 */
+       } else if(mle==3){  /* exponential inter-extrapolation */
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+         lli=log(out[s1][s2]); /* Original formula */
+       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+         lli=log(out[s1][s2]); /* Original formula */
+       } /* End of if */
+       ipmx +=1;
+       sw += weight[i];
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       if(globpr){
+         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+  %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++){
+           llt +=ll[k]*gipmx/gsw;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         }
+         fprintf(ficresilk," %10.6f\n", -llt);
+       }
+     } /* end of wave */
+   } /* end of individual */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   if(globpr==0){ /* First time we count the contributions and weights */
+     gipmx=ipmx;
+     gsw=sw;
+   }
+   return -l;
+ }
+ /*************** function likelione ***********/
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+ {
+   /* This routine should help understanding what is done with
+      the selection of individuals/waves and
+      to check the exact contribution to the likelihood.
+      Plotting could be done.
+    */
+   int k;
+   if(*globpri !=0){ /* Just counts and sums, no printings */
+     strcpy(fileresilk,"ilk");
+     strcat(fileresilk,fileres);
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", fileresilk);
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+     }
+     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+     for(k=1; k<=nlstate; k++)
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+   }
+   *fretone=(*funcone)(p);
+   if(*globpri !=0){
+     fclose(ficresilk);
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     fflush(fichtm);
+   }
+   return;
+ }
  /*********** Maximum Likelihood Estimation ***************/
- Line 1267  void mlikeli(FILE *ficres,double p[], in
+ Line 1743  void mlikeli(FILE *ficres,double p[], in
    int i,j, iter;
    double **xi;
    double fret;
-   char filerespow[FILENAMELENGTH];
+   double fretone; /* Only one call to likelihood */
+   /*  char filerespow[FILENAMELENGTH];*/
    xi=matrix(1,npar,1,npar);
    for (i=1;i<=npar;i++)
      for (j=1;j<=npar;j++)
- Line 1284  void mlikeli(FILE *ficres,double p[], in
+ Line 1761  void mlikeli(FILE *ficres,double p[], in
      for(j=1;j<=nlstate+ndeath;j++)
        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
    fprintf(ficrespow,"\n");
    powell(p,xi,npar,ftol,&iter,&fret,func);
+   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 1301  void hesscov(double **matcov, double p[]
+ Line 1780  void hesscov(double **matcov, double p[]
    int i, j,jk;
    int *indx;
-   double hessii(double p[], double delta, int theta, double delti[]);
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-   double hessij(double p[], double delti[], int i, int j);
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
    void lubksb(double **a, int npar, int *indx, double b[]) ;
    void ludcmp(double **a, int npar, int *indx, double *d) ;
+   double gompertz(double p[]);
    hess=matrix(1,npar,1,npar);
    printf("\nCalculation of the hessian matrix. Wait...\n");
- Line 1313  void hesscov(double **matcov, double p[]
+ Line 1792  void hesscov(double **matcov, double p[]
    for (i=1;i<=npar;i++){
      printf("%d",i);fflush(stdout);
      fprintf(ficlog,"%d",i);fflush(ficlog);
-     hess[i][i]=hessii(p,ftolhess,i,delti);
-     /*printf(" %f ",p[i]);*/
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-     /*printf(" %lf ",hess[i][i]);*/
+     /*  printf(" %f ",p[i]);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
    }
    for (i=1;i<=npar;i++) {
- Line 1323  void hesscov(double **matcov, double p[]
+ Line 1804  void hesscov(double **matcov, double p[]
        if (j>i) {
          printf(".%d%d",i,j);fflush(stdout);
          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-         hess[i][j]=hessij(p,delti,i,j);
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
          hess[j][i]=hess[i][j];
          /*printf(" %lf ",hess[i][j]);*/
        }
- Line 1394  void hesscov(double **matcov, double p[]
+ Line 1876  void hesscov(double **matcov, double p[]
  }
  /*************** hessian matrix ****************/
- double hessii( double x[], double delta, int theta, double delti[])
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
  {
    int i;
    int l=1, lmax=20;
    double k1,k2;
    double p2[NPARMAX+1];
    double res;
-   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
    double fx;
    int k=0,kmax=10;
    double l1;
- Line 1441  double hessii( double x[], double delta,
+ Line 1923  double hessii( double x[], double delta,
  }
- double hessij( double x[], double delti[], int thetai,int thetaj)
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
  {
    int i;
    int l=1, l1, lmax=20;
- Line 1550  void lubksb(double **a, int n, int *indx
+ Line 2032  void lubksb(double **a, int n, int *indx
    }
  }
+ void pstamp(FILE *fichier)
+ {
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+ }
  /************ Frequencies ********************/
- void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
  {  /* Some frequencies */
    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
- Line 1559  void  freqsummary(char fileres[], int ia
+ Line 2046  void  freqsummary(char fileres[], int ia
    double ***freq; /* Frequencies */
    double *pp, **prop;
    double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   FILE *ficresp;
    char fileresp[FILENAMELENGTH];
    pp=vector(1,nlstate);
- Line 1571  void  freqsummary(char fileres[], int ia
+ Line 2057  void  freqsummary(char fileres[], int ia
      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      exit(0);
    }
-   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
    j1=0;
    j=cptcoveff;
- Line 1584  void  freqsummary(char fileres[], int ia
+ Line 2070  void  freqsummary(char fileres[], int ia
        j1++;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
          scanf("%d", i);*/
-       for (i=-1; i<=nlstate+ndeath; i++)
+       for (i=-5; i<=nlstate+ndeath; i++)
-         for (jk=-1; jk<=nlstate+ndeath; jk++)
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
            for(m=iagemin; m <= iagemax+3; m++)
              freq[i][jk][m]=0;
- Line 1624  void  freqsummary(char fileres[], int ia
+ Line 2110  void  freqsummary(char fileres[], int ia
        }
        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+       pstamp(ficresp);
        if  (cptcovn>0) {
          fprintf(ficresp, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- Line 1710  void  freqsummary(char fileres[], int ia
+ Line 2196  void  freqsummary(char fileres[], int ia
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
-   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
    free_vector(pp,1,nlstate);
    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
    /* End of Freq */
- Line 1782  void prevalence(double ***probs, double
+ Line 2268  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 1819  void  concatwav(int wav[], int **dh, int
+ Line 2306  void  concatwav(int wav[], int **dh, int
      mi=0;
      m=firstpass;
      while(s[m][i] <= nlstate){
-       if(s[m][i]>=1)
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
          mw[++mi][i]=m;
        if(m >=lastpass)
          break;
- Line 1835  void  concatwav(int wav[], int **dh, int
+ Line 2322  void  concatwav(int wav[], int **dh, int
      wav[i]=mi;
      if(mi==0){
+       nbwarn++;
        if(first==0){
-         printf("Warning! None valid information for:%d 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:%d 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 1852  void  concatwav(int wav[], int **dh, int
+ Line 2340  void  concatwav(int wav[], int **dh, int
        else{
          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
            if (agedc[i] < 2*AGESUP) {
-           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-           if(j==0) j=1;  /* Survives at least one month after exam */
+             if(j==0) j=1;  /* Survives at least one month after exam */
-           k=k+1;
+             else if(j<0){
-           if (j >= jmax) jmax=j;
+               nberr++;
-           if (j <= jmin) jmin=j;
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-           sum=sum+j;
+               j=1; /* Temporary Dangerous patch */
-           /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-           /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-           if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+             }
+             k=k+1;
+             if (j >= jmax){
+               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);*/
            }
          }
          else{
            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-           /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+ /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
            k=k+1;
-           if (j >= jmax) jmax=j;
+           if (j >= jmax) {
-           else if (j <= jmin)jmin=j;
+             jmax=j;
+             ijmax=i;
+           }
+           else if (j <= jmin){
+             jmin=j;
+             ijmin=i;
+           }
            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-           if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+           if(j<0){
+             nberr++;
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+           }
            sum=sum+j;
          }
          jk= j/stepm;
          jl= j -jk*stepm;
          ju= j -(jk+1)*stepm;
-         if(mle <=1){
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
            if(jl==0){
              dh[mi][i]=jk;
              bh[mi][i]=0;
- Line 1902  void  concatwav(int wav[], int **dh, int
+ Line 2414  void  concatwav(int wav[], int **dh, int
              bh[mi][i]=ju; /* At least one step */
              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
            }
-         }
+         } /* end if mle */
-       } /* end if mle */
+       }
      } /* end wave */
    }
    jmean=sum/k;
-   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   }
  /*********** Tricode ****************************/
- Line 1954  void tricode(int *Tvar, int **nbcode, in
+ Line 2466  void tricode(int *Tvar, int **nbcode, in
   for (k=0; k< maxncov; k++) Ndum[k]=0;
   for (i=1; i<=ncovmodel-2; i++) {
-    /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     ij=Tvar[i];
     Ndum[ij]++;
   }
- Line 1972  void tricode(int *Tvar, int **nbcode, in
+ Line 2484  void tricode(int *Tvar, int **nbcode, in
  /*********** Health Expectancies ****************/
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
  {
-   /* Health expectancies */
+   /* Health expectancies, no variances */
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+   int nhstepma, nstepma; /* Decreasing with age */
    double age, agelim, hf;
-   double ***p3mat,***varhe;
+   double ***p3mat;
-   double **dnewm,**doldm;
+   double eip;
-   double *xp;
-   double **gp, **gm;
-   double ***gradg, ***trgradg;
-   int theta;
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+   pstamp(ficreseij);
-   xp=vector(1,npar);
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-   fprintf(ficreseij,"# Health expectancies\n");
    fprintf(ficreseij,"# Age");
-   for(i=1; i<=nlstate;i++)
+   for(i=1; i<=nlstate;i++){
-     for(j=1; j<=nlstate;j++)
+     for(j=1; j<=nlstate;j++){
-       fprintf(ficreseij," %1d-%1d (SE)",i,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);
    }
- Line 2027  void evsij(char fileres[], double ***eij
+ Line 2536  void evsij(char fileres[], double ***eij
    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
    agelim=AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   /* If stepm=6 months */
-     /* nhstepm age range expressed in number of stepm */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm);
-     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     /* if (stepm >= YEARM) hstepm=1;*/
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     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);
+ /* nhstepm age range expressed in number of stepm */
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   /* if (stepm >= YEARM) hstepm=1;*/
-     /* Computing Variances of health expectancies */
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-      for(theta=1; theta <=npar; theta++){
-       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, gp[h][cptj]=0.; h<=nhstepm-1; h++){
-             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
-           }
-         }
-       }
-       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];
-         }
-      }
- /* End theta */
-      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 (age=bage; age<=fage; age ++){
-       for(j=1;j<=nlstate*nlstate;j++)
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-         varhe[i][j][(int)age] =0.;
+     /* 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 */
-      printf("%d|",(int)age);fflush(stdout);
+     /* If stepm=6 months */
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-      for(h=0;h<=nhstepm-1;h++){
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-       for(k=0;k<=nhstepm-1;k++){
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-         for(i=1;i<=nlstate*nlstate;i++)
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-           for(j=1;j<=nlstate*nlstate;j++)
-             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
+     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]);*/
+           /* 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 );
-     cptj=0;
+     for(i=1; i<=nlstate;i++){
-     for(i=1; i<=nlstate;i++)
+       eip=0;
        for(j=1; j<=nlstate;j++){
-         cptj++;
+         eip +=eij[i][j][(int)age];
-         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
        }
+       fprintf(ficreseij,"%9.4f", eip );
+     }
      fprintf(ficreseij,"\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_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    printf("\n");
    fprintf(ficlog,"\n");
+ }
-   free_vector(xp,1,npar);
+ 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[] )
+ {
+   /* Covariances of health expectancies eij and of total life expectancies according
+    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 ***p3matp, ***p3matm, ***varhe;
+   double **dnewm,**doldm;
+   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);
+   pstamp(ficresstdeij);
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+   fprintf(ficresstdeij,"# Age");
+   for(i=1; i<=nlstate;i++){
+     for(j=1; j<=nlstate;j++)
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+     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);
+   }
+   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 */
+   /* If stepm=6 months */
+   /* nhstepm age range expressed in number of stepm */
+   agelim=AGESUP;
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   /* if (stepm >= YEARM) hstepm=1;*/
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   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;*/
+     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 */
+     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
+        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(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+       for(j=1; j<= nlstate; j++){
+         for(i=1; i<=nlstate; i++){
+           for(h=0; h<=nhstepm-1; h++){
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[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(h=0; h<=nhstepm-1; h++){
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+         }
+     }/* End theta */
+     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(ij=1;ij<=nlstate*nlstate;ij++)
+       for(ji=1;ji<=nlstate*nlstate;ji++)
+         varhe[ij][ji][(int)age] =0.;
+      printf("%d|",(int)age);fflush(stdout);
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+      for(h=0;h<=nhstepm-1;h++){
+       for(k=0;k<=nhstepm-1;k++){
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+         for(ij=1;ij<=nlstate*nlstate;ij++)
+           for(ji=1;ji<=nlstate*nlstate;ji++)
+             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] += (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]);*/
+         }
+     fprintf(ficresstdeij,"%3.0f",age );
+     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= (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," %.4f", varhe[cptj][cptj2][(int)age]);
+           }
+       }
+     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(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);
    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  }
  /************ Variance ******************/
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
+ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
  {
    /* Variance of health expectancies */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
- Line 2195  void varevsij(char optionfilefiname[], d
+ Line 2853  void varevsij(char optionfilefiname[], d
      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
    }
    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   pstamp(ficresprobmorprev);
    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
- Line 2204  void varevsij(char optionfilefiname[], d
+ Line 2864  void varevsij(char optionfilefiname[], d
        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
    }
    fprintf(ficresprobmorprev,"\n");
-   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+   fprintf(ficgp,"\n# Routine varevsij");
-     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-     exit(0);
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-   }
+ /*   } */
-   else{
-     fprintf(ficgp,"\n# Routine varevsij");
-   }
-   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
-     printf("Problem with html file: %s\n", optionfilehtm);
-     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
-     exit(0);
-   }
-   else{
-     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-   }
    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   pstamp(ficresvij);
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+   if(popbased==1)
+     fprintf(ficresvij,"the age specific prevalence observed (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 2249  void varevsij(char optionfilefiname[], d
+ Line 2901  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 2316  void varevsij(char optionfilefiname[], d
+ Line 2967  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 2432  void varevsij(char optionfilefiname[], d
+ Line 3083  void varevsij(char optionfilefiname[], d
  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
  */
-   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    free_vector(xp,1,npar);
    free_matrix(doldm,1,nlstate,1,nlstate);
- Line 2449  void varevsij(char optionfilefiname[], d
+ Line 3101  void varevsij(char optionfilefiname[], d
    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    fclose(ficresprobmorprev);
-   fclose(ficgp);
+   fflush(ficgp);
-   fclose(fichtm);
+   fflush(fichtm);
  }  /* end varevsij */
  /************ Variance of prevlim ******************/
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
+ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
  {
    /* Variance of prevalence limit */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
- Line 2467  void varprevlim(char fileres[], double *
+ Line 3119  void varprevlim(char fileres[], double *
    double **gradg, **trgradg;
    double age,agelim;
    int theta;
-   fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
+   pstamp(ficresvpl);
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
    fprintf(ficresvpl,"# Age");
    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %1d-%1d",i,i);
- Line 2537  void varprevlim(char fileres[], double *
+ Line 3190  void varprevlim(char fileres[], double *
  }
  /************ Variance of one-step probabilities  ******************/
- void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
  {
    int i, j=0,  i1, k1, l1, t, tj;
    int k2, l2, j1,  z1;
- Line 2582  void varprob(char optionfilefiname[], do
+ Line 3235  void varprob(char optionfilefiname[], do
    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   pstamp(ficresprob);
    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
    fprintf(ficresprob,"# Age");
+   pstamp(ficresprobcov);
    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
    fprintf(ficresprobcov,"# Age");
+   pstamp(ficresprobcor);
    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-   fprintf(ficresprobcov,"# Age");
+   fprintf(ficresprobcor,"# Age");
    for(i=1; i<=nlstate;i++)
- Line 2607  void varprob(char optionfilefiname[], do
+ Line 3262  void varprob(char optionfilefiname[], do
    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
    first=1;
-   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+   fprintf(ficgp,"\n# Routine varprob");
-     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+   fprintf(fichtm,"\n");
-     exit(0);
-   }
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   else{
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-     fprintf(ficgp,"\n# Routine varprob");
+   file %s<br>\n",optionfilehtmcov);
-   }
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+ and drawn. It helps understanding how is the covariance between two incidences.\
-     printf("Problem with html file: %s\n", optionfilehtm);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
-     exit(0);
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-   }
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-   else{
+ standard deviations wide on each axis. <br>\
-     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-     fprintf(fichtm,"\n");
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
-     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
-   }
    cov[1]=1;
    tj=cptcoveff;
- Line 2650  void varprob(char optionfilefiname[], do
+ Line 3300  void varprob(char optionfilefiname[], do
          fprintf(ficgp, "**********\n#\n");
-         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
          fprintf(ficresprobcor, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- Line 2810  void varprob(char optionfilefiname[], do
+ Line 3460  void varprob(char optionfilefiname[], do
                      fprintf(ficgp,"\nset parametric;unset label");
                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
- Line 2821  void varprob(char optionfilefiname[], do
+ Line 3475  void varprob(char optionfilefiname[], do
                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                    }else{
                      first=0;
-                     fprintf(fichtm," %d (%.3f),",(int) age, c12);
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
- Line 2830  void varprob(char optionfilefiname[], do
+ Line 3484  void varprob(char optionfilefiname[], do
                    }/* if first */
                  } /* age mod 5 */
                } /* end loop age */
-               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                first=1;
              } /*l12 */
            } /* k12 */
- Line 2840  void varprob(char optionfilefiname[], do
+ Line 3494  void varprob(char optionfilefiname[], do
    }
    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);
    fclose(ficresprobcor);
-   fclose(ficgp);
+   fflush(ficgp);
-   fclose(fichtm);
+   fflush(fichtmcov);
  }
- Line 2857  void printinghtml(char fileres[], char t
+ Line 3513  void printinghtml(char fileres[], char t
                    double jprev1, double mprev1,double anprev1, \
                    double jprev2, double mprev2,double anprev2){
    int jj1, k1, i1, cpt;
-   /*char optionfilehtm[FILENAMELENGTH];*/
-   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
-     printf("Problem with %s \n",optionfilehtm), exit(0);
-     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
-   }
-    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
+ </ul>");
-  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-  - Life expectancies by age and initial health status (estepm=%2d months):
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-    <a href=\"e%s\">e%s</a> <br>\n</li>", \
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
+    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,"\
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+    fprintf(fichtm,"\
+  - (a) Life expectancies by health status at initial age, 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",
+            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 2887  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3550  fprintf(fichtm," \n<ul><li><b>Graphs</b>
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
       /* Pij */
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
- <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+ <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
       /* Quasi-incidences */
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
-        /* Stable prevalence in each health state */
+ <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+        /* 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=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         }
       for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
+         fprintf(fichtm,"\n<br>- 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=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and
- health expectancies in states (1) and (2): e%s%d.png<br>
- <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     } /* end i1 */
   }/* End k1 */
   fprintf(fichtm,"</ul>");
-  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
+  fprintf(fichtm,"\
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
-  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
+  fprintf(fichtm,"\
-  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+  fprintf(fichtm,"\
+  - 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 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,"\
+  - 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",
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+  fprintf(fichtm,"\
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
- Line 2924  health expectancies in states (1) and (2
+ Line 3607  health expectancies in states (1) and (2
  /*      <br>",fileres,fileres,fileres,fileres); */
  /*  else  */
  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
- fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+  fflush(fichtm);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   m=cptcoveff;
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- Line 2940  fprintf(fichtm," <ul><li><b>Graphs</b></
+ Line 3624  fprintf(fichtm," <ul><li><b>Graphs</b></
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed and period prevalence (with confident
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- interval) in state (%d): v%s%d%d.png <br>
+ prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
- <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
       }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+ health expectancies in states (1) and (2). 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 */
   fprintf(fichtm,"</ul>");
- fclose(fichtm);
+  fflush(fichtm);
  }
  /******************* Gnuplot file **************/
- void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   char dirfileres[132],optfileres[132];
    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
    int ng;
-   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-     printf("Problem with file %s",optionfilegnuplot);
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-   }
+ /*   } */
    /*#ifdef windows */
-     fprintf(ficgp,"cd \"%s\" \n",pathc);
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
      /*#endif */
- m=pow(2,cptcoveff);
+   m=pow(2,cptcoveff);
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
   /* 1eme*/
    for (cpt=1; cpt<= nlstate ; cpt ++) {
     for (k1=1; k1<= m ; k1 ++) {
-      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
+      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+      fprintf(ficgp,"set xlabel \"Age\" \n\
+ set ylabel \"Probability\" \n\
+ set ter png small\n\
+ set size 0.65,0.65\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }
-      fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,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)");
       }
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
+      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }
-      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
+      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     }
    }
    /*2 eme*/
    for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
      for (i=1; i<= nlstate+1 ; i ++) {
        k=2*i;
-       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"\" w l 0,");
-       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
- Line 3023  m=pow(2,cptcoveff);
+ Line 3721  m=pow(2,cptcoveff);
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<= nlstate ; cpt ++) {
-       k=2+nlstate*(2*cpt-2);
+       /*       k=2+nlstate*(2*cpt-2); */
-       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       k=2+(nlstate+1)*(cpt-1);
-       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+       fprintf(ficgp,"set ter png small\n\
+ set size 0.65,0.65\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
- Line 3035  m=pow(2,cptcoveff);
+ Line 3736  m=pow(2,cptcoveff);
        */
        for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+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 3045  m=pow(2,cptcoveff);
+ Line 3748  m=pow(2,cptcoveff);
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<=nlstate ; cpt ++) {
        k=3;
-       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter png small\nset size 0.65,0.65\n\
+ unset log y\n\
+ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
        for (i=1; i< nlstate ; i ++)
          fprintf(ficgp,"+$%d",k+i+1);
        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
        l=3+(nlstate+ndeath)*cpt;
-       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
+       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
        for (i=1; i< nlstate ; i ++) {
          l=3+(nlstate+ndeath)*cpt;
          fprintf(ficgp,"+$%d",l+i+1);
- Line 3077  m=pow(2,cptcoveff);
+ Line 3783  m=pow(2,cptcoveff);
     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       for(jk=1; jk <=m; jk++) {
-        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
+        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
         if (ng==2)
           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
         else
- Line 3124  m=pow(2,cptcoveff);
+ Line 3830  m=pow(2,cptcoveff);
         } /* end k2 */
       } /* end jk */
     } /* end ng */
-    fclose(ficgp);
+    fflush(ficgp);
  }  /* end gnuplot */
- Line 3454  populforecast(char fileres[], double anp
+ Line 4160  populforecast(char fileres[], double anp
    fclose(ficrespop);
  } /* End of popforecast */
+ int fileappend(FILE *fichier, char *optionfich)
+ {
+   if((fichier=fopen(optionfich,"a"))==NULL) {
+     printf("Problem with file: %s\n", optionfich);
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+     return (0);
+   }
+   fflush(fichier);
+   return (1);
+ }
+ /**************** function prwizard **********************/
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+ {
+   /* Wizard to print covariance matrix template */
+   char ca[32], cb[32], cc[32];
+   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+   int numlinepar;
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   for(i=1; i <=nlstate; i++){
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
+       jj++;
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+       printf("%1d%1d",i,j);
+       fprintf(ficparo,"%1d%1d",i,j);
+       for(k=1; k<=ncovmodel;k++){
+         /*        printf(" %lf",param[i][j][k]); */
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+         printf(" 0.");
+         fprintf(ficparo," 0.");
+       }
+       printf("\n");
+       fprintf(ficparo,"\n");
+     }
+   }
+   printf("# Scales (for hessian or gradient estimation)\n");
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   for(i=1; i <=nlstate; i++){
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
+       jj++;
+       fprintf(ficparo,"%1d%1d",i,j);
+       printf("%1d%1d",i,j);
+       fflush(stdout);
+       for(k=1; k<=ncovmodel;k++){
+         /*      printf(" %le",delti3[i][j][k]); */
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+         printf(" 0.");
+         fprintf(ficparo," 0.");
+       }
+       numlinepar++;
+       printf("\n");
+       fprintf(ficparo,"\n");
+     }
+   }
+   printf("# Covariance matrix\n");
+ /* # 121 Var(a12)\n\ */
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   fflush(stdout);
+   fprintf(ficparo,"# Covariance matrix\n");
+   /* # 121 Var(a12)\n\ */
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   /* #   ...\n\ */
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+   for(itimes=1;itimes<=2;itimes++){
+     jj=0;
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j==i) continue;
+         for(k=1; k<=ncovmodel;k++){
+           jj++;
+           ca[0]= k+'a'-1;ca[1]='\0';
+           if(itimes==1){
+             printf("#%1d%1d%d",i,j,k);
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+           }else{
+             printf("%1d%1d%d",i,j,k);
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
+             /*  printf(" %.5le",matcov[i][j]); */
+           }
+           ll=0;
+           for(li=1;li <=nlstate; li++){
+             for(lj=1;lj <=nlstate+ndeath; lj++){
+               if(lj==li) continue;
+               for(lk=1;lk<=ncovmodel;lk++){
+                 ll++;
+                 if(ll<=jj){
+                   cb[0]= lk +'a'-1;cb[1]='\0';
+                   if(ll<jj){
+                     if(itimes==1){
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                     }else{
+                       printf(" 0.");
+                       fprintf(ficparo," 0.");
+                     }
+                   }else{
+                     if(itimes==1){
+                       printf(" Var(%s%1d%1d)",ca,i,j);
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+                     }else{
+                       printf(" 0.");
+                       fprintf(ficparo," 0.");
+                     }
+                   }
+                 }
+               } /* end lk */
+             } /* end lj */
+           } /* end li */
+           printf("\n");
+           fprintf(ficparo,"\n");
+           numlinepar++;
+         } /* end k*/
+       } /*end j */
+     } /* end i */
+   } /* end itimes */
+ } /* end of prwizard */
+ /******************* Gompertz Likelihood ******************************/
+ double gompertz(double x[])
+ {
+   double A,B,L=0.0,sump=0.,num=0.;
+   int i,n=0; /* n is the size of the sample */
+   for (i=0;i<=imx-1 ; i++) {
+     sump=sump+weight[i];
+     /*    sump=sump+1;*/
+     num=num+1;
+   }
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+   for (i=1;i<=imx ; i++)
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+       if (cens[i] == 0 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
+         L=L+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+       }
+     }
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   return -2*L*num/sump;
+ }
+ /******************* Printing html file ***********/
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   int imx,  double p[],double **matcov,double agemortsup){
+   int i,k;
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   for (i=1;i<=2;i++)
+     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+   fprintf(fichtm,"</ul>");
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+  for (k=agegomp;k<(agemortsup-2);k++)
+    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+   fflush(fichtm);
+ }
+ /******************* Gnuplot file **************/
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   char dirfileres[132],optfileres[132];
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   int ng;
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     /*#endif */
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+   fprintf(ficgp, "set ter png small\n set log y\n");
+   fprintf(ficgp, "set size 0.65,0.65\n");
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+ }
  /***********************************************/
  /**************** Main Program *****************/
  /***********************************************/
- Line 3462  int main(int argc, char *argv[])
+ Line 4390  int main(int argc, char *argv[])
  {
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+   int 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];
+   char dummy[]="                         ";
+   /*  FILE *fichtm; *//* Html File */
+   /* FILE *ficgp;*/ /*Gnuplot File */
+   struct stat info;
    double agedeb, agefin,hf;
    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
- Line 3473  int main(int argc, char *argv[])
+ Line 4413  int main(int argc, char *argv[])
    double ***mobaverage;
    int *indx;
    char line[MAXLINE], linepar[MAXLINE];
-   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   char pathr[MAXLINE], pathimach[MAXLINE];
+   char **bp, *tok, *val; /* pathtot */
    int firstobs=1, lastobs=10;
    int sdeb, sfin; /* Status at beginning and end */
    int c,  h , cpt,l;
- Line 3483  int main(int argc, char *argv[])
+ Line 4425  int main(int argc, char *argv[])
    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
    int mobilav=0,popforecast=0;
    int hstepm, nhstepm;
+   int agemortsup;
+   float  sumlpop=0.;
    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
- Line 3500  int main(int argc, char *argv[])
+ Line 4444  int main(int argc, char *argv[])
    double *epj, vepp;
    double kk1, kk2;
    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double **ximort;
    char *alph[]={"a","a","b","c","d","e"}, str[4];
+   int *dcwave;
    char z[1]="c", occ;
- #include <sys/time.h>
- #include <time.h>
    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+   char  *strt, strtend[80];
+   char *stratrunc;
+   int lstra;
+   long total_usecs;
-   /* long total_usecs;
+ /*   setlocale (LC_ALL, ""); */
-      struct timeval start_time, end_time;
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
-      gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   (void) gettimeofday(&start_time,&tzp);
+   curr_time=start_time;
+   tm = *localtime(&start_time.tv_sec);
+   tmg = *gmtime(&start_time.tv_sec);
+   strcpy(strstart,asctime(&tm));
+ /*  printf("Localtime (at start)=%s",strstart); */
+ /*  tp.tv_sec = tp.tv_sec +86400; */
+ /*  tm = *localtime(&start_time.tv_sec); */
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ /*   tp.tv_sec = mktime(&tmg); */
+ /*   strt=asctime(&tmg); */
+ /*   printf("Time(after) =%s",strstart);  */
+ /*  (void) time (&time_value);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+ *  tm = *localtime(&time_value);
+ *  strstart=asctime(&tm);
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+ */
+   nberr=0; /* Number of errors and warnings */
+   nbwarn=0;
    getcwd(pathcd, size);
    printf("\n%s\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]);
    }
-   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
    /*cygwin_split_path(pathtot,path,optionfile);
      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
    /* cutv(path,optionfile,pathtot,'\\');*/
+   /* Split argv[0], imach program to get pathimach */
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+  /*   strcpy(pathimach,argv[0]); */
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-   chdir(path);
+   chdir(path); /* Can be a relative path */
-   replace(pathc,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){
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+     /* fclose(ficlog); */
+ /*     exit(1); */
+   }
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
+ /*     perror("mkdir"); */
+ /*   } */
    /*-------- arguments in the command line --------*/
- Line 3543  int main(int argc, char *argv[])
+ Line 4546  int main(int argc, char *argv[])
      goto end;
    }
    fprintf(ficlog,"Log filename:%s\n",filelog);
-   fprintf(ficlog,"\n%s",version);
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-   fprintf(ficlog,"\nEnter the parameter file name: ");
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+  path=%s \n\
+  optionfile=%s\n\
+  optionfilext=%s\n\
+  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("Local time (at start):%s",strstart);
+   fprintf(ficlog,"Local time (at start): %s",strstart);
    fflush(ficlog);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
    /* */
    strcpy(fileres,"r");
- Line 3558  int main(int argc, char *argv[])
+ Line 4570  int main(int argc, char *argv[])
    if((ficpar=fopen(optionfile,"r"))==NULL)    {
      printf("Problem with optionfile %s\n",optionfile);
      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+     fflush(ficlog);
      goto end;
    }
    strcpy(filereso,"o");
    strcat(filereso,fileres);
-   if((ficparo=fopen(filereso,"w"))==NULL) {
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
      printf("Problem with Output resultfile: %s\n", filereso);
      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     fflush(ficlog);
      goto end;
    }
    /* Reads comments: lines beginning with '#' */
+   numlinepar=0;
    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
+     numlinepar++;
      puts(line);
      fputs(line,ficparo);
+     fputs(line,ficlog);
    }
    ungetc(c,ficpar);
    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   numlinepar++;
    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fflush(ficlog);
    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
+     numlinepar++;
      puts(line);
      fputs(line,ficparo);
+     fputs(line,ficlog);
    }
    ungetc(c,ficpar);
    covar=matrix(0,NCOVMAX,1,n);
    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
- Line 3596  int main(int argc, char *argv[])
+ Line 4620  int main(int argc, char *argv[])
    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-   /* Read guess parameters */
-   /* Reads comments: lines beginning with '#' */
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+   delti=delti3[1][1];
-     ungetc(c,ficpar);
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-     fgets(line, MAXLINE, ficpar);
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-     puts(line);
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     fputs(line,ficparo);
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     fclose (ficparo);
+     fclose (ficlog);
+     goto end;
+     exit(0);
    }
-   ungetc(c,ficpar);
+   else if(mle==-3) {
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-   for(i=1; i <=nlstate; i++)
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     for(j=1; j <=nlstate+ndeath-1; j++){
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
+     matcov=matrix(1,npar,1,npar);
-       fprintf(ficparo,"%1d%1d",i1,j1);
+   }
-       if(mle==1)
+   else{
-         printf("%1d%1d",i,j);
+     /* Read guess parameters */
-       fprintf(ficlog,"%1d%1d",i,j);
+     /* Reads comments: lines beginning with '#' */
-       for(k=1; k<=ncovmodel;k++){
+     while((c=getc(ficpar))=='#' && c!= EOF){
-         fscanf(ficpar," %lf",&param[i][j][k]);
+       ungetc(c,ficpar);
-         if(mle==1){
+       fgets(line, MAXLINE, ficpar);
-           printf(" %lf",param[i][j][k]);
+       numlinepar++;
-           fprintf(ficlog," %lf",param[i][j][k]);
+       puts(line);
-         }
+       fputs(line,ficparo);
-         else
+       fputs(line,ficlog);
-           fprintf(ficlog," %lf",param[i][j][k]);
-         fprintf(ficparo," %lf",param[i][j][k]);
-       }
-       fscanf(ficpar,"\n");
-       if(mle==1)
-         printf("\n");
-       fprintf(ficlog,"\n");
-       fprintf(ficparo,"\n");
      }
+     ungetc(c,ficpar);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     for(i=1; i <=nlstate; i++){
+       j=0;
+       for(jj=1; jj <=nlstate+ndeath; jj++){
+         if(jj==i) continue;
+         j++;
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ((i1 != i) && (j1 != j)){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+ 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);
+         if(mle==1)
+           printf("%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i,j);
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar," %lf",&param[i][j][k]);
+           if(mle==1){
+             printf(" %lf",param[i][j][k]);
+             fprintf(ficlog," %lf",param[i][j][k]);
+           }
+           else
+             fprintf(ficlog," %lf",param[i][j][k]);
+           fprintf(ficparo," %lf",param[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         if(mle==1)
+           printf("\n");
+         fprintf(ficlog,"\n");
+         fprintf(ficparo,"\n");
+       }
+     }
+     fflush(ficlog);
-   p=param[1][1];
+     p=param[1][1];
-   /* Reads comments: lines beginning with '#' */
+     /* Reads comments: lines beginning with '#' */
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       puts(line);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     for(i=1; i <=nlstate; i++){
-   /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
+       for(j=1; j <=nlstate+ndeath-1; j++){
-   for(i=1; i <=nlstate; i++){
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     for(j=1; j <=nlstate+ndeath-1; j++){
+         if ((i1-i)*(j1-j)!=0){
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-       printf("%1d%1d",i,j);
+           exit(1);
-       fprintf(ficparo,"%1d%1d",i1,j1);
+         }
-       for(k=1; k<=ncovmodel;k++){
+         printf("%1d%1d",i,j);
-         fscanf(ficpar,"%le",&delti3[i][j][k]);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-         printf(" %le",delti3[i][j][k]);
+         fprintf(ficlog,"%1d%1d",i1,j1);
-         fprintf(ficparo," %le",delti3[i][j][k]);
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
+           printf(" %le",delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
+           fprintf(ficlog," %le",delti3[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         printf("\n");
+         fprintf(ficparo,"\n");
+         fprintf(ficlog,"\n");
        }
-       fscanf(ficpar,"\n");
-       printf("\n");
-       fprintf(ficparo,"\n");
      }
-   }
+     fflush(ficlog);
-   delti=delti3[1][1];
+     delti=delti3[1][1];
-   /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-   /* Reads comments: lines beginning with '#' */
+     /* Reads comments: lines beginning with '#' */
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       puts(line);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   matcov=matrix(1,npar,1,npar);
+     matcov=matrix(1,npar,1,npar);
-   for(i=1; i <=npar; i++){
+     for(i=1; i <=npar; i++){
-     fscanf(ficpar,"%s",&str);
+       fscanf(ficpar,"%s",&str);
-     if(mle==1)
+       if(mle==1)
-       printf("%s",str);
+         printf("%s",str);
-     fprintf(ficlog,"%s",str);
+       fprintf(ficlog,"%s",str);
-     fprintf(ficparo,"%s",str);
+       fprintf(ficparo,"%s",str);
-     for(j=1; j <=i; j++){
+       for(j=1; j <=i; j++){
-       fscanf(ficpar," %le",&matcov[i][j]);
+         fscanf(ficpar," %le",&matcov[i][j]);
-       if(mle==1){
+         if(mle==1){
-         printf(" %.5le",matcov[i][j]);
+           printf(" %.5le",matcov[i][j]);
+         }
          fprintf(ficlog," %.5le",matcov[i][j]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
        }
-       else
+       fscanf(ficpar,"\n");
-         fprintf(ficlog," %.5le",matcov[i][j]);
+       numlinepar++;
-       fprintf(ficparo," %.5le",matcov[i][j]);
+       if(mle==1)
+         printf("\n");
+       fprintf(ficlog,"\n");
+       fprintf(ficparo,"\n");
      }
-     fscanf(ficpar,"\n");
+     for(i=1; i <=npar; i++)
+       for(j=i+1;j<=npar;j++)
+         matcov[i][j]=matcov[j][i];
      if(mle==1)
        printf("\n");
      fprintf(ficlog,"\n");
-     fprintf(ficparo,"\n");
-   }
-   for(i=1; i <=npar; i++)
-     for(j=i+1;j<=npar;j++)
-       matcov[i][j]=matcov[j][i];
-   if(mle==1)
-     printf("\n");
-   fprintf(ficlog,"\n");
-   /*-------- Rewriting paramater file ----------*/
-   strcpy(rfileres,"r");    /* "Rparameterfile */
-   strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-   strcat(rfileres,".");    /* */
-   strcat(rfileres,optionfilext);    /* Other files have txt extension */
-   if((ficres =fopen(rfileres,"w"))==NULL) {
-     printf("Problem writing new parameter file: %s\n", fileres);goto end;
-     fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-   }
-   fprintf(ficres,"#%s\n",version);
+     fflush(ficlog);
+     /*-------- Rewriting parameter file ----------*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     strcat(rfileres,".");    /* */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     if((ficres =fopen(rfileres,"w"))==NULL) {
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+     }
+     fprintf(ficres,"#%s\n",version);
+   }    /* End of mle != -3 */
    /*-------- data file ----------*/
    if((fic=fopen(datafile,"r"))==NULL)    {
-     printf("Problem with datafile: %s\n", datafile);goto end;
+     printf("Problem while opening datafile: %s\n", datafile);goto end;
-     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
    }
    n= lastobs;
    severity = vector(1,maxwav);
    outcome=imatrix(1,maxwav+1,1,n);
-   num=ivector(1,n);
+   num=lvector(1,n);
    moisnais=vector(1,n);
    annais=vector(1,n);
    moisdc=vector(1,n);
- Line 3744  int main(int argc, char *argv[])
+ Line 4815  int main(int argc, char *argv[])
    ncodemax=ivector(1,8);
    i=1;
-   while (fgets(line, MAXLINE, fic) != NULL)    {
+   linei=0;
-     if ((i >= firstobs) && (i <=lastobs)) {
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+     linei=linei+1;
-       for (j=maxwav;j>=1;j--){
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-         cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
+       if(line[j] == '\t')
-         strcpy(line,stra);
+         line[j] = ' ';
-         cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+     }
-         cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+       ;
+     };
+     line[j+1]=0;  /* Trims blanks at end of line */
+     if(line[0]=='#'){
+       fprintf(ficlog,"Comment line\n%s\n",line);
+       printf("Comment line\n%s\n",line);
+       continue;
+     }
+     for (j=maxwav;j>=1;j--){
+       cutv(stra, strb,line,' ');
+       errno=0;
+       lval=strtol(strb,&endptr,10);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+       if( strb[0]=='\0' || (*endptr != '\0')){
+         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+         exit(1);
        }
+       s[j][i]=lval;
-       cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
+       strcpy(line,stra);
+       cutv(stra, strb,line,' ');
-       cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-       cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
+       }
+       else  if(iout=sscanf(strb,"%s.") != 0){
-       cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
+         month=99;
-       for (j=ncovcol;j>=1;j--){
+         year=9999;
-         cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+       }else{
-       }
+         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-       num[i]=atol(stra);
+         exit(1);
+       }
-       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+       anint[j][i]= (double) year;
-         printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+       mint[j][i]= (double)month;
+       strcpy(line,stra);
-       i=i+1;
+     } /* 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 %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+       exit(1);
+     }
+     andc[i]=(double) year;
+     moisdc[i]=(double) month;
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
+     else  if(iout=sscanf(strb,"%s.") != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
+       exit(1);
+     }
+     annais[i]=(double)(year);
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     errno=0;
+     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);
+       exit(1);
+     }
+     weight[i]=dval;
+     strcpy(line,stra);
+     for (j=ncovcol;j>=1;j--){
+       cutv(stra, strb,line,' ');
+       errno=0;
+       lval=strtol(strb,&endptr,10);
+       if( strb[0]=='\0' || (*endptr != '\0')){
+         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
+         exit(1);
+       }
+       if(lval <-1 || lval >1){
+         printf("Error reading data around '%d' at line number %ld 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);
+         exit(1);
+       }
+       covar[j][i]=(double)(lval);
+       strcpy(line,stra);
+     }
+     lstra=strlen(stra);
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       stratrunc = &(stra[lstra-9]);
+       num[i]=atol(stratrunc);
+     }
+     else
+       num[i]=atol(stra);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+     i=i+1;
+   } /* End loop reading  data */
+   fclose(fic);
    /* printf("ii=%d", ij);
       scanf("%d",i);*/
    imx=i-1; /* Number of individuals */
- Line 3783  int main(int argc, char *argv[])
+ Line 4945  int main(int argc, char *argv[])
      }*/
     /*  for (i=1; i<=imx; i++){
       if (s[4][i]==9)  s[4][i]=-1;
-      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
-  for (i=1; i<=imx; i++)
+   /* for (i=1; i<=imx; i++) */
     /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
       else weight[i]=1;*/
-   /* Calculation of the number of parameter from char model*/
+   /* Calculation of the number of parameters from char model */
    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
    Tprod=ivector(1,15);
    Tvaraff=ivector(1,15);
- Line 3869  int main(int argc, char *argv[])
+ Line 5031  int main(int argc, char *argv[])
    printf("cptcovprod=%d ", cptcovprod);
    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-   scanf("%d ",i);
+   scanf("%d ",i);*/
-   fclose(fic);*/
      /*  if(mle==1){*/
    if (weightopt != 1) { /* Maximisation without weights*/
- Line 3886  int main(int argc, char *argv[])
+ Line 5047  int main(int argc, char *argv[])
          s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         printf("Error! Date of death (month %2d and year %4d) of individual %d 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);
+         nberr++;
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d 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);
+         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
          s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-         printf("Error! Month of death of individual %d 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]);
+         nberr++;
-         fprintf(ficlog,"Error! Month of death of individual %d 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]);
+         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 */
        }
      }
- Line 3901  int main(int argc, char *argv[])
+ Line 5064  int main(int argc, char *argv[])
    for (i=1; i<=imx; i++)  {
      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
      for(m=firstpass; (m<= lastpass); m++){
-       if(s[m][i] >0){
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
          if (s[m][i] >= nlstate+1) {
            if(agedc[i]>0)
              if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
- Line 3909  int main(int argc, char *argv[])
+ Line 5072  int main(int argc, char *argv[])
            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
              else {
                if ((int)andc[i]!=9999){
-                 printf("Warning negative age at death: %d line:%d\n",num[i],i);
+                 nbwarn++;
-                 fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+                 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
+                                  years but with the precision of a month */
-                                  month */
            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
            if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
              agev[m][i]=1;
- Line 3945  int main(int argc, char *argv[])
+ Line 5108  int main(int argc, char *argv[])
    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;
- Line 3954  int main(int argc, char *argv[])
+ Line 5118  int main(int argc, char *argv[])
    /*for (i=1; i<=imx; i++){
    for (m=firstpass; (m<lastpass); m++){
-      printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+      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);
- Line 4013  int main(int argc, char *argv[])
+ Line 5179  int main(int argc, char *argv[])
       }
       scanf("%d",i);*/
+   /*------------ gnuplot -------------*/
+   strcpy(optionfilegnuplot,optionfilefiname);
+   if(mle==-3)
+     strcat(optionfilegnuplot,"-mort");
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+   else{
+     fprintf(ficgp,"\n# %s\n", version);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     fprintf(ficgp,"set missing 'NaNq'\n");
+   }
+   /*  fclose(ficgp);*/
+   /*--------- index.htm --------*/
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   if(mle==-3)
+     strcat(optionfilehtm,"-mort");
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm), exit(0);
+   }
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   strcat(optionfilehtmcov,"-cov.htm");
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   }
+   else{
+   fprintf(fichtmcov,"<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",\
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   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",\
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+           fileres,fileres,\
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+   fflush(fichtm);
+   strcpy(pathr,path);
+   strcat(pathr,optionfilefiname);
+   chdir(optionfilefiname); /* Move to directory named optionfile */
    /* Calculates basic frequencies. Computes observed prevalence at single age
       and prints on file fileres'p'. */
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   fprintf(fichtm,"\n");
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+           imx,agemin,agemax,jmin,jmax,jmean);
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
- Line 4028  int main(int argc, char *argv[])
+ Line 5257  int main(int argc, char *argv[])
       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-   if(mle>=1){ /* Could be 1 or 2 */
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
-   }
+   if (mle==-3){
+     ximort=matrix(1,NDIM,1,NDIM);
+     cens=ivector(1,n);
+     ageexmed=vector(1,n);
+     agecens=vector(1,n);
+     dcwave=ivector(1,n);
+     for (i=1; i<=imx; i++){
+       dcwave[i]=-1;
+       for (m=firstpass; m<=lastpass; m++)
+         if (s[m][i]>nlstate) {
+           dcwave[i]=m;
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+           break;
+         }
+     }
+     for (i=1; i<=imx; i++) {
+       if (wav[i]>0){
+         ageexmed[i]=agev[mw[1][i]][i];
+         j=wav[i];
+         agecens[i]=1.;
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
+           cens[i]= 1;
+         }else if (ageexmed[i]< 1)
+           cens[i]= -1;
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+           cens[i]=0 ;
+       }
+       else cens[i]=-1;
+     }
-   /*--------- results files --------------*/
+     for (i=1;i<=NDIM;i++) {
-   fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+       for (j=1;j<=NDIM;j++)
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     }
+     p[1]=0.0268; p[NDIM]=0.083;
+     /*printf("%lf %lf", p[1], p[2]);*/
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+     strcpy(filerespow,"pow-mort");
+     strcat(filerespow,fileres);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", filerespow);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+     }
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+     /*  for (i=1;i<=nlstate;i++)
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     */
+     fprintf(ficrespow,"\n");
+     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+     fclose(ficrespow);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
-   jk=1;
+     for(i=1; i <=NDIM; i++)
-   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       for(j=i+1;j<=NDIM;j++)
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+         matcov[i][j]=matcov[j][i];
-   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   for(i=1,jk=1; i <=nlstate; i++){
+     printf("\nCovariance matrix\n ");
-     for(k=1; k <=(nlstate+ndeath); k++){
+     for(i=1; i <=NDIM; i++) {
-       if (k != i)
+       for(j=1;j<=NDIM;j++){
-         {
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\n ");
+     }
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     for (i=1;i<=NDIM;i++)
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     lsurv=vector(1,AGESUP);
+     lpop=vector(1,AGESUP);
+     tpop=vector(1,AGESUP);
+     lsurv[agegomp]=100000;
+     for (k=agegomp;k<=AGESUP;k++) {
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
+     }
+     tpop[agegomp]=sumlpop;
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+                      stepm, weightopt,\
+                      model,imx,p,matcov,agemortsup);
+     free_vector(lsurv,1,AGESUP);
+     free_vector(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+   } /* Endof if mle==-3 */
+   else{ /* For mle >=1 */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     globpr=1; /* to print the contributions */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     if(mle>=1){ /* Could be 1 or 2 */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     /*--------- results files --------------*/
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
            printf("%d%d ",i,k);
            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);
            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");
            fprintf(ficlog,"\n");
            fprintf(ficres,"\n");
          }
+       }
      }
-   }
+     if(mle!=0){
-   if(mle!=0){
+       /* Computing hessian and covariance matrix */
-     /* Computing hessian and covariance matrix */
+       ftolhess=ftol; /* Usually correct */
-     ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, p, npar, delti, ftolhess, func);
-     hesscov(matcov, p, npar, delti, ftolhess, func);
+     }
-   }
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
-   fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
-   printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
-   for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
-     for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
-       if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
-         fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
-         printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
-         fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
-         for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
-           printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
-           fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
-           fprintf(ficres," %.5e",delti[jk]);
+             jk++;
-           jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
          }
-         printf("\n");
-         fprintf(ficlog,"\n");
-         fprintf(ficres,"\n");
        }
      }
-   }
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-   fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     if(mle>=1)
-   if(mle==1)
+       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-   fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     /* # 121 Var(a12)\n\ */
-   for(i=1,k=1;i<=npar;i++){
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     /*  if (k>nlstate) k=1;
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-         i1=(i-1)/(ncovmodel*nlstate)+1;
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-         fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-         printf("%s%d%d",alph[k],i1,tab[i]);
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
      */
-     fprintf(ficres,"%3d",i);
+     for(itimes=1;itimes<=2;itimes++){
-     if(mle==1)
+       jj=0;
-       printf("%3d",i);
+       for(i=1; i <=nlstate; i++){
-     fprintf(ficlog,"%3d",i);
+         for(j=1; j <=nlstate+ndeath; j++){
-     for(j=1; j<=i;j++){
+           if(j==i) continue;
-       fprintf(ficres," %.5e",matcov[i][j]);
+           for(k=1; k<=ncovmodel;k++){
-       if(mle==1)
+             jj++;
-         printf(" %.5e",matcov[i][j]);
+             ca[0]= k+'a'-1;ca[1]='\0';
-       fprintf(ficlog," %.5e",matcov[i][j]);
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       puts(line);
+       fputs(line,ficparo);
      }
-     fprintf(ficres,"\n");
-     if(mle==1)
-       printf("\n");
-     fprintf(ficlog,"\n");
-     k++;
-   }
-   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
+     estepm=0;
-     fputs(line,ficparo);
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
-   }
+     if (estepm==0 || estepm < stepm) estepm=stepm;
-   ungetc(c,ficpar);
+     if (fage <= 2) {
+       bage = ageminpar;
-   estepm=0;
+       fage = agemaxpar;
-   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     }
-   if (estepm==0 || estepm < stepm) estepm=stepm;
-   if (fage <= 2) {
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     bage = ageminpar;
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-     fage = agemaxpar;
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-   }
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+       ungetc(c,ficpar);
-   fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+       fgets(line, MAXLINE, ficpar);
-   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+       puts(line);
+       fputs(line,ficparo);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     }
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
-   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
+     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
-     fputs(line,ficparo);
+     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   }
+     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   ungetc(c,ficpar);
+     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-   fscanf(ficpar,"pop_based=%d\n",&popbased);
+       puts(line);
-   fprintf(ficparo,"pop_based=%d\n",popbased);
+       fputs(line,ficparo);
-   fprintf(ficres,"pop_based=%d\n",popbased);
+     }
-   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-   }
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-   ungetc(c,ficpar);
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
-   fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+     fprintf(ficparo,"pop_based=%d\n",popbased);
-   fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficres,"pop_based=%d\n",popbased);
-   printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+       ungetc(c,ficpar);
-   /* day and month of proj2 are not used but only year anproj2.*/
+       fgets(line, MAXLINE, ficpar);
+       puts(line);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       fputs(line,ficparo);
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
+     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
-     fputs(line,ficparo);
+     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   }
+     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   ungetc(c,ficpar);
+     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
+     /* day and month of proj2 are not used but only year anproj2.*/
-   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
+     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
-   /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-   /*------------ gnuplot -------------*/
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-   strcpy(optionfilegnuplot,optionfilefiname);
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-   strcat(optionfilegnuplot,".gp");
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
-     printf("Problem with file %s",optionfilegnuplot);
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
-   }
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
-   else{
-     fprintf(ficgp,"\n# %s\n", version);
+    /*------------ free_vector  -------------*/
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+    /*  chdir(path); */
-     fprintf(ficgp,"set missing 'NaNq'\n");
-   }
-   fclose(ficgp);
-   printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
-   /*--------- index.htm --------*/
-   strcpy(optionfilehtm,optionfile);
-   strcat(optionfilehtm,".htm");
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-     printf("Problem with %s \n",optionfilehtm), exit(0);
-   }
-   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
- \n
- Total number of observations=%d <br>\n
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
- <hr  size=\"2\" color=\"#EC5E5E\">
-  <ul><li><h4>Parameter files</h4>\n
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n
-  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
-    fclose(fichtm);
-   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
-   /*------------ free_vector  -------------*/
-   chdir(path);
-   free_ivector(wav,1,imx);
+     free_ivector(wav,1,imx);
-   free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-   free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
-   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-   free_ivector(num,1,n);
+     free_lvector(num,1,n);
-   free_vector(agedc,1,n);
+     free_vector(agedc,1,n);
-   /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
-   /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
-   fclose(ficparo);
+     fclose(ficparo);
-   fclose(ficres);
+     fclose(ficres);
-   /*--------------- Prevalence limit  (stable prevalence) --------------*/
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-   strcpy(filerespl,"pl");
+     strcpy(filerespl,"pl");
-   strcat(filerespl,fileres);
+     strcat(filerespl,fileres);
-   if((ficrespl=fopen(filerespl,"w"))==NULL) {
+     if((ficrespl=fopen(filerespl,"w"))==NULL) {
-     printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
+       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-     fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
+       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-   }
+     }
-   printf("Computing stable prevalence: result on file '%s' \n", filerespl);
+     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
+     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficrespl,"#Stable prevalence \n");
+     pstamp(ficrespl);
-   fprintf(ficrespl,"#Age ");
+     fprintf(ficrespl,"# Period (stable) prevalence \n");
-   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     fprintf(ficrespl,"#Age ");
-   fprintf(ficrespl,"\n");
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     fprintf(ficrespl,"\n");
-   prlim=matrix(1,nlstate,1,nlstate);
+     prlim=matrix(1,nlstate,1,nlstate);
-   agebase=ageminpar;
-   agelim=agemaxpar;
+     agebase=ageminpar;
-   ftolpl=1.e-10;
+     agelim=agemaxpar;
-   i1=cptcoveff;
+     ftolpl=1.e-10;
-   if (cptcovn < 1){i1=1;}
+     i1=cptcoveff;
+     if (cptcovn < 1){i1=1;}
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       k=k+1;
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+         k=k+1;
-       fprintf(ficrespl,"\n#******");
+         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
-       printf("\n#******");
+         fprintf(ficrespl,"\n#******");
-       fprintf(ficlog,"\n#******");
+         printf("\n#******");
-       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficlog,"\n#******");
-         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         for(j=1;j<=cptcoveff;j++) {
-         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       }
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficrespl,"******\n");
+         }
-       printf("******\n");
+         fprintf(ficrespl,"******\n");
-       fprintf(ficlog,"******\n");
+         printf("******\n");
+         fprintf(ficlog,"******\n");
-       for (age=agebase; age<=agelim; age++){
+         for (age=agebase; age<=agelim; age++){
-         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-         fprintf(ficrespl,"%.0f ",age );
+           fprintf(ficrespl,"%.0f ",age );
-         for(j=1;j<=cptcoveff;j++)
+           for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         for(i=1; i<=nlstate;i++)
+           for(i=1; i<=nlstate;i++)
-           fprintf(ficrespl," %.5f", prlim[i][i]);
+             fprintf(ficrespl," %.5f", prlim[i][i]);
-         fprintf(ficrespl,"\n");
+           fprintf(ficrespl,"\n");
+         }
        }
      }
-   }
+     fclose(ficrespl);
-   fclose(ficrespl);
-   /*------------- h Pij x at various ages ------------*/
+     /*------------- h Pij x at various ages ------------*/
-   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-   if((ficrespij=fopen(filerespij,"w"))==NULL) {
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
-     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-   }
+     }
-   printf("Computing pij: result on file '%s' \n", filerespij);
+     printf("Computing pij: result on file '%s' \n", filerespij);
-   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
-   /*if (stepm<=24) stepsize=2;*/
+     /*if (stepm<=24) stepsize=2;*/
-   agelim=AGESUP;
-   hstepm=stepsize*YEARM; /* Every year of age */
-   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-   /* hstepm=1;   aff par mois*/
+     agelim=AGESUP;
+     hstepm=stepsize*YEARM; /* Every year of age */
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     /* hstepm=1;   aff par mois*/
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     pstamp(ficrespij);
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-       k=k+1;
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       fprintf(ficrespij,"\n#****** ");
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-       for(j=1;j<=cptcoveff;j++)
+         k=k+1;
-         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrespij,"\n#****** ");
-       fprintf(ficrespij,"******\n");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrespij,"******\n");
-       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-         /*        nhstepm=nhstepm*YEARM; aff par mois*/
+           /*      nhstepm=nhstepm*YEARM; aff par mois*/
-         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         oldm=oldms;savm=savms;
+           oldm=oldms;savm=savms;
-         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-         for(i=1; i<=nlstate;i++)
-           for(j=1; j<=nlstate+ndeath;j++)
-             fprintf(ficrespij," %1d-%1d",i,j);
-         fprintf(ficrespij,"\n");
-         for (h=0; h<=nhstepm; h++){
-           fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
            for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate+ndeath;j++)
-               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+               fprintf(ficrespij," %1d-%1d",i,j);
+           fprintf(ficrespij,"\n");
+           for (h=0; h<=nhstepm; h++){
+             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+             for(i=1; i<=nlstate;i++)
+               for(j=1; j<=nlstate+ndeath;j++)
+                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+             fprintf(ficrespij,"\n");
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            fprintf(ficrespij,"\n");
          }
-         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         fprintf(ficrespij,"\n");
        }
      }
-   }
-   varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
-   fclose(ficrespij);
+     fclose(ficrespij);
-   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(i=1;i<=AGESUP;i++)
-   /*---------- Forecasting ------------------*/
+       for(j=1;j<=NCOVMAX;j++)
-   /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+         for(k=1;k<=NCOVMAX;k++)
-   if(prevfcast==1){
+           probs[i][j][k]=0.;
-     /*    if(stepm ==1){*/
+     /*---------- Forecasting ------------------*/
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
        prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
        /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
- /*      }  */
+       /*      }  */
- /*      else{ */
+       /*      else{ */
- /*        erreur=108; */
+       /*        erreur=108; */
- /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
- /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
- /*      } */
+       /*      } */
-   }
+     }
-   /*---------- Health expectancies and variances ------------*/
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
-   strcpy(filerest,"t");
-   strcat(filerest,fileres);
-   if((ficrest=fopen(filerest,"w"))==NULL) {
-     printf("Problem with total LE resultfile: %s\n", filerest);goto end;
-     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
-   }
-   printf("Computing Total LEs with variances: file '%s' \n", filerest);
-   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
+     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);
+     */
-   strcpy(filerese,"e");
+     if (mobilav!=0) {
-   strcat(filerese,fileres);
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   if((ficreseij=fopen(filerese,"w"))==NULL) {
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   }
+       }
-   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     }
-   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
-   strcpy(fileresv,"v");
-   strcat(fileresv,fileres);
-   if((ficresvij=fopen(fileresv,"w"))==NULL) {
-     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
-     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
-   }
-   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-   /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     /*---------- Health expectancies, no variances ------------*/
-   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) {
+     strcpy(filerese,"e");
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     strcat(filerese,fileres);
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+     if((ficreseij=fopen(filerese,"w"))==NULL) {
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
      }
-   }
+     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     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");
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         oldm=oldms;savm=savms;
-       k=k+1;
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
-       fprintf(ficrest,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficrest,"******\n");
-       fprintf(ficreseij,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficreseij,"******\n");
-       fprintf(ficresvij,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficresvij,"******\n");
-       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
-       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
-       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
-       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
-       if(popbased==1){
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
        }
+     }
+     fclose(ficreseij);
-       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+     /*---------- Health expectancies and variances ------------*/
-       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-       fprintf(ficrest,"\n");
+     strcpy(filerest,"t");
-       epj=vector(1,nlstate+1);
+     strcat(filerest,fileres);
-       for(age=bage; age <=fage ;age++){
+     if((ficrest=fopen(filerest,"w"))==NULL) {
-         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
-         if (popbased==1) {
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
-           if(mobilav ==0){
+     }
-             for(i=1; i<=nlstate;i++)
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
-               prlim[i][i]=probs[(int)age][i][k];
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
-           }else{ /* mobilav */
-             for(i=1; i<=nlstate;i++)
-               prlim[i][i]=mobaverage[(int)age][i][k];
+     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);
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     }
+     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
+         fprintf(ficrest,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrest,"******\n");
+         fprintf(ficresstdeij,"\n#****** ");
+         fprintf(ficrescveij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           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++)
+           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         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);
+         pstamp(ficrest);
+         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=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,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);
+           else
+             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"# Age e.. (std) ");
+           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           fprintf(ficrest,"\n");
+           epj=vector(1,nlstate+1);
+           for(age=bage; age <=fage ;age++){
+             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+             if (vpopbased==1) {
+               if(mobilav ==0){
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=probs[(int)age][i][k];
+               }else{ /* mobilav */
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=mobaverage[(int)age][i][k];
+               }
+             }
-         fprintf(ficrest," %4.0f",age);
+             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];
+             }
+             for(i=1, vepp=0.;i <=nlstate;i++)
+               for(j=1;j <=nlstate;j++)
+                 vepp += vareij[i][j][(int)age];
+             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+             for(j=1;j <=nlstate;j++){
+               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             }
+             fprintf(ficrest,"\n");
            }
-           epj[nlstate+1] +=epj[j];
          }
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         for(i=1, vepp=0.;i <=nlstate;i++)
+         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-           for(j=1;j <=nlstate;j++)
+         free_vector(epj,1,nlstate+1);
-             vepp += vareij[i][j][(int)age];
+       }
-         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+     }
-         for(j=1;j <=nlstate;j++){
+     free_vector(weight,1,n);
-           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+     free_imatrix(Tvard,1,15,1,2);
-         }
+     free_imatrix(s,1,maxwav+1,1,n);
-         fprintf(ficrest,"\n");
+     free_matrix(anint,1,maxwav,1,n);
-       }
+     free_matrix(mint,1,maxwav,1,n);
-       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     free_ivector(cod,1,n);
-       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     free_ivector(tab,1,NCOVMAX);
-       free_vector(epj,1,nlstate+1);
+     fclose(ficresstdeij);
-     }
+     fclose(ficrescveij);
-   }
+     fclose(ficresvij);
-   free_vector(weight,1,n);
+     fclose(ficrest);
-   free_imatrix(Tvard,1,15,1,2);
+     fclose(ficpar);
-   free_imatrix(s,1,maxwav+1,1,n);
-   free_matrix(anint,1,maxwav,1,n);
+     /*------- Variance of period (stable) prevalence------*/
-   free_matrix(mint,1,maxwav,1,n);
-   free_ivector(cod,1,n);
+     strcpy(fileresvpl,"vpl");
-   free_ivector(tab,1,NCOVMAX);
+     strcat(fileresvpl,fileres);
-   fclose(ficreseij);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-   fclose(ficresvij);
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
-   fclose(ficrest);
+       exit(0);
-   fclose(ficpar);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
-   /*------- Variance of stable prevalence------*/
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-   strcpy(fileresvpl,"vpl");
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-   strcat(fileresvpl,fileres);
+         k=k+1;
-   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+         fprintf(ficresvpl,"\n#****** ");
-     printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
+         for(j=1;j<=cptcoveff;j++)
-     exit(0);
+           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   }
+         fprintf(ficresvpl,"******\n");
-   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-       k=k+1;
-       fprintf(ficresvpl,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficresvpl,"******\n");
-       varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         varpl=matrix(1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
+         oldm=oldms;savm=savms;
-       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
+         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
-       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       }
      }
-   }
-   fclose(ficresvpl);
+     fclose(ficresvpl);
-   /*---------- End : free ----------------*/
-   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(covar,0,NCOVMAX,1,n);
-   free_matrix(matcov,1,npar,1,npar);
-   /*free_vector(delti,1,npar);*/
-   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-   free_matrix(agev,1,maxwav,1,imx);
-   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ivector(ncodemax,1,8);
+     /*---------- End : free ----------------*/
-   free_ivector(Tvar,1,15);
+     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ivector(Tprod,1,15);
+     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ivector(Tvaraff,1,15);
-   free_ivector(Tage,1,15);
+   }  /* mle==-3 arrives here for freeing */
-   free_ivector(Tcode,1,100);
+   free_matrix(prlim,1,nlstate,1,nlstate);
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
-   /*  fclose(fichtm);*/
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   /*  fclose(ficgp);*/ /* ALready done */
+     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);
-   if(erreur >0){
+     free_matrix(matcov,1,npar,1,npar);
-     printf("End of Imach with error or warning %d\n",erreur);
+     /*free_vector(delti,1,npar);*/
-     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_ivector(ncodemax,1,8);
+     free_ivector(Tvar,1,15);
+     free_ivector(Tprod,1,15);
+     free_ivector(Tvaraff,1,15);
+     free_ivector(Tage,1,15);
+     free_ivector(Tcode,1,100);
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     free_imatrix(codtab,1,100,1,10);
+   fflush(fichtm);
+   fflush(ficgp);
+   if((nberr >0) || (nbwarn>0)){
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
    }else{
-    printf("End of Imach\n");
+     printf("End of Imach\n");
-    fprintf(ficlog,"End of Imach\n");
+     fprintf(ficlog,"End of Imach\n");
    }
    printf("See log file on %s\n",filelog);
-   fclose(ficlog);
    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   (void) gettimeofday(&end_time,&tzp);
-   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
+   tm = *localtime(&end_time.tv_sec);
-   /*printf("Total time was %d uSec.\n", total_usecs);*/
+   tmg = *gmtime(&end_time.tv_sec);
+   strcpy(strtend,asctime(&tm));
+   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ /*   if(fileappend(fichtm,optionfilehtm)){ */
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\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 -----------*/
-   end:
- #ifdef windows
-   /* chdir(pathcd);*/
- #endif
-  /*system("wgnuplot graph.plt");*/
-  /*system("../gp37mgw/wgnuplot graph.plt");*/
-  /*system("cd ../gp37mgw");*/
-  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
-   strcpy(plotcmd,GNUPLOTPROGRAM);
-   strcat(plotcmd," ");
-   strcat(plotcmd,optionfilegnuplot);
-   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
-   system(plotcmd);
-   printf(" Wait...");
-  /*#ifdef windows*/
+    printf("Before Current directory %s!\n",pathcd);
+    if(chdir(pathcd) != 0)
+     printf("Can't move to directory %s!\n",path);
+   if(getcwd(pathcd,MAXLINE) > 0)
+     printf("Current directory %s!\n",pathcd);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
+   sprintf(plotcmd,"gnuplot");
+ #ifndef UNIX
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef UNIX
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+   if((outcmd=system(plotcmd)) != 0){
+     printf("\n Problem with gnuplot\n");
+   }
+   printf(" Wait...");
    while (z[0] != 'q') {
      /* chdir(path); */
-     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
+     printf("\nType e to edit output files, g to graph again and q for exiting: ");
      scanf("%s",z);
-     if (z[0] == 'c') system("./imach");
+ /*     if (z[0] == 'c') system("./imach"); */
-     else if (z[0] == 'e') system(optionfilehtm);
+     if (z[0] == 'e') {
+       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+       system(optionfilehtm);
+     }
      else if (z[0] == 'g') system(plotcmd);
      else if (z[0] == 'q') exit(0);
    }
-   /*#endif */
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: ");
+     scanf("%s",z);
+   }
  }

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