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Diff for /imach/src/imach.c between versions 1.94 and 1.143

-version 1.94, 2003/06/27 13:00:02
+version 1.143, 2014/01/26 09:45:38
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.143  2014/01/26 09:45:38  brouard
+   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
+   Revision 1.142  2014/01/26 03:57:36  brouard
+   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.141  2014/01/26 02:42:01  brouard
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.140  2011/09/02 10:37:54  brouard
+   Summary: times.h is ok with mingw32 now.
+   Revision 1.139  2010/06/14 07:50:17  brouard
+   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
+   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
+   Revision 1.138  2010/04/30 18:19:40  brouard
+   *** empty log message ***
+   Revision 1.137  2010/04/29 18:11:38  brouard
+   (Module): Checking covariates for more complex models
+   than V1+V2. A lot of change to be done. Unstable.
+   Revision 1.136  2010/04/26 20:30:53  brouard
+   (Module): merging some libgsl code. Fixing computation
+   of likelione (using inter/intrapolation if mle = 0) in order to
+   get same likelihood as if mle=1.
+   Some cleaning of code and comments added.
+   Revision 1.135  2009/10/29 15:33:14  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.134  2009/10/29 13:18:53  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.133  2009/07/06 10:21:25  brouard
+   just nforces
+   Revision 1.132  2009/07/06 08:22:05  brouard
+   Many tings
+   Revision 1.131  2009/06/20 16:22:47  brouard
+   Some dimensions resccaled
+   Revision 1.130  2009/05/26 06:44:34  brouard
+   (Module): Max Covariate is now set to 20 instead of 8. A
+   lot of cleaning with variables initialized to 0. Trying to make
+   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
+   Revision 1.129  2007/08/31 13:49:27  lievre
+   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
+   Revision 1.128  2006/06/30 13:02:05  brouard
+   (Module): Clarifications on computing e.j
+   Revision 1.127  2006/04/28 18:11:50  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   (Module): In order to speed up (in case of numerous covariates) we
+   compute health expectancies (without variances) in a first step
+   and then all the health expectancies with variances or standard
+   deviation (needs data from the Hessian matrices) which slows the
+   computation.
+   In the future we should be able to stop the program is only health
+   expectancies and graph are needed without standard deviations.
+   Revision 1.126  2006/04/28 17:23:28  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   Version 0.98h
+   Revision 1.125  2006/04/04 15:20:31  lievre
+   Errors in calculation of health expectancies. Age was not initialized.
+   Forecasting file added.
+   Revision 1.124  2006/03/22 17:13:53  lievre
+   Parameters are printed with %lf instead of %f (more numbers after the comma).
+   The log-likelihood is printed in the log file
+   Revision 1.123  2006/03/20 10:52:43  brouard
+   * imach.c (Module): <title> changed, corresponds to .htm file
+   name. <head> headers where missing.
+   * imach.c (Module): Weights can have a decimal point as for
+   English (a comma might work with a correct LC_NUMERIC environment,
+   otherwise the weight is truncated).
+   Modification of warning when the covariates values are not 0 or
+.
+   Version 0.98g
+   Revision 1.122  2006/03/20 09:45:41  brouard
+   (Module): Weights can have a decimal point as for
+   English (a comma might work with a correct LC_NUMERIC environment,
+   otherwise the weight is truncated).
+   Modification of warning when the covariates values are not 0 or
+.
+   Version 0.98g
+   Revision 1.121  2006/03/16 17:45:01  lievre
+   * imach.c (Module): Comments concerning covariates added
+   * imach.c (Module): refinements in the computation of lli if
+   status=-2 in order to have more reliable computation if stepm is
+   not 1 month. Version 0.98f
+   Revision 1.120  2006/03/16 15:10:38  lievre
+   (Module): refinements in the computation of lli if
+   status=-2 in order to have more reliable computation if stepm is
+   not 1 month. Version 0.98f
+   Revision 1.119  2006/03/15 17:42:26  brouard
+   (Module): Bug if status = -2, the loglikelihood was
+   computed as likelihood omitting the logarithm. Version O.98e
+   Revision 1.118  2006/03/14 18:20:07  brouard
+   (Module): varevsij Comments added explaining the second
+   table of variances if popbased=1 .
+   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+   (Module): Function pstamp added
+   (Module): Version 0.98d
+   Revision 1.117  2006/03/14 17:16:22  brouard
+   (Module): varevsij Comments added explaining the second
+   table of variances if popbased=1 .
+   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+   (Module): Function pstamp added
+   (Module): Version 0.98d
+   Revision 1.116  2006/03/06 10:29:27  brouard
+   (Module): Variance-covariance wrong links and
+   varian-covariance of ej. is needed (Saito).
+   Revision 1.115  2006/02/27 12:17:45  brouard
+   (Module): One freematrix added in mlikeli! 0.98c
+   Revision 1.114  2006/02/26 12:57:58  brouard
+   (Module): Some improvements in processing parameter
+   filename with strsep.
+   Revision 1.113  2006/02/24 14:20:24  brouard
+   (Module): Memory leaks checks with valgrind and:
+   datafile was not closed, some imatrix were not freed and on matrix
+   allocation too.
+   Revision 1.112  2006/01/30 09:55:26  brouard
+   (Module): Back to gnuplot.exe instead of wgnuplot.exe
+   Revision 1.111  2006/01/25 20:38:18  brouard
+   (Module): Lots of cleaning and bugs added (Gompertz)
+   (Module): Comments can be added in data file. Missing date values
+   can be a simple dot '.'.
+   Revision 1.110  2006/01/25 00:51:50  brouard
+   (Module): Lots of cleaning and bugs added (Gompertz)
+   Revision 1.109  2006/01/24 19:37:15  brouard
+   (Module): Comments (lines starting with a #) are allowed in data.
+   Revision 1.108  2006/01/19 18:05:42  lievre
+   Gnuplot problem appeared...
+   To be fixed
+   Revision 1.107  2006/01/19 16:20:37  brouard
+   Test existence of gnuplot in imach path
+   Revision 1.106  2006/01/19 13:24:36  brouard
+   Some cleaning and links added in html output
+   Revision 1.105  2006/01/05 20:23:19  lievre
+   *** empty log message ***
+   Revision 1.104  2005/09/30 16:11:43  lievre
+   (Module): sump fixed, loop imx fixed, and simplifications.
+   (Module): If the status is missing at the last wave but we know
+   that the person is alive, then we can code his/her status as -2
+   (instead of missing=-1 in earlier versions) and his/her
+   contributions to the likelihood is 1 - Prob of dying from last
+   health status (= 1-p13= p11+p12 in the easiest case of somebody in
+   the healthy state at last known wave). Version is 0.98
+   Revision 1.103  2005/09/30 15:54:49  lievre
+   (Module): sump fixed, loop imx fixed, and simplifications.
+   Revision 1.102  2004/09/15 17:31:30  brouard
+   Add the possibility to read data file including tab characters.
+   Revision 1.101  2004/09/15 10:38:38  brouard
+   Fix on curr_time
+   Revision 1.100  2004/07/12 18:29:06  brouard
+   Add version for Mac OS X. Just define UNIX in Makefile
+   Revision 1.99  2004/06/05 08:57:40  brouard
+   *** empty log message ***
+   Revision 1.98  2004/05/16 15:05:56  brouard
+   New version 0.97 . First attempt to estimate force of mortality
+   directly from the data i.e. without the need of knowing the health
+   state at each age, but using a Gompertz model: log u =a + b*age .
+   This is the basic analysis of mortality and should be done before any
+   other analysis, in order to test if the mortality estimated from the
+   cross-longitudinal survey is different from the mortality estimated
+   from other sources like vital statistic data.
+   The same imach parameter file can be used but the option for mle should be -3.
+   Agnès, who wrote this part of the code, tried to keep most of the
+   former routines in order to include the new code within the former code.
+   The output is very simple: only an estimate of the intercept and of
+   the slope with 95% confident intervals.
+   Current limitations:
+   A) Even if you enter covariates, i.e. with the
+   model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
+   B) There is no computation of Life Expectancy nor Life Table.
+   Revision 1.97  2004/02/20 13:25:42  lievre
+   Version 0.96d. Population forecasting command line is (temporarily)
+   suppressed.
+   Revision 1.96  2003/07/15 15:38:55  brouard
+   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
+   rewritten within the same printf. Workaround: many printfs.
+   Revision 1.95  2003/07/08 07:54:34  brouard
+   * imach.c (Repository):
+   (Repository): Using imachwizard code to output a more meaningful covariance
+   matrix (cov(a12,c31) instead of numbers.
    Revision 1.94  2003/06/27 13:00:02  brouard
    Just cleaning
- Line 108
+ Line 345
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
-   of the life expectancies. It also computes the stable prevalence.
+   of the life expectancies. It also computes the period (stable) prevalence.
-   Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
-            Institut national d'�tudes d�mographiques, Paris.
+            Institut national d'études démographiques, Paris.
    This software have been partly granted by Euro-REVES, a concerted action
    from the European Union.
    It is copyrighted identically to a GNU software product, ie programme and
- Line 137
+ Line 374
        begin-prev-date,...
    open gnuplot file
    open html file
-   stable prevalence
+   period (stable) prevalence
     for age prevalim()
    h Pij x
    variance of p varprob
- Line 149
+ Line 386
    varevsij()
    if popbased==1 varevsij(,popbased)
    total life expectancies
-   Variance of stable prevalence
+   Variance of period (stable) prevalence
   end
  */
- Line 159
+ Line 396
  #include <math.h>
  #include <stdio.h>
  #include <stdlib.h>
+ #include <string.h>
  #include <unistd.h>
- #include <sys/time.h>
+ #include <limits.h>
+ #include <sys/types.h>
+ #include <sys/stat.h>
+ #include <errno.h>
+ extern int errno;
+ #ifdef LINUX
  #include <time.h>
  #include "timeval.h"
+ #else
+ #include <sys/time.h>
+ #endif
+ #ifdef GSL
+ #include <gsl/gsl_errno.h>
+ #include <gsl/gsl_multimin.h>
+ #endif
+ /* #include <libintl.h> */
+ /* #define _(String) gettext (String) */
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- #define MAXLINE 256
  #define GNUPLOTPROGRAM "gnuplot"
  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
  #define FILENAMELENGTH 132
- /*#define DEBUG*/
- /*#define windows*/
  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+ #define MAXPARM 128 /* Maximum number of parameters for the optimization */
  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
  #define NINTERVMAX 8
  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
- #define NCOVMAX 8 /* Maximum number of covariates */
+ #define NCOVMAX 20 /* Maximum number of covariates */
  #define MAXN 20000
  #define YEARM 12. /* Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
- #ifdef unix
+ #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ #ifdef UNIX
  #define DIRSEPARATOR '/'
+ #define CHARSEPARATOR "/"
  #define ODIRSEPARATOR '\\'
  #else
  #define DIRSEPARATOR '\\'
+ #define CHARSEPARATOR "\\"
  #define ODIRSEPARATOR '/'
  #endif
  /* $Id$ */
  /* $State$ */
- char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
+ char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
  char fullversion[]="$Revision$ $Date$";
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ char strstart[80];
- int nvar;
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
+ int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
  int npar=NPARMAX;
  int nlstate=2; /* Number of live states */
  int ndeath=1; /* Number of dead states */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
- int maxwav; /* Maxim number of waves */
+ int maxwav=0; /* Maxim number of waves */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- int gipmx, gsw; /* Global variables on the number of contributions
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
                     to the likelihood and the sum of weights (done by funcone)*/
- int mle, weightopt;
+ int mle=1, weightopt=0;
  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
             * wave mi and wave mi+1 is not an exact multiple of stepm. */
- double jmean; /* Mean space between 2 waves */
+ double jmean=1; /* Mean space between 2 waves */
  double **oldm, **newm, **savm; /* Working pointers to matrices */
  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ /*FILE *fic ; */ /* Used in readdata only */
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
  FILE *ficlog, *ficrespow;
- int globpr; /* Global variable for printing or not */
+ int globpr=0; /* Global variable for printing or not */
  double fretone; /* Only one call to likelihood */
- long ipmx; /* Number of contributions */
+ long ipmx=0; /* Number of contributions */
  double sw; /* Sum of weights */
+ char filerespow[FILENAMELENGTH];
  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
  FILE *ficresilk;
  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- Line 233  FILE *ficresprobmorprev;
+ Line 496  FILE *ficresprobmorprev;
  FILE *fichtm, *fichtmcov; /* Html File */
  FILE *ficreseij;
  char filerese[FILENAMELENGTH];
+ FILE *ficresstdeij;
+ char fileresstde[FILENAMELENGTH];
+ FILE *ficrescveij;
+ char filerescve[FILENAMELENGTH];
  FILE  *ficresvij;
  char fileresv[FILENAMELENGTH];
  FILE  *ficresvpl;
  char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- char tmpout[FILENAMELENGTH];
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
  char command[FILENAMELENGTH];
  int  outcmd=0;
- Line 261  long time_value;
+ Line 528  long time_value;
  extern long time();
  char strcurr[80], strfor[80];
+ char *endptr;
+ long lval;
+ double dval;
  #define NR_END 1
  #define FREE_ARG char*
  #define FTOL 1.0e-10
- Line 288  static double maxarg1,maxarg2;
+ Line 559  static double maxarg1,maxarg2;
  static double sqrarg;
  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ int agegomp= AGEGOMP;
  int imx;
- int stepm;
+ int stepm=1;
  /* Stepm, step in month: minimum step interpolation*/
  int estepm;
- Line 298  int estepm;
+ Line 570  int estepm;
  int m,nb;
  long *num;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  double **pmmij, ***probs;
+ double *ageexmed,*agecens;
  double dateintmean=0;
  double *weight;
  int **s; /* Status */
- double *agedc, **covar, idx;
+ double *agedc;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double  **covar; /**< covar[i,j], value of jth covariate for individual i,
+                   * covar=matrix(0,NCOVMAX,1,n);
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
+ double  idx;
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double *lsurv, *lpop, *tpop;
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
- double ftolhess; /* Tolerance for computing hessian */
+ double ftolhess; /**< Tolerance for computing hessian */
  /**************** split *************************/
  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
  {
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+   */
    char  *ss;                            /* pointer */
    int   l1, l2;                         /* length counters */
    l1 = strlen(path );                   /* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   if ( ss == NULL ) {                   /* no directory, so use current */
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+     strcpy( name, path );               /* we got the fullname name because no directory */
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      /* get current working directory */
- Line 328  static int split( char *path, char *dirc
+ Line 612  static int split( char *path, char *dirc
      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
        return( GLOCK_ERROR_GETCWD );
      }
-     strcpy( name, path );               /* we've got it */
+     /* got dirc from getcwd*/
+     printf(" DIRC = %s \n",dirc);
    } else {                              /* strip direcotry from path */
      ss++;                               /* after this, the filename */
      l2 = strlen( ss );                  /* length of filename */
- Line 336  static int split( char *path, char *dirc
+ Line 621  static int split( char *path, char *dirc
      strcpy( name, ss );         /* save file name */
      strncpy( dirc, path, l1 - l2 );     /* now the directory */
      dirc[l1-l2] = 0;                    /* add zero */
+     printf(" DIRC2 = %s \n",dirc);
    }
+   /* We add a separator at the end of dirc if not exists */
    l1 = strlen( dirc );                  /* length of directory */
-   /*#ifdef windows
+   if( dirc[l1-1] != DIRSEPARATOR ){
-   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
+     dirc[l1] =  DIRSEPARATOR;
- #else
+     dirc[l1+1] = 0;
-   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
+     printf(" DIRC3 = %s \n",dirc);
- #endif
+   }
-   */
    ss = strrchr( name, '.' );            /* find last / */
-   ss++;
+   if (ss >0){
-   strcpy(ext,ss);                       /* save extension */
+     ss++;
-   l1= strlen( name);
+     strcpy(ext,ss);                     /* save extension */
-   l2= strlen(ss)+1;
+     l1= strlen( name);
-   strncpy( finame, name, l1-l2);
+     l2= strlen(ss)+1;
-   finame[l1-l2]= 0;
+     strncpy( finame, name, l1-l2);
+     finame[l1-l2]= 0;
+   }
    return( 0 );                          /* we're done */
  }
- Line 369  void replace_back_to_slash(char *s, char
+ Line 658  void replace_back_to_slash(char *s, char
    }
  }
+ char *trimbb(char *out, char *in)
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
+   char *s;
+   s=out;
+   while (*in != '\0'){
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
+       in++;
+     }
+     *out++ = *in++;
+   }
+   *out='\0';
+   return s;
+ }
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
+ {
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+      gives blocc="abcdef2ghi" and alocc="j".
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
+   */
+   char *s, *t;
+   t=in;s=in;
+   while (*in != '\0'){
+     while( *in == occ){
+       *blocc++ = *in++;
+       s=in;
+     }
+     *blocc++ = *in++;
+   }
+   if (s == t) /* occ not found */
+     *(blocc-(in-s))='\0';
+   else
+     *(blocc-(in-s)-1)='\0';
+   in=s;
+   while ( *in != '\0'){
+     *alocc++ = *in++;
+   }
+   *alocc='\0';
+   return s;
+ }
  int nbocc(char *s, char occ)
  {
    int i,j=0;
- Line 381  int nbocc(char *s, char occ)
+ Line 713  int nbocc(char *s, char occ)
    return j;
  }
- void cutv(char *u,char *v, char*t, char occ)
+ /* void cutv(char *u,char *v, char*t, char occ) */
- {
+ /* { */
-   /* cuts string t into u and v where u is ended by char occ excluding it
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-      gives u="abcedf" and v="ghi2j" */
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   int i,lg,j,p=0;
+ /*   int i,lg,j,p=0; */
-   i=0;
+ /*   i=0; */
-   for(j=0; j<=strlen(t)-1; j++) {
+ /*   lg=strlen(t); */
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+ /*   for(j=0; j<=lg-1; j++) { */
-   }
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
+ /*   } */
-   lg=strlen(t);
+ /*   for(j=0; j<p; j++) { */
-   for(j=0; j<p; j++) {
+ /*     (u[j] = t[j]); */
-     (u[j] = t[j]);
+ /*   } */
-   }
+ /*      u[p]='\0'; */
-      u[p]='\0';
-    for(j=0; j<= lg; j++) {
+ /*    for(j=0; j<= lg; j++) { */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   }
+ /*   } */
- }
+ /* } */
  /********************** nrerror ********************/
- Line 784  char *asc_diff_time(long time_sec, char
+ Line 1116  char *asc_diff_time(long time_sec, char
    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);
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
    return ascdiff;
  }
- Line 813  void powell(double p[], double **xi, int
+ Line 1145  void powell(double p[], double **xi, int
      last_time=curr_time;
      (void) gettimeofday(&curr_time,&tzp);
      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
-     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
-     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
-     for (i=1;i<=n;i++) {
+    for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12lf",i, p[i]);
        fprintf(ficrespow," %.12lf", p[i]);
- Line 825  void powell(double p[], double **xi, int
+ Line 1157  void powell(double p[], double **xi, int
      fprintf(ficrespow,"\n");fflush(ficrespow);
      if(*iter <=3){
        tm = *localtime(&curr_time.tv_sec);
-       strcpy(strcurr,asctime(&tmf));
+       strcpy(strcurr,asctime(&tm));
  /*       asctime_r(&tm,strcurr); */
        forecast_time=curr_time;
        itmp = strlen(strcurr);
-       if(strcurr[itmp-1]=='\n')
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
          strcurr[itmp-1]='\0';
        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
- Line 841  void powell(double p[], double **xi, int
+ Line 1173  void powell(double p[], double **xi, int
          itmp = strlen(strfor);
          if(strfor[itmp-1]=='\n')
          strfor[itmp-1]='\0';
-         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
-         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
        }
      }
      for (i=1;i<=n;i++) {
- Line 936  void powell(double p[], double **xi, int
+ Line 1268  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 946  double **prevalim(double **prlim, int nl
+ Line 1278  double **prevalim(double **prlim, int nl
    int i, ii,j,k;
    double min, max, maxmin, maxmax,sumnew=0.;
    double **matprod2();
-   double **out, cov[NCOVMAX], **pmij();
+   double **out, cov[NCOVMAX+1], **pmij();
    double **newm;
    double agefin, delaymax=50 ; /* Max number of years to converge */
- Line 961  double **prevalim(double **prlim, int nl
+ Line 1293  double **prevalim(double **prlim, int nl
    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
      newm=savm;
      /* Covariates have to be included here again */
-      cov[2]=agefin;
+     cov[2]=agefin;
-       for (k=1; k<=cptcovn;k++) {
+     for (k=1; k<=cptcovn;k++) {
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+       /*        printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
-       }
+     }
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+     for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       for (k=1; k<=cptcovprod;k++)
+     for (k=1; k<=cptcovprod;k++)
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      savm=oldm;
      oldm=newm;
      maxmax=0.;
- Line 1002  double **prevalim(double **prlim, int nl
+ Line 1334  double **prevalim(double **prlim, int nl
  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
  {
-   double s1, s2;
+   /* According to parameters values stored in x and the covariate's values stored in cov,
+      computes the probability to be observed in state j being in state i by appying the
+      model to the ncovmodel covariates (including constant and age).
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+      ncth covariate in the global vector x is given by the formula:
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+      Outputs ps[i][j] the probability to be observed in j being in j according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
+   double s1, lnpijopii;
    /*double t34;*/
    int i,j,j1, nc, ii, jj;
      for(i=1; i<= nlstate; i++){
-     for(j=1; j<i;j++){
+       for(j=1; j<i;j++){
-       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         /*s2 += param[i][j][nc]*cov[nc];*/
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-       }
+         }
-       ps[i][j]=s2;
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-     }
+       }
-     for(j=i+1; j<=nlstate+ndeath;j++){
+       for(j=i+1; j<=nlstate+ndeath;j++){
-       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-       }
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-       ps[i][j]=s2;
+         }
-     }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-   }
+       }
-     /*ps[3][2]=1;*/
-   for(i=1; i<= nlstate; i++){
-      s1=0;
-     for(j=1; j<i; j++)
-       s1+=exp(ps[i][j]);
-     for(j=i+1; j<=nlstate+ndeath; j++)
-       s1+=exp(ps[i][j]);
-     ps[i][i]=1./(s1+1.);
-     for(j=1; j<i; j++)
-       ps[i][j]= exp(ps[i][j])*ps[i][i];
-     for(j=i+1; j<=nlstate+ndeath; j++)
-       ps[i][j]= exp(ps[i][j])*ps[i][i];
-     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-   } /* end i */
-   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-     for(jj=1; jj<= nlstate+ndeath; jj++){
-       ps[ii][jj]=0;
-       ps[ii][ii]=1;
      }
-   }
+     for(i=1; i<= nlstate; i++){
+       s1=0;
-   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
+       for(j=1; j<i; j++){
-     for(jj=1; jj<= nlstate+ndeath; jj++){
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-      printf("%lf ",ps[ii][jj]);
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-    }
+       }
-     printf("\n ");
+       for(j=i+1; j<=nlstate+ndeath; j++){
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       }
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
+       ps[i][i]=1./(s1+1.);
+       /* Computing other pijs */
+       for(j=1; j<i; j++)
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       for(j=i+1; j<=nlstate+ndeath; j++)
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+     } /* end i */
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       for(jj=1; jj<= nlstate+ndeath; jj++){
+         ps[ii][jj]=0;
+         ps[ii][ii]=1;
+       }
      }
-     printf("\n ");printf("%lf ",cov[2]);*/
- /*
-   for(i=1; i<= npar; i++) printf("%f ",x[i]);
+ /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
-   goto end;*/
+ /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+ /*         printf("ddd %lf ",ps[ii][jj]); */
+ /*       } */
+ /*       printf("\n "); */
+ /*        } */
+ /*        printf("\n ");printf("%lf ",cov[2]); */
+        /*
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       goto end;*/
      return ps;
  }
- Line 1097  double ***hpxij(double ***po, int nhstep
+ Line 1448  double ***hpxij(double ***po, int nhstep
       */
    int i, j, d, h, k;
-   double **out, cov[NCOVMAX];
+   double **out, cov[NCOVMAX+1];
    double **newm;
    /* Hstepm could be zero and should return the unit matrix */
- Line 1113  double ***hpxij(double ***po, int nhstep
+ Line 1464  double ***hpxij(double ***po, int nhstep
        /* Covariates have to be included here again */
        cov[1]=1.;
        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       for (k=1; k<=cptcovn;k++)
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        for (k=1; k<=cptcovage;k++)
          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        for (k=1; k<=cptcovprod;k++)
- Line 1130  double ***hpxij(double ***po, int nhstep
+ Line 1482  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 1142  double ***hpxij(double ***po, int nhstep
+ Line 1495  double ***hpxij(double ***po, int nhstep
  double func( double *x)
  {
    int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double sw; /* Sum of weights */
    double lli; /* Individual log likelihood */
- Line 1161  double func( double *x)
+ Line 1514  double func( double *x)
    if(mle==1){
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       /* Computes the values of the ncovmodel covariates of the model
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
+          to be observed in j being in i according to the model.
+        */
        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
+          has been calculated etc */
        for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 1172  double func( double *x)
+ Line 1533  double func( double *x)
            newm=savm;
            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 1181  double func( double *x)
+ Line 1542  double func( double *x)
          } /* end mult */
          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         /* But now since version 0.9 we anticipate for bias and large stepm.
+         /* But now since version 0.9 we anticipate for bias at large stepm.
           * If stepm is larger than one month (smallest stepm) and if the exact delay
           * (in months) between two waves is not a multiple of stepm, we rounded to
           * the nearest (and in case of equal distance, to the lowest) interval but now
           * we keep into memory the bias bh[mi][i] and also the previous matrix product
-          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           * -stepm/2 to stepm/2 .
           * For stepm=1 the results are the same as for previous versions of Imach.
           * For stepm > 1 the results are less biased than in previous versions.
- Line 1196  double func( double *x)
+ Line 1557  double func( double *x)
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
-         /* bias is positive if real duration
+         /* bias bh is positive if real duration
           * is higher than the multiple of stepm and negative otherwise.
           */
          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
          if( s2 > nlstate){
-           /* i.e. if s2 is a death state and if the date of death is known then the contribution
+           /* i.e. if s2 is a death state and if the date of death is known
-              to the likelihood is the probability to die between last step unit time and current
+              then the contribution to the likelihood is the probability to
-              step unit time, which is also the differences between probability to die before dh
+              die between last step unit time and current  step unit time,
-              and probability to die before dh-stepm .
+              which is also equal to probability to die before dh
+              minus probability to die before dh-stepm .
               In version up to 0.92 likelihood was computed
          as if date of death was unknown. Death was treated as any other
          health state: the date of the interview describes the actual state
- Line 1224  double func( double *x)
+ Line 1586  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 1374  double funcone( double *x)
+ Line 1757  double funcone( double *x)
  {
    /* Same as likeli but slower because of a lot of printf and if */
    int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double lli; /* Individual log likelihood */
    double llt;
- Line 1418  double funcone( double *x)
+ Line 1801  double funcone( double *x)
         */
        if( s2 > nlstate && (mle <5) ){  /* Jackson */
          lli=log(out[s1][s2] - savm[s1][s2]);
-       } else if (mle==1){
+       } else if  (s2==-2) {
+         for (j=1,survp=0. ; j<=nlstate; j++)
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         lli= log(survp);
+       }else if (mle==1){
          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
        } else if(mle==2){
          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
- Line 1426  double funcone( double *x)
+ Line 1813  double funcone( double *x)
          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
        } else if (mle==4){  /* mle=4 no inter-extrapolation */
          lli=log(out[s1][s2]); /* Original formula */
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+       } else{  /* mle=0 back to 1 */
-         lli=log(out[s1][s2]); /* Original formula */
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         /*lli=log(out[s1][s2]); */ /* Original formula */
        } /* End of if */
        ipmx +=1;
        sw += weight[i];
        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
        if(globpr){
-         fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-  %10.6f %10.6f %10.6f ", \
+  %11.6f %11.6f %11.6f ", \
                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
 *weight[i]*lli,out[s1][s2],savm[s1][s2]);
          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
- Line 1500  void mlikeli(FILE *ficres,double p[], in
+ Line 1888  void mlikeli(FILE *ficres,double p[], in
    double **xi;
    double fret;
    double fretone; /* Only one call to likelihood */
-   char filerespow[FILENAMELENGTH];
+   /*  char filerespow[FILENAMELENGTH];*/
    xi=matrix(1,npar,1,npar);
    for (i=1;i<=npar;i++)
      for (j=1;j<=npar;j++)
- Line 1520  void mlikeli(FILE *ficres,double p[], in
+ Line 1908  void mlikeli(FILE *ficres,double p[], in
    powell(p,xi,npar,ftol,&iter,&fret,func);
+   free_matrix(xi,1,npar,1,npar);
    fclose(ficrespow);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
- Line 1535  void hesscov(double **matcov, double p[]
+ Line 1924  void hesscov(double **matcov, double p[]
    int i, j,jk;
    int *indx;
-   double hessii(double p[], double delta, int theta, double delti[]);
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-   double hessij(double p[], double delti[], int i, int j);
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
    void lubksb(double **a, int npar, int *indx, double b[]) ;
    void ludcmp(double **a, int npar, int *indx, double *d) ;
+   double gompertz(double p[]);
    hess=matrix(1,npar,1,npar);
    printf("\nCalculation of the hessian matrix. Wait...\n");
- Line 1547  void hesscov(double **matcov, double p[]
+ Line 1936  void hesscov(double **matcov, double p[]
    for (i=1;i<=npar;i++){
      printf("%d",i);fflush(stdout);
      fprintf(ficlog,"%d",i);fflush(ficlog);
-     hess[i][i]=hessii(p,ftolhess,i,delti);
-     /*printf(" %f ",p[i]);*/
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-     /*printf(" %lf ",hess[i][i]);*/
+     /*  printf(" %f ",p[i]);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
    }
    for (i=1;i<=npar;i++) {
- Line 1557  void hesscov(double **matcov, double p[]
+ Line 1948  void hesscov(double **matcov, double p[]
        if (j>i) {
          printf(".%d%d",i,j);fflush(stdout);
          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-         hess[i][j]=hessij(p,delti,i,j);
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
          hess[j][i]=hess[i][j];
          /*printf(" %lf ",hess[i][j]);*/
        }
- Line 1628  void hesscov(double **matcov, double p[]
+ Line 2020  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 p2[MAXPARM+1]; /* identical to x */
    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 1654  double hessii( double x[], double delta,
+ Line 2046  double hessii( double x[], double delta,
        /*res= (k1-2.0*fx+k2)/delt/delt; */
        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
- #ifdef DEBUG
+ #ifdef DEBUGHESS
        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
  #endif
- Line 1675  double hessii( double x[], double delta,
+ Line 2067  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;
    double k1,k2,k3,k4,res,fx;
-   double p2[NPARMAX+1];
+   double p2[MAXPARM+1];
    int k;
    fx=func(x);
- Line 1784  void lubksb(double **a, int n, int *indx
+ Line 2176  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;
+   int i, m, jk, k1,i1, j1, bool, z1,j;
    int first;
    double ***freq; /* Frequencies */
    double *pp, **prop;
    double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   FILE *ficresp;
    char fileresp[FILENAMELENGTH];
    pp=vector(1,nlstate);
- Line 1805  void  freqsummary(char fileres[], int ia
+ Line 2201  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 1813  void  freqsummary(char fileres[], int ia
+ Line 2209  void  freqsummary(char fileres[], int ia
    first=1;
-   for(k1=1; k1<=j;k1++){
+   for(k1=1; k1<=j;k1++){   /* Loop on covariates */
-     for(i1=1; i1<=ncodemax[k1];i1++){
+     for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
        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;
-     for (i=1; i<=nlstate; i++)
+       for (i=1; i<=nlstate; i++)
-       for(m=iagemin; m <= iagemax+3; m++)
+         for(m=iagemin; m <= iagemax+3; m++)
-         prop[i][m]=0;
+           prop[i][m]=0;
        dateintsum=0;
        k2cpt=0;
- Line 1858  void  freqsummary(char fileres[], int ia
+ Line 2254  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]]);
          fprintf(ficresp, "**********\n#");
+         fprintf(ficlog, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficlog, "**********\n#");
        }
        for(i=1; i<=nlstate;i++)
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
- Line 1887  void  freqsummary(char fileres[], int ia
+ Line 2286  void  freqsummary(char fileres[], int ia
              pos += freq[jk][m][i];
            if(pp[jk]>=1.e-10){
              if(first==1){
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              }
              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
            }else{
- Line 1944  void  freqsummary(char fileres[], int ia
+ Line 2343  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 1958  void prevalence(double ***probs, double
+ Line 2357  void prevalence(double ***probs, double
       We still use firstpass and lastpass as another selection.
    */
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+   int i, m, jk, k1, i1, j1, bool, z1,j;
    double ***freq; /* Frequencies */
    double *pp, **prop;
    double pos,posprop;
- Line 2016  void prevalence(double ***probs, double
+ Line 2415  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 2053  void  concatwav(int wav[], int **dh, int
+ Line 2453  void  concatwav(int wav[], int **dh, int
      mi=0;
      m=firstpass;
      while(s[m][i] <= nlstate){
-       if(s[m][i]>=1)
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
          mw[++mi][i]=m;
        if(m >=lastpass)
          break;
- Line 2071  void  concatwav(int wav[], int **dh, int
+ Line 2471  void  concatwav(int wav[], int **dh, int
      if(mi==0){
        nbwarn++;
        if(first==0){
-         printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
          first=1;
        }
        if(first==1){
-         fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
        }
      } /* end mi==0 */
    } /* End individuals */
- Line 2093  void  concatwav(int wav[], int **dh, int
+ Line 2493  void  concatwav(int wav[], int **dh, int
                nberr++;
                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                j=1; /* Temporary Dangerous patch */
-               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
+               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
              }
              k=k+1;
-             if (j >= jmax) jmax=j;
+             if (j >= jmax){
-             if (j <= jmin) jmin=j;
+               jmax=j;
+               ijmax=i;
+             }
+             if (j <= jmin){
+               jmin=j;
+               ijmin=i;
+             }
              sum=sum+j;
              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
- Line 2107  void  concatwav(int wav[], int **dh, int
+ Line 2513  void  concatwav(int wav[], int **dh, int
          }
          else{
            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-           /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+ /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
            k=k+1;
-           if (j >= jmax) jmax=j;
+           if (j >= jmax) {
-           else if (j <= jmin)jmin=j;
+             jmax=j;
+             ijmax=i;
+           }
+           else if (j <= jmin){
+             jmin=j;
+             ijmin=i;
+           }
            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
            if(j<0){
- Line 2128  void  concatwav(int wav[], int **dh, int
+ Line 2541  void  concatwav(int wav[], int **dh, int
              dh[mi][i]=jk;
              bh[mi][i]=0;
            }else{ /* We want a negative bias in order to only have interpolation ie
-                   * at the price of an extra matrix product in likelihood */
+                   * to avoid the price of an extra matrix product in likelihood */
              dh[mi][i]=jk+1;
              bh[mi][i]=ju;
            }
- Line 2153  void  concatwav(int wav[], int **dh, int
+ Line 2566  void  concatwav(int wav[], int **dh, int
      } /* end wave */
    }
    jmean=sum/k;
-   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   }
  /*********** Tricode ****************************/
  void tricode(int *Tvar, int **nbcode, int imx)
  {
+   /* Uses cptcovn+2*cptcovprod as the number of covariates */
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+   /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
-   int cptcode=0;
+   int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+   int modmaxcovj=0; /* Modality max of covariates j */
    cptcoveff=0;
    for (k=0; k<maxncov; k++) Ndum[k]=0;
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+   for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+   for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
-                                modality*/
+                                modality of this covariate Vj*/
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
-       Ndum[ij]++; /*store the modality */
+                                       modality of the nth covariate of individual i. */
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+       if (ij > modmaxcovj) modmaxcovj=ij;
-                                        Tvar[j]. If V=sex and male is 0 and
+       /* getting the maximum value of the modality of the covariate
-                                        female is 1, then  cptcode=1.*/
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-     }
+          female is 1, then modmaxcovj=1.*/
+     }
-     for (i=0; i<=cptcode; i++) {
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+     for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
-     }
+       if( Ndum[i] != 0 )
+         ncodemax[j]++;
+       /* Number of modalities of the j th covariate. In fact
+          ncodemax[j]=2 (dichotom. variables only) but it could be more for
+          historical reasons */
+     } /* Ndum[-1] number of undefined modalities */
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
      ij=1;
-     for (i=1; i<=ncodemax[j]; i++) {
+     for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
-       for (k=0; k<= maxncov; k++) {
+       for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
-         if (Ndum[k] != 0) {
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-           nbcode[Tvar[j]][ij]=k;
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+                                      k is a modality. If we have model=V1+V1*sex
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
            ij++;
          }
          if (ij > ncodemax[j]) break;
-       }
+       }  /* end of loop on */
-     }
+     } /* end of loop on modality */
-   }
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+   for (k=0; k< maxncov; k++) Ndum[k]=0;
-  for (i=1; i<=ncovmodel-2; i++) {
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-    /* Listing of all covariables in 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];
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
     Ndum[ij]++;
   }
   ij=1;
-  for (i=1; i<= maxncov; i++) {
+  for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     if((Ndum[i]!=0) && (i<=ncovcol)){
       Tvaraff[ij]=i; /*For printing */
       ij++;
     }
   }
+  ij--;
-  cptcoveff=ij-1; /*Number of simple covariates*/
+  cptcoveff=ij; /*Number of simple covariates*/
  }
  /*********** Health Expectancies ****************/
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+ {
+   /* Health expectancies, no variances */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+   int nhstepma, nstepma; /* Decreasing with age */
+   double age, agelim, hf;
+   double ***p3mat;
+   double eip;
+   pstamp(ficreseij);
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+   fprintf(ficreseij,"# Age");
+   for(i=1; i<=nlstate;i++){
+     for(j=1; j<=nlstate;j++){
+       fprintf(ficreseij," e%1d%1d ",i,j);
+     }
+     fprintf(ficreseij," e%1d. ",i);
+   }
+   fprintf(ficreseij,"\n");
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else  hstepm=estepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
+    * if stepm=24 months pijx are given only every 2 years and by summing them
+    * we are calculating an estimate of the Life Expectancy assuming a linear
+    * progression in between and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+    * to compare the new estimate of Life expectancy with the same linear
+    * hypothesis. A more precise result, taking into account a more precise
+    * curvature will be obtained if estepm is as small as stepm. */
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like estepm months */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed only each two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+      results. So we changed our mind and took the option of the best precision.
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   agelim=AGESUP;
+   /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+ /* nhstepm age range expressed in number of stepm */
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   /* if (stepm >= YEARM) hstepm=1;*/
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   for (age=bage; age<=fage; age ++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     /* if (stepm >= YEARM) hstepm=1;*/
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
+     /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     printf("%d|",(int)age);fflush(stdout);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+     /* Computing expectancies */
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++)
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+         }
+     fprintf(ficreseij,"%3.0f",age );
+     for(i=1; i<=nlstate;i++){
+       eip=0;
+       for(j=1; j<=nlstate;j++){
+         eip +=eij[i][j][(int)age];
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       }
+       fprintf(ficreseij,"%9.4f", eip );
+     }
+     fprintf(ficreseij,"\n");
+   }
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   printf("\n");
+   fprintf(ficlog,"\n");
+ }
+ void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
  {
-   /* Health expectancies */
+   /* Covariances of health expectancies eij and of total life expectancies according
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
+    to initial status i, ei. .
+   */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+   int nhstepma, nstepma; /* Decreasing with age */
    double age, agelim, hf;
-   double ***p3mat,***varhe;
+   double ***p3matp, ***p3matm, ***varhe;
    double **dnewm,**doldm;
-   double *xp;
+   double *xp, *xm;
    double **gp, **gm;
    double ***gradg, ***trgradg;
    int theta;
+   double eip, vip;
    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
    xp=vector(1,npar);
+   xm=vector(1,npar);
    dnewm=matrix(1,nlstate*nlstate,1,npar);
    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-   fprintf(ficreseij,"# Health expectancies\n");
+   pstamp(ficresstdeij);
-   fprintf(ficreseij,"# Age");
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-   for(i=1; i<=nlstate;i++)
+   fprintf(ficresstdeij,"# Age");
+   for(i=1; i<=nlstate;i++){
      for(j=1; j<=nlstate;j++)
-       fprintf(ficreseij," %1d-%1d (SE)",i,j);
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-   fprintf(ficreseij,"\n");
+     fprintf(ficresstdeij," e%1d. ",i);
+   }
+   fprintf(ficresstdeij,"\n");
+   pstamp(ficrescveij);
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   fprintf(ficrescveij,"# Age");
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++){
+       cptj= (j-1)*nlstate+i;
+       for(i2=1; i2<=nlstate;i2++)
+         for(j2=1; j2<=nlstate;j2++){
+           cptj2= (j2-1)*nlstate+i2;
+           if(cptj2 <= cptj)
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+         }
+     }
+   fprintf(ficrescveij,"\n");
    if(estepm < stepm){
      printf ("Problem %d lower than %d\n",estepm, stepm);
    }
- Line 2272  void evsij(char fileres[], double ***eij
+ Line 2826  void evsij(char fileres[], double ***eij
    */
    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   /* If stepm=6 months */
+   /* nhstepm age range expressed in number of stepm */
    agelim=AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-     /* nhstepm age range expressed in number of stepm */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm);
+   /* if (stepm >= YEARM) hstepm=1;*/
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+   for (age=bage; age<=fage; age ++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      /* Typically if 20 years nstepm = 20*12/6=40 stepm */
      /* if (stepm >= YEARM) hstepm=1;*/
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-     gp=matrix(0,nhstepm,1,nlstate*nlstate);
-     gm=matrix(0,nhstepm,1,nlstate*nlstate);
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
+     /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     /* Computing Variances of health expectancies */
+     /* Computing  Variances of health expectancies */
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-      for(theta=1; theta <=npar; theta++){
+        decrease memory allocation */
+     for(theta=1; theta <=npar; theta++){
        for(i=1; i<=npar; i++){
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-       cptj=0;
        for(j=1; j<= nlstate; j++){
          for(i=1; i<=nlstate; i++){
-           cptj=cptj+1;
+           for(h=0; h<=nhstepm-1; h++){
-           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
            }
          }
        }
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-       for(i=1; i<=npar; i++)
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       cptj=0;
-       for(j=1; j<= nlstate; j++){
-         for(i=1;i<=nlstate;i++){
-           cptj=cptj+1;
-           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
-             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
-           }
-         }
-       }
-       for(j=1; j<= nlstate*nlstate; j++)
          for(h=0; h<=nhstepm-1; h++){
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
          }
-      }
+     }/* End theta */
- /* End theta */
+     for(h=0; h<=nhstepm-1; h++)
-      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-      for(h=0; h<=nhstepm-1; h++)
        for(j=1; j<=nlstate*nlstate;j++)
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
-      for(i=1;i<=nlstate*nlstate;i++)
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-       for(j=1;j<=nlstate*nlstate;j++)
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-         varhe[i][j][(int)age] =0.;
+         varhe[ij][ji][(int)age] =0.;
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
- Line 2350  void evsij(char fileres[], double ***eij
+ Line 2896  void evsij(char fileres[], double ***eij
        for(k=0;k<=nhstepm-1;k++){
          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-         for(i=1;i<=nlstate*nlstate;i++)
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-           for(j=1;j<=nlstate*nlstate;j++)
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
        }
      }
      /* Computing expectancies */
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
- /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
          }
-     fprintf(ficreseij,"%3.0f",age );
+     fprintf(ficresstdeij,"%3.0f",age );
-     cptj=0;
+     for(i=1; i<=nlstate;i++){
+       eip=0.;
+       vip=0.;
+       for(j=1; j<=nlstate;j++){
+         eip += eij[i][j][(int)age];
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+       }
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+     }
+     fprintf(ficresstdeij,"\n");
+     fprintf(ficrescveij,"%3.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
-         cptj++;
+         cptj= (j-1)*nlstate+i;
-         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
+         for(i2=1; i2<=nlstate;i2++)
+           for(j2=1; j2<=nlstate;j2++){
+             cptj2= (j2-1)*nlstate+i2;
+             if(cptj2 <= cptj)
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+           }
        }
-     fprintf(ficreseij,"\n");
+     fprintf(ficrescveij,"\n");
-     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    printf("\n");
    fprintf(ficlog,"\n");
+   free_vector(xm,1,npar);
    free_vector(xp,1,npar);
    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
- Line 2390  void evsij(char fileres[], double ***eij
+ Line 2958  void evsij(char fileres[], double ***eij
  }
  /************ Variance ******************/
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
+ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
  {
    /* Variance of health expectancies */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
- Line 2441  void varevsij(char optionfilefiname[], d
+ Line 3009  void varevsij(char optionfilefiname[], d
      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
    }
    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   pstamp(ficresprobmorprev);
    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
- Line 2451  void varevsij(char optionfilefiname[], d
+ Line 3021  void varevsij(char optionfilefiname[], d
    }
    fprintf(ficresprobmorprev,"\n");
    fprintf(ficgp,"\n# Routine varevsij");
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
  /*   } */
    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   pstamp(ficresvij);
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+   if(popbased==1)
+     fprintf(ficresvij,"the age specific prevalence observed (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 2482  void varevsij(char optionfilefiname[], d
+ Line 3057  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 2549  void varevsij(char optionfilefiname[], d
+ Line 3123  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 2659  void varevsij(char optionfilefiname[], d
+ Line 3233  void varevsij(char optionfilefiname[], d
    free_vector(gmp,nlstate+1,nlstate+ndeath);
    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 2 ",subdirf(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)) t \"95\%% interval\" w l lt 3 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 3 ",subdirf(fileresprobmorprev));
    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
- Line 2688  void varevsij(char optionfilefiname[], d
+ Line 3262  void varevsij(char optionfilefiname[], d
  }  /* end varevsij */
  /************ Variance of prevlim ******************/
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
+ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
  {
    /* Variance of prevalence limit */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
- Line 2701  void varprevlim(char fileres[], double *
+ Line 3275  void varprevlim(char fileres[], double *
    double **gradg, **trgradg;
    double age,agelim;
    int theta;
-   fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
+   pstamp(ficresvpl);
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
    fprintf(ficresvpl,"# Age");
    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %1d-%1d",i,i);
- Line 2771  void varprevlim(char fileres[], double *
+ Line 3346  void varprevlim(char fileres[], double *
  }
  /************ Variance of one-step probabilities  ******************/
- void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
  {
    int i, j=0,  i1, k1, l1, t, tj;
    int k2, l2, j1,  z1;
- Line 2816  void varprob(char optionfilefiname[], do
+ Line 3391  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 2835  void varprob(char optionfilefiname[], do
+ Line 3412  void varprob(char optionfilefiname[], do
    fprintf(ficresprobcov,"\n");
    fprintf(ficresprobcor,"\n");
   */
-  xp=vector(1,npar);
+   xp=vector(1,npar);
    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
- Line 2845  void varprob(char optionfilefiname[], do
+ Line 3422  void varprob(char optionfilefiname[], do
    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
    fprintf(fichtm,"\n");
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
    file %s<br>\n",optionfilehtmcov);
    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
  and drawn. It helps understanding how is the covariance between two incidences.\
- Line 2879  To be simple, these graphs help to under
+ Line 3456  To be simple, these graphs help to under
          fprintf(ficgp, "**********\n#\n");
-         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
          fprintf(ficresprobcor, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- Line 2988  To be simple, these graphs help to under
+ Line 3565  To be simple, these graphs help to under
        /* Confidence intervalle of pij  */
        /*
-         fprintf(ficgp,"\nset noparametric;unset label");
+         fprintf(ficgp,"\nunset parametric;unset label");
          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
- Line 3019  To be simple, these graphs help to under
+ Line 3596  To be simple, these graphs help to under
                    /* Computing eigen value of matrix of covariance */
                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                   if ((lc2 <0) || (lc1 <0) ){
+                     printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+                     fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
+                     lc1=fabs(lc1);
+                     lc2=fabs(lc2);
+                   }
                    /* Eigen vectors */
                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                    /*v21=sqrt(1.-v11*v11); *//* error */
- Line 3073  To be simple, these graphs help to under
+ Line 3657  To be simple, these graphs help to under
    }
    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
    free_vector(xp,1,npar);
    fclose(ficresprob);
    fclose(ficresprobcov);
- Line 3090  void printinghtml(char fileres[], char t
+ Line 3676  void printinghtml(char fileres[], char t
                    double jprev1, double mprev1,double anprev1, \
                    double jprev2, double mprev2,double anprev2){
    int jj1, k1, i1, cpt;
-   /*char optionfilehtm[FILENAMELENGTH];*/
- /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
- /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
- /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
- /*   } */
-    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
+ </ul>");
-  - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-  - Life expectancies by age and initial health status (estepm=%2d months): \
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-    <a href=\"%s\">%s</a> <br>\n</li>", \
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
+    fprintf(fichtm,"\
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+    fprintf(fichtm,"\
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+    fprintf(fichtm,"\
+  - (a) Life expectancies by health status at initial age, 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 3123  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3713  fprintf(fichtm," \n<ul><li><b>Graphs</b>
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
       /* Pij */
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
       /* Quasi-incidences */
       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-        /* Stable prevalence in each health state */
+        /* Period (stable) prevalence in each health state */
         for(cpt=1; cpt<nlstate;cpt++){
-          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
+          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+ <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         }
       for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
+         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
- health expectancies in states (1) and (2): %s%d.png<br>\
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     } /* end i1 */
   }/* End k1 */
   fprintf(fichtm,"</ul>");
-  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
+  fprintf(fichtm,"\
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-  - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-  - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
+  fprintf(fichtm,"\
-  - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          rfileres,rfileres,\
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
+  fprintf(fichtm,"\
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+  fprintf(fichtm,"\
+  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), 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 */
- Line 3168  health expectancies in states (1) and (2
+ Line 3770  health expectancies in states (1) and (2
  /*      <br>",fileres,fileres,fileres,fileres); */
  /*  else  */
  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
- fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+  fflush(fichtm);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   m=cptcoveff;
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- Line 3184  fprintf(fichtm," <ul><li><b>Graphs</b></
+ Line 3787  fprintf(fichtm," <ul><li><b>Graphs</b></
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- interval) in state (%d): %s%d%d.png <br>\
+ prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
       }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+ health expectancies in states (1) and (2). 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>");
- Line 3198  interval) in state (%d): %s%d%d.png <br>
+ Line 3807  interval) in state (%d): %s%d%d.png <br>
  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-   int ng;
+   int ng=0;
  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
- Line 3225  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 3834  plot [%.f:%.f] \"%s\" every :::%d::%d u
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+        else        fprintf(ficgp," \%%*lf (\%%*lf)");
       }
-      fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 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\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 2,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+      fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     }
    }
    /*2 eme*/
- Line 3260  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 3869  plot [%.f:%.f] \"%s\" every :::%d::%d u
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
-       fprintf(ficgp,"\" t\"\" w l 0,");
+       fprintf(ficgp,"\" t\"\" w l lt 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)");
        }
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+       else fprintf(ficgp,"\" t\"\" w l lt 1,");
      }
    }
- Line 3275  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 3884  plot [%.f:%.f] \"%s\" every :::%d::%d u
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<= nlstate ; cpt ++) {
-       k=2+nlstate*(2*cpt-2);
+       /*       k=2+nlstate*(2*cpt-2); */
+       k=2+(nlstate+1)*(cpt-1);
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
        fprintf(ficgp,"set ter png small\n\
  set size 0.65,0.65\n\
- Line 3289  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 3899  plot [%.f:%.f] \"%s\" every :::%d::%d u
        */
        for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
        }
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
      }
    }
- Line 3349  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
+ Line 3961  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
               else
                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-              ij=1;
+              ij=1;/* To be checked else nbcode[0][0] wrong */
               for(j=3; j <=ncovmodel; j++) {
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                   ij++;
                 }
- Line 3842  void prwizard(int ncovmodel, int nlstate
+ Line 4454  void prwizard(int ncovmodel, int nlstate
          } /* end k*/
        } /*end j */
      } /* end i */
-   }
+   } /* end itimes */
  } /* end of prwizard */
+ /******************* Gompertz Likelihood ******************************/
+ double gompertz(double x[])
+ {
+   double A,B,L=0.0,sump=0.,num=0.;
+   int i,n=0; /* n is the size of the sample */
+   for (i=0;i<=imx-1 ; i++) {
+     sump=sump+weight[i];
+     /*    sump=sump+1;*/
+     num=num+1;
+   }
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+   for (i=1;i<=imx ; i++)
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+       if (cens[i] == 0 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
+         L=L+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+       }
+     }
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   return -2*L*num/sump;
+ }
+ #ifdef GSL
+ /******************* Gompertz_f Likelihood ******************************/
+ double gompertz_f(const gsl_vector *v, void *params)
+ {
+   double A,B,LL=0.0,sump=0.,num=0.;
+   double *x= (double *) v->data;
+   int i,n=0; /* n is the size of the sample */
+   for (i=0;i<=imx-1 ; i++) {
+     sump=sump+weight[i];
+     /*    sump=sump+1;*/
+     num=num+1;
+   }
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
+   for (i=1;i<=imx ; i++)
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
+       if (cens[i] == 0 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
+         LL=LL+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+       }
+     }
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
+   return -2*LL*num/sump;
+ }
+ #endif
+ /******************* Printing html file ***********/
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   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);
+ }
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
+ {
+   /*-------- data file ----------*/
+   FILE *fic;
+   char dummy[]="                         ";
+   int i, j, n;
+   int linei, month, year,iout;
+   char line[MAXLINE], linetmp[MAXLINE];
+   char stra[80], strb[80];
+   char *stratrunc;
+   int lstra;
+   if((fic=fopen(datafile,"r"))==NULL)    {
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+   }
+   i=1;
+   linei=0;
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+     linei=linei+1;
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+       if(line[j] == '\t')
+         line[j] = ' ';
+     }
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+       ;
+     };
+     line[j+1]=0;  /* Trims blanks at end of line */
+     if(line[0]=='#'){
+       fprintf(ficlog,"Comment line\n%s\n",line);
+       printf("Comment line\n%s\n",line);
+       continue;
+     }
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
+     for (j=0; line[j]!='\0';j++){
+       line[j]=linetmp[j];
+     }
+     for (j=maxwav;j>=1;j--){
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
+       }else{
+         errno=0;
+         lval=strtol(strb,&endptr,10);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
+           return 1;
+         }
+       }
+       s[j][i]=lval;
+       strcpy(line,stra);
+       cutv(stra, strb,line,' ');
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       }
+       else  if(iout=sscanf(strb,"%s.") != 0){
+         month=99;
+         year=9999;
+       }else{
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
+         return 1;
+       }
+       anint[j][i]= (double) year;
+       mint[j][i]= (double)month;
+       strcpy(line,stra);
+     } /* ENd Waves */
+     cutv(stra, strb,line,' ');
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     andc[i]=(double) year;
+     moisdc[i]=(double) month;
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
+     else  if(iout=sscanf(strb,"%s.") != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     if (year==9999) {
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     annais[i]=(double)(year);
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     errno=0;
+     dval=strtod(strb,&endptr);
+     if( strb[0]=='\0' || (*endptr != '\0')){
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fflush(ficlog);
+       return 1;
+     }
+     weight[i]=dval;
+     strcpy(line,stra);
+     for (j=ncovcol;j>=1;j--){
+       cutv(stra, strb,line,' ');
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
+       }else{
+         errno=0;
+         lval=strtol(strb,&endptr,10);
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
+           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
+           return 1;
+         }
+       }
+       if(lval <-1 || lval >1){
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n \
+  Exiting.\n",lval,linei, i,line,j);
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n \
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
+         return 1;
+       }
+       covar[j][i]=(double)(lval);
+       strcpy(line,stra);
+     }
+     lstra=strlen(stra);
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       stratrunc = &(stra[lstra-9]);
+       num[i]=atol(stratrunc);
+     }
+     else
+       num[i]=atol(stra);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+     i=i+1;
+   } /* End loop reading  data */
+   *imax=i-1; /* Number of individuals */
+   fclose(fic);
+   return (0);
+   endread:
+     printf("Exiting readdata: ");
+     fclose(fic);
+     return (1);
+ }
+ int decodemodel ( char model[], int lastobs)
+ {
+   int i, j, k;
+   int i1, j1, k1, k2;
+   char modelsav[80];
+    char stra[80], strb[80], strc[80], strd[80],stre[80];
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
+     j=0, j1=0, k1=1, k2=1;
+     j=nbocc(model,'+'); /* j=Number of '+' */
+     j1=nbocc(model,'*'); /* j1=Number of '*' */
+     cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
+                   but the covariates which are product must be computed and stored. */
+     cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
+     strcpy(modelsav,model);
+     if (strstr(model,"AGE") !=0){
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
+       return 1;
+     }
+     if (strstr(model,"v") !=0){
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
+       return 1;
+     }
+     /* This loop fills the array Tvar from the string 'model'.*/
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
+     /*  k=1 Tvar[1]=2 (from V2) */
+     /*  k=5 Tvar[5] */
+     /* for (k=1; k<=cptcovn;k++) { */
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+     /*  } */
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+     for(k=cptcovn; k>=1;k--){
+       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4
+                                     */
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+       /*scanf("%d",i);*/
+       if (strchr(strb,'*')) {  /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
+         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+         if (strcmp(strc,"age")==0) { /* Vn*age */
+           cptcovprod--;
+           cutv(strb,stre,strd,'V'); /* stre="V3" */
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
+           cptcovage++; /* Sums the number of covariates which include age as a product */
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
+           /*printf("stre=%s ", stre);*/
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+           cptcovprod--;
+           cutv(strb,stre,strc,'V');
+           Tvar[k]=atoi(stre);
+           cptcovage++;
+           Tage[cptcovage]=k;
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+           Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
+                                   because this model-covariate is a construction we invent a new column
+                                   ncovcol + k1
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+           Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
+           Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
+           Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
+           Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
+           for (i=1; i<=lastobs;i++){
+             /* Computes the new covariate which is a product of
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+           }
+           k1++;
+           k2=k2+2;
+         } /* End age is not in the model */
+       } /* End if model includes a product */
+       else { /* no more sum */
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+        /*  scanf("%d",i);*/
+         cutv(strd,strc,strb,'V');
+         Tvar[k]=atoi(strc);
+       }
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+         scanf("%d",i);*/
+     } /* end of loop + */
+   } /* end model */
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   printf("cptcovprod=%d ", cptcovprod);
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   scanf("%d ",i);*/
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
+   endread:
+     printf("Exiting decodemodel: ");
+     return (1);
+ }
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+ {
+   int i, m;
+   for (i=1; i<=imx; i++) {
+     for(m=2; (m<= maxwav); m++) {
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+         anint[m][i]=9999;
+         s[m][i]=-1;
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+         *nberr++;
+         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+         s[m][i]=-1;
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+         *nberr++;
+         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+       }
+     }
+   }
+   for (i=1; i<=imx; i++)  {
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     for(m=firstpass; (m<= lastpass); m++){
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+         if (s[m][i] >= nlstate+1) {
+           if(agedc[i]>0)
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+               agev[m][i]=agedc[i];
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+             else {
+               if ((int)andc[i]!=9999){
+                 nbwarn++;
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+                 agev[m][i]=-1;
+               }
+             }
+         }
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
+                                  years but with the precision of a month */
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+             agev[m][i]=1;
+           else if(agev[m][i] < *agemin){
+             *agemin=agev[m][i];
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
+           }
+           else if(agev[m][i] >*agemax){
+             *agemax=agev[m][i];
+             printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
+           }
+           /*agev[m][i]=anint[m][i]-annais[i];*/
+           /*     agev[m][i] = age[i]+2*m;*/
+         }
+         else { /* =9 */
+           agev[m][i]=1;
+           s[m][i]=-1;
+         }
+       }
+       else /*= 0 Unknown */
+         agev[m][i]=1;
+     }
+   }
+   for (i=1; i<=imx; i++)  {
+     for(m=firstpass; (m<=lastpass); m++){
+       if (s[m][i] > (nlstate+ndeath)) {
+         *nberr++;
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         return 1;
+       }
+     }
+   }
+   /*for (i=1; i<=imx; i++){
+   for (m=firstpass; (m<lastpass); m++){
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+ }
+ }*/
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
+   return (0);
+   endread:
+     printf("Exiting calandcheckages: ");
+     return (1);
+ }
  /***********************************************/
- Line 3853  void prwizard(int ncovmodel, int nlstate
+ Line 4985  void prwizard(int ncovmodel, int nlstate
  int main(int argc, char *argv[])
  {
+ #ifdef GSL
+   const gsl_multimin_fminimizer_type *T;
+   size_t iteri = 0, it;
+   int rval = GSL_CONTINUE;
+   int status = GSL_SUCCESS;
+   double ssval;
+ #endif
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-   int jj, imk;
+   int linei, month, year,iout;
+   int jj, ll, li, lj, lk, imk;
    int numlinepar=0; /* Current linenumber of parameter file */
+   int itimes;
+   int NDIM=2;
+   int vpopbased=0;
+   char ca[32], cb[32], cc[32];
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
+   struct stat info;
    double agedeb, agefin,hf;
    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
- Line 3871  int main(int argc, char *argv[])
+ Line 5017  int main(int argc, char *argv[])
    int *indx;
    char line[MAXLINE], linepar[MAXLINE];
    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-   char pathr[MAXLINE];
+   char pathr[MAXLINE], pathimach[MAXLINE];
+   char **bp, *tok, *val; /* pathtot */
    int firstobs=1, lastobs=10;
    int sdeb, sfin; /* Status at beginning and end */
    int c,  h , cpt,l;
    int ju,jl, mi;
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   int i1,j1, jk,aa,bb, stepsize, ij;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
    int mobilav=0,popforecast=0;
    int hstepm, nhstepm;
+   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;
    double bage, fage, age, agelim, agebase;
    double ftolpl=FTOL;
    double **prlim;
-   double *severity;
    double ***param; /* Matrix of parameters */
    double  *p;
    double **matcov; /* Matrix of covariance */
- Line 3898  int main(int argc, char *argv[])
+ Line 5046  int main(int argc, char *argv[])
    double *epj, vepp;
    double kk1, kk2;
    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double **ximort;
    char *alph[]={"a","a","b","c","d","e"}, str[4];
+   int *dcwave;
    char z[1]="c", occ;
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+   /*char  *strt;*/
-   char strstart[80], *strt, strtend[80];
+   char strtend[80];
-   char *stratrunc;
-   int lstra;
    long total_usecs;
+ /*   setlocale (LC_ALL, ""); */
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
    (void) gettimeofday(&start_time,&tzp);
    curr_time=start_time;
- Line 3941  int main(int argc, char *argv[])
+ Line 5093  int main(int argc, char *argv[])
    printf("\n%s\n%s",version,fullversion);
    if(argc <=1){
      printf("\nEnter the parameter file name: ");
-     scanf("%s",pathtot);
+     fgets(pathr,FILENAMELENGTH,stdin);
+     i=strlen(pathr);
+     if(pathr[i-1]=='\n')
+       pathr[i-1]='\0';
+    for (tok = pathr; tok != NULL; ){
+       printf("Pathr |%s|\n",pathr);
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+       printf("val= |%s| pathr=%s\n",val,pathr);
+       strcpy (pathtot, val);
+       if(pathr[0] == '\0') break; /* Dirty */
+     }
    }
    else{
      strcpy(pathtot,argv[1]);
- Line 3951  int main(int argc, char *argv[])
+ Line 5113  int main(int argc, char *argv[])
      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
    /* cutv(path,optionfile,pathtot,'\\');*/
+   /* Split argv[0], imach program to get pathimach */
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+  /*   strcpy(pathimach,argv[0]); */
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-   chdir(path);
+   chdir(path); /* Can be a relative path */
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+     printf("Current directory %s!\n",pathcd);
    strcpy(command,"mkdir ");
    strcat(command,optionfilefiname);
    if((outcmd=system(command)) != 0){
- Line 3977  int main(int argc, char *argv[])
+ Line 5147  int main(int argc, char *argv[])
    }
    fprintf(ficlog,"Log filename:%s\n",filelog);
    fprintf(ficlog,"\n%s\n%s",version,fullversion);
-   fprintf(ficlog,"\nEnter the parameter file name: ");
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-   fprintf(ficlog,"pathtot=%s\n\
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
   path=%s \n\
   optionfile=%s\n\
   optionfilext=%s\n\
-  optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
    printf("Local time (at start):%s",strstart);
    fprintf(ficlog,"Local time (at start): %s",strstart);
- Line 4021  int main(int argc, char *argv[])
+ Line 5191  int main(int argc, char *argv[])
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
      numlinepar++;
-     puts(line);
+     fputs(line,stdout);
      fputs(line,ficparo);
      fputs(line,ficlog);
    }
- Line 4037  int main(int argc, char *argv[])
+ Line 5207  int main(int argc, char *argv[])
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
      numlinepar++;
-     puts(line);
+     fputs(line, stdout);
+     //puts(line);
      fputs(line,ficparo);
      fputs(line,ficlog);
    }
- Line 4045  int main(int argc, char *argv[])
+ Line 5216  int main(int argc, char *argv[])
    covar=matrix(0,NCOVMAX,1,n);
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
+      v1+v2*age+v2*v3 makes cptcovn = 3
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+   */
+   if (strlen(model)>1)
+     cptcovn=nbocc(model,'+')+1;
+   /* ncovprod */
+   ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
+     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fflush(stdout);
+     fclose (ficlog);
+     goto end;
+   }
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   delti=delti3[1][1];
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
      printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
      fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
      fclose (ficparo);
      fclose (ficlog);
+     goto end;
      exit(0);
    }
-   /* Read guess parameters */
+   else if(mle==-3) {
-   /* Reads comments: lines beginning with '#' */
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     ungetc(c,ficpar);
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     fgets(line, MAXLINE, ficpar);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     numlinepar++;
+     matcov=matrix(1,npar,1,npar);
-     puts(line);
-     fputs(line,ficparo);
-     fputs(line,ficlog);
    }
-   ungetc(c,ficpar);
+   else{
+     /* Read guess parameters */
-   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     /* Reads comments: lines beginning with '#' */
-   for(i=1; i <=nlstate; i++){
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     j=0;
+       ungetc(c,ficpar);
-     for(jj=1; jj <=nlstate+ndeath; jj++){
+       fgets(line, MAXLINE, ficpar);
-       if(jj==i) continue;
-       j++;
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
-       if ((i1 != i) && (j1 != j)){
-         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-         exit(1);
-       }
-       fprintf(ficparo,"%1d%1d",i1,j1);
-       if(mle==1)
-         printf("%1d%1d",i,j);
-       fprintf(ficlog,"%1d%1d",i,j);
-       for(k=1; k<=ncovmodel;k++){
-         fscanf(ficpar," %lf",&param[i][j][k]);
-         if(mle==1){
-           printf(" %lf",param[i][j][k]);
-           fprintf(ficlog," %lf",param[i][j][k]);
-         }
-         else
-           fprintf(ficlog," %lf",param[i][j][k]);
-         fprintf(ficparo," %lf",param[i][j][k]);
-       }
-       fscanf(ficpar,"\n");
        numlinepar++;
-       if(mle==1)
+       fputs(line,stdout);
-         printf("\n");
+       fputs(line,ficparo);
-       fprintf(ficlog,"\n");
+       fputs(line,ficlog);
-       fprintf(ficparo,"\n");
      }
-   }
+     ungetc(c,ficpar);
-   fflush(ficlog);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+     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++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
-     puts(line);
-     fputs(line,ficparo);
-     fputs(line,ficlog);
-   }
-   ungetc(c,ficpar);
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     for(i=1; i <=nlstate; i++){
-   /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
+       for(j=1; j <=nlstate+ndeath-1; j++){
-   for(i=1; i <=nlstate; i++){
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     for(j=1; j <=nlstate+ndeath-1; j++){
+         if ((i1-i)*(j1-j)!=0){
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-       if ((i1-i)*(j1-j)!=0){
+           exit(1);
-         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+         }
-         exit(1);
+         printf("%1d%1d",i,j);
-       }
+         fprintf(ficparo,"%1d%1d",i1,j1);
-       printf("%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i1,j1);
-       fprintf(ficparo,"%1d%1d",i1,j1);
+         for(k=1; k<=ncovmodel;k++){
-       fprintf(ficlog,"%1d%1d",i1,j1);
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-       for(k=1; k<=ncovmodel;k++){
+           printf(" %le",delti3[i][j][k]);
-         fscanf(ficpar,"%le",&delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
-         printf(" %le",delti3[i][j][k]);
+           fprintf(ficlog," %le",delti3[i][j][k]);
-         fprintf(ficparo," %le",delti3[i][j][k]);
+         }
-         fprintf(ficlog," %le",delti3[i][j][k]);
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         printf("\n");
+         fprintf(ficparo,"\n");
+         fprintf(ficlog,"\n");
        }
-       fscanf(ficpar,"\n");
-       numlinepar++;
-       printf("\n");
-       fprintf(ficparo,"\n");
-       fprintf(ficlog,"\n");
      }
-   }
+     fflush(ficlog);
-   fflush(ficlog);
-   delti=delti3[1][1];
+     delti=delti3[1][1];
-   /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-   /* Reads comments: lines beginning with '#' */
+     /* Reads comments: lines beginning with '#' */
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
-     puts(line);
-     fputs(line,ficparo);
-     fputs(line,ficlog);
-   }
-   ungetc(c,ficpar);
-   matcov=matrix(1,npar,1,npar);
+     matcov=matrix(1,npar,1,npar);
-   for(i=1; i <=npar; i++){
+     for(i=1; i <=npar; i++)
-     fscanf(ficpar,"%s",&str);
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-     if(mle==1)
-       printf("%s",str);
+     for(i=1; i <=npar; i++){
-     fprintf(ficlog,"%s",str);
+       fscanf(ficpar,"%s",&str);
-     fprintf(ficparo,"%s",str);
+       if(mle==1)
-     for(j=1; j <=i; j++){
+         printf("%s",str);
-       fscanf(ficpar," %le",&matcov[i][j]);
+       fprintf(ficlog,"%s",str);
-       if(mle==1){
+       fprintf(ficparo,"%s",str);
-         printf(" %.5le",matcov[i][j]);
+       for(j=1; j <=i; j++){
+         fscanf(ficpar," %le",&matcov[i][j]);
+         if(mle==1){
+           printf(" %.5le",matcov[i][j]);
+         }
+         fprintf(ficlog," %.5le",matcov[i][j]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
        }
-       fprintf(ficlog," %.5le",matcov[i][j]);
+       fscanf(ficpar,"\n");
-       fprintf(ficparo," %.5le",matcov[i][j]);
+       numlinepar++;
+       if(mle==1)
+         printf("\n");
+       fprintf(ficlog,"\n");
+       fprintf(ficparo,"\n");
      }
-     fscanf(ficpar,"\n");
+     for(i=1; i <=npar; i++)
-     numlinepar++;
+       for(j=i+1;j<=npar;j++)
+         matcov[i][j]=matcov[j][i];
      if(mle==1)
        printf("\n");
      fprintf(ficlog,"\n");
-     fprintf(ficparo,"\n");
-   }
-   for(i=1; i <=npar; i++)
-     for(j=i+1;j<=npar;j++)
-       matcov[i][j]=matcov[j][i];
-   if(mle==1)
-     printf("\n");
-   fprintf(ficlog,"\n");
-   fflush(ficlog);
-   /*-------- Rewriting paramater file ----------*/
-   strcpy(rfileres,"r");    /* "Rparameterfile */
-   strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-   strcat(rfileres,".");    /* */
-   strcat(rfileres,optionfilext);    /* Other files have txt extension */
-   if((ficres =fopen(rfileres,"w"))==NULL) {
-     printf("Problem writing new parameter file: %s\n", fileres);goto end;
-     fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-   }
-   fprintf(ficres,"#%s\n",version);
-   /*-------- data file ----------*/
+     fflush(ficlog);
-   if((fic=fopen(datafile,"r"))==NULL)    {
-     printf("Problem with datafile: %s\n", datafile);goto end;
+     /*-------- Rewriting parameter file ----------*/
-     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
+     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 */
    n= lastobs;
-   severity = vector(1,maxwav);
-   outcome=imatrix(1,maxwav+1,1,n);
    num=lvector(1,n);
    moisnais=vector(1,n);
    annais=vector(1,n);
- Line 4227  int main(int argc, char *argv[])
+ Line 5418  int main(int argc, char *argv[])
    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
    mint=matrix(1,maxwav,1,n);
    anint=matrix(1,maxwav,1,n);
-   s=imatrix(1,maxwav+1,1,n);
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
    tab=ivector(1,NCOVMAX);
-   ncodemax=ivector(1,8);
+   ncodemax=ivector(1,8); /* hard coded ? */
-   i=1;
-   while (fgets(line, MAXLINE, fic) != NULL)    {
-     if ((i >= firstobs) && (i <=lastobs)) {
-       for (j=maxwav;j>=1;j--){
-         cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
-         strcpy(line,stra);
-         cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
-         cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
-       }
-       cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
-       for (j=ncovcol;j>=1;j--){
-         cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
-       }
-       lstra=strlen(stra);
-       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-         stratrunc = &(stra[lstra-9]);
-         num[i]=atol(stratrunc);
-       }
-       else
-         num[i]=atol(stra);
-       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
-       i=i+1;
-     }
-   }
-   /* printf("ii=%d", ij);
-      scanf("%d",i);*/
-   imx=i-1; /* Number of individuals */
-   /* for (i=1; i<=imx; i++){
+   /* Reads data from file datafile */
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+     goto end;
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
-     }*/
-    /*  for (i=1; i<=imx; i++){
-      if (s[4][i]==9)  s[4][i]=-1;
-      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
-  for (i=1; i<=imx; i++)
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
-      else weight[i]=1;*/
-   /* Calculation of the number of parameter from char model*/
+   /* Calculation of the number of parameters from char model */
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
-   Tprod=ivector(1,15);
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
+         k=3 V4 Tvar[k=3]= 4 (from V4)
+         k=2 V1 Tvar[k=2]= 1 (from V1)
+         k=1 Tvar[1]=2 (from V2)
+     */
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+   */
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
+     Tvar[3=V1*V4]=4+1 etc */
+   Tprod=ivector(1,15); /* Gives the position of a product */
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+   */
    Tvaraff=ivector(1,15);
-   Tvard=imatrix(1,15,1,2);
+   Tvard=imatrix(1,15,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
-   Tage=ivector(1,15);
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+   Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
-     j=0, j1=0, k1=1, k2=1;
+covariates (3 plus signs)
-     j=nbocc(model,'+'); /* j=Number of '+' */
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+                       */
-     cptcovn=j+1;
-     cptcovprod=j1; /*Number of products */
-     strcpy(modelsav,model);
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
-       printf("Error. Non available option model=%s ",model);
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
-       goto end;
-     }
-     /* This loop fills the array Tvar from the string 'model'.*/
-     for(i=(j+1); i>=1;i--){
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-       /*scanf("%d",i);*/
-       if (strchr(strb,'*')) {  /* Model includes a product */
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
-         if (strcmp(strc,"age")==0) { /* Vn*age */
-           cptcovprod--;
-           cutv(strb,stre,strd,'V');
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
-           cptcovage++;
-             Tage[cptcovage]=i;
-             /*printf("stre=%s ", stre);*/
-         }
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
-           cptcovprod--;
-           cutv(strb,stre,strc,'V');
-           Tvar[i]=atoi(stre);
-           cptcovage++;
-           Tage[cptcovage]=i;
-         }
-         else {  /* Age is not in the model */
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
-           Tvar[i]=ncovcol+k1;
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
-           Tprod[k1]=i;
-           Tvard[k1][1]=atoi(strc); /* m*/
-           Tvard[k1][2]=atoi(stre); /* n */
-           Tvar[cptcovn+k2]=Tvard[k1][1];
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
-           for (k=1; k<=lastobs;k++)
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
-           k1++;
-           k2=k2+2;
-         }
-       }
-       else { /* no more sum */
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-        /*  scanf("%d",i);*/
-       cutv(strd,strc,strb,'V');
-       Tvar[i]=atoi(strc);
-       }
-       strcpy(modelsav,stra);
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-         scanf("%d",i);*/
-     } /* end of loop + */
-   } /* end model */
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-   printf("cptcovprod=%d ", cptcovprod);
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-   scanf("%d ",i);
+   if(decodemodel(model, lastobs) == 1)
-   fclose(fic);*/
+     goto end;
+   if((double)(lastobs-imx)/(double)imx > 1.10){
+     nbwarn++;
+     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+   }
      /*  if(mle==1){*/
-   if (weightopt != 1) { /* Maximisation without weights*/
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
-     for(i=1;i<=n;i++) weight[i]=1.0;
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
    }
      /*-calculation of age at interview from date of interview and age at death -*/
    agev=matrix(1,maxwav,1,imx);
-   for (i=1; i<=imx; i++) {
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
-     for(m=2; (m<= maxwav); m++) {
+     goto end;
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-         anint[m][i]=9999;
-         s[m][i]=-1;
-       }
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         nberr++;
-         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-         s[m][i]=-1;
-       }
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-         nberr++;
-         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-       }
-     }
-   }
-   for (i=1; i<=imx; i++)  {
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-     for(m=firstpass; (m<= lastpass); m++){
-       if(s[m][i] >0){
-         if (s[m][i] >= nlstate+1) {
-           if(agedc[i]>0)
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-               agev[m][i]=agedc[i];
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-             else {
-               if ((int)andc[i]!=9999){
-                 nbwarn++;
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-                 agev[m][i]=-1;
-               }
-             }
-         }
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
-                                  years but with the precision of a
-                                  month */
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-             agev[m][i]=1;
-           else if(agev[m][i] <agemin){
-             agemin=agev[m][i];
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
-           }
-           else if(agev[m][i] >agemax){
-             agemax=agev[m][i];
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
-           }
-           /*agev[m][i]=anint[m][i]-annais[i];*/
-           /*     agev[m][i] = age[i]+2*m;*/
-         }
-         else { /* =9 */
-           agev[m][i]=1;
-           s[m][i]=-1;
-         }
-       }
-       else /*= 0 Unknown */
-         agev[m][i]=1;
-     }
-   }
-   for (i=1; i<=imx; i++)  {
-     for(m=firstpass; (m<=lastpass); m++){
-       if (s[m][i] > (nlstate+ndeath)) {
-         nberr++;
-         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-         goto end;
-       }
-     }
-   }
-   /*for (i=1; i<=imx; i++){
-   for (m=firstpass; (m<lastpass); m++){
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
- }
- }*/
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-   free_vector(severity,1,maxwav);
+   agegomp=(int)agemin;
-   free_imatrix(outcome,1,maxwav+1,1,n);
    free_vector(moisnais,1,n);
    free_vector(annais,1,n);
    /* free_matrix(mint,1,maxwav,1,n);
- Line 4480  int main(int argc, char *argv[])
+ Line 5495  int main(int argc, char *argv[])
    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-   Tcode=ivector(1,100);
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
    ncodemax[1]=1;
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);
- Line 4490  int main(int argc, char *argv[])
+ Line 5504  int main(int argc, char *argv[])
    h=0;
    m=pow(2,cptcoveff);
-   for(k=1;k<=cptcoveff; k++){
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-     for(i=1; i <=(m/pow(2,k));i++){
+     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
-       for(j=1; j <= ncodemax[k]; j++){
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
            h++;
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+           if (h>m)
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+             h=1;
+           /**< codtab(h,k)  k
+            *     h     1     2     3     4
+            *______________________________
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
+            *     2     2     1     1     1
+            *     3 i=2 1     2     1     1
+            *     4     2     2     1     1
+            *     5 i=3 1 i=2 1     2     1
+            *     6     2     1     2     1
+            *     7 i=4 1     2     2     1
+            *     8     2     2     2     1
+            *     9 i=5 1 i=3 1 i=2 1     1
+            *    10     2     1     1     1
+            *    11 i=6 1     2     1     1
+            *    12     2     2     1     1
+            *    13 i=7 1 i=4 1     2     1
+            *    14     2     1     2     1
+            *    15 i=8 1     2     2     1
+            *    16     2     2     2     1
+            */
+           codtab[h][k]=j;
+           codtab[h][Tvar[k]]=j;
+           printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
          }
        }
      }
- Line 4505  int main(int argc, char *argv[])
+ Line 5542  int main(int argc, char *argv[])
       codtab[1][2]=1;codtab[2][2]=2; */
    /* for(i=1; i <=m ;i++){
       for(k=1; k <=cptcovn; k++){
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
       }
       printf("\n");
       }
- Line 4513  int main(int argc, char *argv[])
+ Line 5550  int main(int argc, char *argv[])
    /*------------ gnuplot -------------*/
    strcpy(optionfilegnuplot,optionfilefiname);
+   if(mle==-3)
+     strcat(optionfilegnuplot,"-mort");
    strcat(optionfilegnuplot,".gp");
    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
      printf("Problem with file %s",optionfilegnuplot);
    }
    else{
      fprintf(ficgp,"\n# %s\n", version);
      fprintf(ficgp,"# %s\n", optionfilegnuplot);
-     fprintf(ficgp,"set missing 'NaNq'\n");
+     //fprintf(ficgp,"set missing 'NaNq'\n");
+     fprintf(ficgp,"set datafile 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);
+     printf("Problem with %s \n",optionfilehtm);
+     exit(0);
    }
    strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
- Line 4537  int main(int argc, char *argv[])
+ Line 5581  int main(int argc, char *argv[])
      printf("Problem with %s \n",optionfilehtmcov), exit(0);
    }
    else{
-   fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
-           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
  \n\
  <hr  size=\"2\" color=\"#EC5E5E\">\
   <ul><li><h4>Parameter files</h4>\n\
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
   - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
   - Log file of the run: <a href=\"%s\">%s</a><br>\n\
   - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
   - Date and time at start: %s</ul>\n",\
-           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
            fileres,fileres,\
            filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
    fflush(fichtm);
- Line 4564  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5610  Title=%s <br>Datafile=%s Firstpass=%d La
    /* Calculates basic frequencies. Computes observed prevalence at single age
       and prints on file fileres'p'. */
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
    fprintf(fichtm,"\n");
    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
- Line 4583  Interval (in months) between two waves:
+ Line 5629  Interval (in months) between two waves:
    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-   likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
-   printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+   if (mle==-3){
-   for (k=1; k<=npar;k++)
+     ximort=matrix(1,NDIM,1,NDIM);
-     printf(" %d %8.5f",k,p[k]);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-   printf("\n");
+     cens=ivector(1,n);
-   globpr=1; /* to print the contributions */
+     ageexmed=vector(1,n);
-   likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     agecens=vector(1,n);
-   printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     dcwave=ivector(1,n);
-   for (k=1; k<=npar;k++)
-     printf(" %d %8.5f",k,p[k]);
+     for (i=1; i<=imx; i++){
-   printf("\n");
+       dcwave[i]=-1;
-   if(mle>=1){ /* Could be 1 or 2 */
+       for (m=firstpass; m<=lastpass; m++)
-     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+         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;
+     }
+     for (i=1;i<=NDIM;i++) {
+       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]);*/
+ #ifdef GSL
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
+ #elsedef
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ #endif
+     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);
+     }
+ #ifdef GSL
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+ #elsedef
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
+     /*  for (i=1;i<=nlstate;i++)
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     */
+     fprintf(ficrespow,"\n");
+ #ifdef GSL
+     /* gsl starts here */
+     T = gsl_multimin_fminimizer_nmsimplex;
+     gsl_multimin_fminimizer *sfm = NULL;
+     gsl_vector *ss, *x;
+     gsl_multimin_function minex_func;
+     /* Initial vertex size vector */
+     ss = gsl_vector_alloc (NDIM);
+     if (ss == NULL){
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+     }
+     /* Set all step sizes to 1 */
+     gsl_vector_set_all (ss, 0.001);
+     /* Starting point */
+     x = gsl_vector_alloc (NDIM);
-   /*--------- results files --------------*/
+     if (x == NULL){
-   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);
+       gsl_vector_free(ss);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+     }
+     /* Initialize method and iterate */
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
+ /*     gsl_vector_set(x, 0, 0.0268); */
+ /*     gsl_vector_set(x, 1, 0.083); */
+     gsl_vector_set(x, 0, p[1]);
+     gsl_vector_set(x, 1, p[2]);
+     minex_func.f = &gompertz_f;
+     minex_func.n = NDIM;
+     minex_func.params = (void *)&p; /* ??? */
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+     printf("Iterations beginning .....\n\n");
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
-   jk=1;
+     iteri=0;
-   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     while (rval == GSL_CONTINUE){
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       iteri++;
-   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       status = gsl_multimin_fminimizer_iterate(sfm);
-   for(i=1,jk=1; i <=nlstate; i++){
-     for(k=1; k <=(nlstate+ndeath); k++){
+       if (status) printf("error: %s\n", gsl_strerror (status));
-       if (k != i)
+       fflush(0);
-         {
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+     gsl_vector_free(x); /* initial values */
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ #endif
+     fclose(ficrespow);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+     for(i=1; i <=NDIM; i++)
+       for(j=i+1;j<=NDIM;j++)
+         matcov[i][j]=matcov[j][i];
+     printf("\nCovariance matrix\n ");
+     for(i=1; i <=NDIM; 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);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
+   } /* Endof if mle==-3 */
+   else{ /* For mle >=1 */
+     globpr=0;/* debug */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       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);
+       fputs(line,stdout);
+       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);
+       fputs(line,stdout);
+       fputs(line,ficparo);
-   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);
-   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);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   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);
+       fgets(line, MAXLINE, ficpar);
-   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);
+       fputs(line,stdout);
+       fputs(line,ficparo);
-   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);
+     fprintf(ficparo,"pop_based=%d\n",popbased);
+     fprintf(ficres,"pop_based=%d\n",popbased);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     /* day and month of proj2 are not used but only year anproj2.*/
+     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+    /*------------ free_vector  -------------*/
+    /*  chdir(path); */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     free_lvector(num,1,n);
+     free_vector(agedc,1,n);
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     fclose(ficparo);
+     fclose(ficres);
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+     strcpy(filerespl,"pl");
+     strcat(filerespl,fileres);
+     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+     }
+     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     pstamp(ficrespl);
+     fprintf(ficrespl,"# Period (stable) prevalence \n");
+     fprintf(ficrespl,"#Age ");
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     fprintf(ficrespl,"\n");
+     prlim=matrix(1,nlstate,1,nlstate);
+     agebase=ageminpar;
+     agelim=agemaxpar;
+     ftolpl=1.e-10;
+     i1=pow(2,cptcoveff);
+     if (cptcovn < 1){i1=1;}
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
+         /* to clean */
+         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
+         fprintf(ficrespl,"\n#******");
+         printf("\n#******");
+         fprintf(ficlog,"\n#******");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficrespl,"******\n");
+         printf("******\n");
+         fprintf(ficlog,"******\n");
+         for (age=agebase; age<=agelim; age++){
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           fprintf(ficrespl,"%.0f ",age );
+           for(j=1;j<=cptcoveff;j++)
+             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           for(i=1; i<=nlstate;i++)
+             fprintf(ficrespl," %.5f", prlim[i][i]);
+           fprintf(ficrespl,"\n");
+         } /* Age */
+         /* was end of cptcod */
+     } /* cptcov */
+     fclose(ficrespl);
+     /*------------- h Pij x at various ages ------------*/
+     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+     }
+     printf("Computing pij: result on file '%s' \n", filerespij);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     /*if (stepm<=24) stepsize=2;*/
+     agelim=AGESUP;
+     hstepm=stepsize*YEARM; /* Every year of age */
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     /* hstepm=1;   aff par mois*/
+     pstamp(ficrespij);
+     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
+         fprintf(ficrespij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrespij,"******\n");
+         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-   dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+           /*      nhstepm=nhstepm*YEARM; aff par mois*/
-   dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-   fscanf(ficpar,"pop_based=%d\n",&popbased);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   fprintf(ficparo,"pop_based=%d\n",popbased);
+           oldm=oldms;savm=savms;
-   fprintf(ficres,"pop_based=%d\n",popbased);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-   while((c=getc(ficpar))=='#' && c!= EOF){
+           for(i=1; i<=nlstate;i++)
-     ungetc(c,ficpar);
+             for(j=1; j<=nlstate+ndeath;j++)
-     fgets(line, MAXLINE, ficpar);
+               fprintf(ficrespij," %1d-%1d",i,j);
-     puts(line);
+           fprintf(ficrespij,"\n");
-     fputs(line,ficparo);
+           for (h=0; h<=nhstepm; h++){
-   }
+             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
-   ungetc(c,ficpar);
+             for(i=1; i<=nlstate;i++)
+               for(j=1; j<=nlstate+ndeath;j++)
-   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(ficrespij," %.5f", p3mat[i][j][h]);
-   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(ficrespij,"\n");
-   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);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   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);
+           fprintf(ficrespij,"\n");
-   /* day and month of proj2 are not used but only year anproj2.*/
+         }
+       }
+     }
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
+     fclose(ficrespij);
-   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-   /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
-   /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-   replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
-   printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
-                model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
-                jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
-   /*------------ free_vector  -------------*/
-   /*  chdir(path); */
-   free_ivector(wav,1,imx);
-   free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-   free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
-   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-   free_lvector(num,1,n);
-   free_vector(agedc,1,n);
-   /*free_matrix(covar,0,NCOVMAX,1,n);*/
-   /*free_matrix(covar,1,NCOVMAX,1,n);*/
-   fclose(ficparo);
-   fclose(ficres);
-   /*--------------- Prevalence limit  (stable prevalence) --------------*/
-   strcpy(filerespl,"pl");
-   strcat(filerespl,fileres);
-   if((ficrespl=fopen(filerespl,"w"))==NULL) {
-     printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
-     fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
-   }
-   printf("Computing stable prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficrespl,"#Stable prevalence \n");
-   fprintf(ficrespl,"#Age ");
-   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-   fprintf(ficrespl,"\n");
-   prlim=matrix(1,nlstate,1,nlstate);
-   agebase=ageminpar;
-   agelim=agemaxpar;
-   ftolpl=1.e-10;
-   i1=cptcoveff;
-   if (cptcovn < 1){i1=1;}
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     for(i=1;i<=AGESUP;i++)
-       k=k+1;
+       for(j=1;j<=NCOVMAX;j++)
-       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+         for(k=1;k<=NCOVMAX;k++)
-       fprintf(ficrespl,"\n#******");
+           probs[i][j][k]=0.;
-       printf("\n#******");
-       fprintf(ficlog,"\n#******");
+     /*---------- Forecasting ------------------*/
-       for(j=1;j<=cptcoveff;j++) {
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
-         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     if(prevfcast==1){
-         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       /*    if(stepm ==1){*/
-         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       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);*/
-       fprintf(ficrespl,"******\n");
+       /*      }  */
-       printf("******\n");
+       /*      else{ */
-       fprintf(ficlog,"******\n");
+       /*        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); */
-       for (age=agebase; age<=agelim; age++){
+       /*        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); */
-         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+       /*      } */
-         fprintf(ficrespl,"%.0f ",age );
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         for(i=1; i<=nlstate;i++)
-           fprintf(ficrespl," %.5f", prlim[i][i]);
-         fprintf(ficrespl,"\n");
-       }
      }
-   }
-   fclose(ficrespl);
-   /*------------- h Pij x at various ages ------------*/
-   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-   if((ficrespij=fopen(filerespij,"w"))==NULL) {
-     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-   }
-   printf("Computing pij: result on file '%s' \n", filerespij);
-   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   /*if (stepm<=24) stepsize=2;*/
-   agelim=AGESUP;
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
-   hstepm=stepsize*YEARM; /* Every year of age */
-   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-   /* hstepm=1;   aff par mois*/
+     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);
+     */
-   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     if (mobilav!=0) {
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-       k=k+1;
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       fprintf(ficrespij,"\n#****** ");
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       for(j=1;j<=cptcoveff;j++)
+       }
-         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     }
-       fprintf(ficrespij,"******\n");
-       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-         /*        nhstepm=nhstepm*YEARM; aff par mois*/
-         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     /*---------- Health expectancies, no variances ------------*/
-         oldm=oldms;savm=savms;
-         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+     strcpy(filerese,"e");
-         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+     strcat(filerese,fileres);
-         for(i=1; i<=nlstate;i++)
+     if((ficreseij=fopen(filerese,"w"))==NULL) {
-           for(j=1; j<=nlstate+ndeath;j++)
+       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
-             fprintf(ficrespij," %1d-%1d",i,j);
+       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
-         fprintf(ficrespij,"\n");
+     }
-         for (h=0; h<=nhstepm; h++){
+     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
-           fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
-           for(i=1; i<=nlstate;i++)
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-             for(j=1; j<=nlstate+ndeath;j++)
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+         k=k+1;
-           fprintf(ficrespij,"\n");
+         fprintf(ficreseij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          }
-         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficreseij,"******\n");
-         fprintf(ficrespij,"\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        }
      }
-   }
+     fclose(ficreseij);
-   varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
-   fclose(ficrespij);
+     /*---------- Health expectancies and variances ------------*/
-   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   /*---------- Forecasting ------------------*/
+     strcpy(filerest,"t");
-   /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     strcat(filerest,fileres);
-   if(prevfcast==1){
+     if((ficrest=fopen(filerest,"w"))==NULL) {
-     /*    if(stepm ==1){*/
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+     }
- /*      }  */
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
- /*      else{ */
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
- /*        erreur=108; */
- /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
- /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
- /*      } */
-   }
-   /*---------- Health expectancies and variances ------------*/
-   strcpy(filerest,"t");
+     strcpy(fileresstde,"stde");
-   strcat(filerest,fileres);
+     strcat(fileresstde,fileres);
-   if((ficrest=fopen(filerest,"w"))==NULL) {
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
-     printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
-     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
-   }
+     }
-   printf("Computing Total LEs with variances: file '%s' \n", filerest);
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
-   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
+     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(filerese,"e");
+     strcpy(fileresv,"v");
-   strcat(filerese,fileres);
+     strcat(fileresv,fileres);
-   if((ficreseij=fopen(filerese,"w"))==NULL) {
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
-     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
-     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
-   }
+     }
-   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-   strcpy(fileresv,"v");
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-   strcat(fileresv,fileres);
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-   if((ficresvij=fopen(fileresv,"w"))==NULL) {
+         k=k+1;
-     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+         fprintf(ficrest,"\n#****** ");
-     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+         for(j=1;j<=cptcoveff;j++)
-   }
+           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+         fprintf(ficrest,"******\n");
-   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-   /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+         fprintf(ficresstdeij,"\n#****** ");
-   prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+         fprintf(ficrescveij,"\n#****** ");
-   /*  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",\
+         for(j=1;j<=cptcoveff;j++) {
- ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+           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");
-   if (mobilav!=0) {
+         fprintf(ficresvij,"\n#****** ");
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         for(j=1;j<=cptcoveff;j++)
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         fprintf(ficresvij,"******\n");
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
-   }
-   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;
+         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
-       fprintf(ficrest,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficrest,"******\n");
-       fprintf(ficreseij,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficreseij,"******\n");
-       fprintf(ficresvij,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficresvij,"******\n");
-       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
-       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
-       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
+         pstamp(ficrest);
-       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
+         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-       if(popbased==1){
+           oldm=oldms;savm=savms;
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
+           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);
+             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+               for(i=1, epj[j]=0.;i <=nlstate;i++) {
+                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
+                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               }
+               epj[nlstate+1] +=epj[j];
+             }
+             for(i=1, vepp=0.;i <=nlstate;i++)
-       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+               for(j=1;j <=nlstate;j++)
-       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+                 vepp += vareij[i][j][(int)age];
-       fprintf(ficrest,"\n");
+             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+             for(j=1;j <=nlstate;j++){
-       epj=vector(1,nlstate+1);
+               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
-       for(age=bage; age <=fage ;age++){
+             }
-         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+             fprintf(ficrest,"\n");
-         if (popbased==1) {
-           if(mobilav ==0){
-             for(i=1; i<=nlstate;i++)
-               prlim[i][i]=probs[(int)age][i][k];
-           }else{ /* mobilav */
-             for(i=1; i<=nlstate;i++)
-               prlim[i][i]=mobaverage[(int)age][i][k];
            }
          }
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         fprintf(ficrest," %4.0f",age);
+         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+         free_vector(epj,1,nlstate+1);
-           for(i=1, epj[j]=0.;i <=nlstate;i++) {
+       }
-             epj[j] += prlim[i][i]*eij[i][j][(int)age];
+     }
-             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+     free_vector(weight,1,n);
-           }
+     free_imatrix(Tvard,1,15,1,2);
-           epj[nlstate+1] +=epj[j];
+     free_imatrix(s,1,maxwav+1,1,n);
-         }
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
-         for(i=1, vepp=0.;i <=nlstate;i++)
+     free_ivector(cod,1,n);
-           for(j=1;j <=nlstate;j++)
+     free_ivector(tab,1,NCOVMAX);
-             vepp += vareij[i][j][(int)age];
+     fclose(ficresstdeij);
-         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+     fclose(ficrescveij);
-         for(j=1;j <=nlstate;j++){
+     fclose(ficresvij);
-           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+     fclose(ficrest);
-         }
+     fclose(ficpar);
-         fprintf(ficrest,"\n");
-       }
+     /*------- Variance of period (stable) prevalence------*/
-       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     strcpy(fileresvpl,"vpl");
-       free_vector(epj,1,nlstate+1);
+     strcat(fileresvpl,fileres);
-     }
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-   }
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
-   free_vector(weight,1,n);
+       exit(0);
-   free_imatrix(Tvard,1,15,1,2);
+     }
-   free_imatrix(s,1,maxwav+1,1,n);
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
-   free_matrix(anint,1,maxwav,1,n);
-   free_matrix(mint,1,maxwav,1,n);
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-   free_ivector(cod,1,n);
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-   free_ivector(tab,1,NCOVMAX);
+         k=k+1;
-   fclose(ficreseij);
+         fprintf(ficresvpl,"\n#****** ");
-   fclose(ficresvij);
+         for(j=1;j<=cptcoveff;j++)
-   fclose(ficrest);
+           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   fclose(ficpar);
+         fprintf(ficresvpl,"******\n");
-   /*------- Variance of stable prevalence------*/
-   strcpy(fileresvpl,"vpl");
-   strcat(fileresvpl,fileres);
-   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-     printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
-     exit(0);
-   }
-   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-       k=k+1;
-       fprintf(ficresvpl,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficresvpl,"******\n");
-       varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         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);
+   }  /* mle==-3 arrives here for freeing */
-   free_ivector(Tage,1,15);
+  endfree:
-   free_ivector(Tcode,1,100);
+     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(covar,0,NCOVMAX,1,n);
+     free_matrix(matcov,1,npar,1,npar);
+     /*free_vector(delti,1,npar);*/
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_ivector(ncodemax,1,8);
+     free_ivector(Tvar,1,15);
+     free_ivector(Tprod,1,15);
+     free_ivector(Tvaraff,1,15);
+     free_ivector(Tage,1,15);
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     free_imatrix(codtab,1,100,1,10);
    fflush(fichtm);
    fflush(ficgp);
    if((nberr >0) || (nbwarn>0)){
-     printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
      fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
    }else{
      printf("End of Imach\n");
- Line 5101  ageminpar, agemax, s[lastpass][imx], age
+ Line 6466  ageminpar, agemax, s[lastpass][imx], age
    tm = *localtime(&end_time.tv_sec);
    tmg = *gmtime(&end_time.tv_sec);
    strcpy(strtend,asctime(&tm));
-   printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend);
+   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
    fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
    printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   printf("Total time was %ld 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);
+   fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
    /*  printf("Total time was %d uSec.\n", total_usecs);*/
  /*   if(fileappend(fichtm,optionfilehtm)){ */
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
    fclose(fichtm);
+   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
    fclose(fichtmcov);
    fclose(ficgp);
    fclose(ficlog);
    /*------ End -----------*/
-   chdir(path);
-   strcpy(plotcmd,GNUPLOTPROGRAM);
+    printf("Before Current directory %s!\n",pathcd);
-   strcat(plotcmd," ");
+    if(chdir(pathcd) != 0)
-   strcat(plotcmd,optionfilegnuplot);
+     printf("Can't move to directory %s!\n",path);
-   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
+   if(getcwd(pathcd,MAXLINE) > 0)
+     printf("Current directory %s!\n",pathcd);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
+   sprintf(plotcmd,"gnuplot");
+ #ifndef UNIX
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef UNIX
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
    if((outcmd=system(plotcmd)) != 0){
-     printf(" Problem with gnuplot\n");
+     printf("\n Problem with gnuplot\n");
    }
    printf(" Wait...");
    while (z[0] != 'q') {
- Line 5131  ageminpar, agemax, s[lastpass][imx], age
+ Line 6522  ageminpar, agemax, s[lastpass][imx], age
      printf("\nType e to edit output files, g to graph again and q for exiting: ");
      scanf("%s",z);
  /*     if (z[0] == 'c') system("./imach"); */
-     if (z[0] == 'e') system(optionfilehtm);
+     if (z[0] == 'e') {
+       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+       system(optionfilehtm);
+     }
      else if (z[0] == 'g') system(plotcmd);
      else if (z[0] == 'q') exit(0);
    }

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

Removed from v.1.94
changed lines
	Added in v.1.143