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Diff for /imach/src/imach.c between versions 1.102 and 1.146

-version 1.102, 2004/09/15 17:31:30
+version 1.146, 2014/06/16 10:20:28
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.146  2014/06/16 10:20:28  brouard
+   Summary: Merge
+   Author: Brouard
+   Merge, before building revised version.
+   Revision 1.145  2014/06/10 21:23:15  brouard
+   Summary: Debugging with valgrind
+   Author: Nicolas Brouard
+   Lot of changes in order to output the results with some covariates
+   After the Edimburgh REVES conference 2014, it seems mandatory to
+   improve the code.
+   No more memory valgrind error but a lot has to be done in order to
+   continue the work of splitting the code into subroutines.
+   Also, decodemodel has been improved. Tricode is still not
+   optimal. nbcode should be improved. Documentation has been added in
+   the source code.
+   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.
- Line 24
+ Line 233
    The same imach parameter file can be used but the option for mle should be -3.
-   Agn�s, who wrote this part of the code, tried to keep most of the
+   Agnès, who wrote this part of the code, tried to keep most of the
    former routines in order to include the new code within the former code.
    The output is very simple: only an estimate of the intercept and of
- Line 155
+ Line 364
    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 184
+ Line 393
        begin-prev-date,...
    open gnuplot file
    open html file
-   stable prevalence
+   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
-    for age prevalim()
+    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
-   h Pij x
+                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
-   variance of p varprob
+     freexexit2 possible for memory heap.
+   h Pij x                         | pij_nom  ficrestpij
+    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
+ 85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
+ 85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
+ 65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
+ 65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
+   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
+    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
+    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
    forecasting if prevfcast==1 prevforecast call prevalence()
    health expectancies
    Variance-covariance of DFLE
- Line 196
+ Line 417
    varevsij()
    if popbased==1 varevsij(,popbased)
    total life expectancies
-   Variance of stable prevalence
+   Variance of period (stable) prevalence
   end
  */
- Line 206
+ Line 427
  #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 256
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
  #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 NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
  #define NINTERVMAX 8
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- #define NDEATHMAX 8 /* Maximum number of dead 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, including generated covariates V1*V2 */
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
  #define MAXN 20000
- #define YEARM 12. /* Number of months per year */
+ #define YEARM 12. /**< Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
  #ifdef UNIX
  #define DIRSEPARATOR '/'
+ #define CHARSEPARATOR "/"
  #define ODIRSEPARATOR '\\'
  #else
  #define DIRSEPARATOR '\\'
+ #define CHARSEPARATOR "\\"
  #define ODIRSEPARATOR '/'
  #endif
+ <<<<<<< imach.c
  /* $Id$ */
+ =======
+ /* $Id$ */
+ >>>>>>> 1.145
  /* $State$ */
- char version[]="Imach version 0.97c, September 2004, INED-EUROREVES ";
+ <<<<<<< imach.c
+ 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[]="$Revision$ $Date$";
+ =======
+ 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  */
+ >>>>>>> 1.145
- int nvar;
+ char strstart[80];
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ 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 */
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
+ int cptcov=0; /* Working variable */
  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 **matprod2(); /* test */
  double **oldm, **newm, **savm; /* Working pointers to matrices */
  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ /*FILE *fic ; */ /* Used in readdata only */
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
  FILE *ficlog, *ficrespow;
- int globpr; /* Global variable for printing or not */
+ int globpr=0; /* Global variable for printing or not */
  double fretone; /* Only one call to likelihood */
- long ipmx; /* Number of contributions */
+ long ipmx=0; /* Number of contributions */
  double sw; /* Sum of weights */
  char filerespow[FILENAMELENGTH];
  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- Line 285  FILE *ficresprobmorprev;
+ Line 545  FILE *ficresprobmorprev;
  FILE *fichtm, *fichtmcov; /* Html File */
  FILE *ficreseij;
  char filerese[FILENAMELENGTH];
+ FILE *ficresstdeij;
+ char fileresstde[FILENAMELENGTH];
+ FILE *ficrescveij;
+ char filerescve[FILENAMELENGTH];
  FILE  *ficresvij;
  char fileresv[FILENAMELENGTH];
  FILE  *ficresvpl;
  char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
  char command[FILENAMELENGTH];
  int  outcmd=0;
- Line 313  long time_value;
+ Line 577  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 359  double dateintmean=0;
+ Line 627  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[j,i], 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 *Ndum; /** Freq of modality (tricode */
+ 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)
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       the name of the file (name), its extension only (ext) and its first part of the name (finame)
    */
    char  *ss;                            /* pointer */
- Line 377  static int split( char *path, char *dirc
+ Line 653  static int split( char *path, char *dirc
    l1 = strlen(path );                   /* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   if ( ss == NULL ) {                   /* no directory, so use current */
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+     strcpy( name, path );               /* we got the fullname name because no directory */
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      /* get current working directory */
- Line 385  static int split( char *path, char *dirc
+ Line 662  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 393  static int split( char *path, char *dirc
+ Line 671  static int split( char *path, char *dirc
      strcpy( name, ss );         /* save file name */
      strncpy( dirc, path, l1 - l2 );     /* now the directory */
      dirc[l1-l2] = 0;                    /* add zero */
+     printf(" DIRC2 = %s \n",dirc);
    }
+   /* We add a separator at the end of dirc if not exists */
    l1 = strlen( dirc );                  /* length of directory */
-   /*#ifdef windows
+   if( dirc[l1-1] != DIRSEPARATOR ){
-   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
+     dirc[l1] =  DIRSEPARATOR;
- #else
+     dirc[l1+1] = 0;
-   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
+     printf(" DIRC3 = %s \n",dirc);
- #endif
+   }
-   */
    ss = strrchr( name, '.' );            /* find last / */
    if (ss >0){
      ss++;
- Line 410  static int split( char *path, char *dirc
+ Line 689  static int split( char *path, char *dirc
      strncpy( finame, name, l1-l2);
      finame[l1-l2]= 0;
    }
    return( 0 );                          /* we're done */
  }
- Line 428  void replace_back_to_slash(char *s, char
+ Line 708  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 *cutl(char *blocc, char *alocc, char *in, char occ)
+ {
+   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
+      and alocc starts after first 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 blocc
+   */
+   char *s, *t, *bl;
+   t=in;s=in;
+   while ((*in != occ) && (*in != '\0')){
+     *alocc++ = *in++;
+   }
+   if( *in == occ){
+     *(alocc)='\0';
+     s=++in;
+   }
+   if (s == t) {/* occ not found */
+     *(alocc-(in-s))='\0';
+     in=s;
+   }
+   while ( *in != '\0'){
+     *blocc++ = *in++;
+   }
+   *blocc='\0';
+   return t;
+ }
+ 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 440  int nbocc(char *s, char occ)
+ Line 791  int nbocc(char *s, char occ)
    return j;
  }
- void cutv(char *u,char *v, char*t, char occ)
+ /* void cutv(char *u,char *v, char*t, char occ) */
- {
+ /* { */
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-      gives u="abcedf" and v="ghi2j" */
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   int i,lg,j,p=0;
+ /*   int i,lg,j,p=0; */
-   i=0;
+ /*   i=0; */
-   for(j=0; j<=strlen(t)-1; j++) {
+ /*   lg=strlen(t); */
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+ /*   for(j=0; j<=lg-1; j++) { */
-   }
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
+ /*   } */
-   lg=strlen(t);
+ /*   for(j=0; j<p; j++) { */
-   for(j=0; j<p; j++) {
+ /*     (u[j] = t[j]); */
-     (u[j] = t[j]);
+ /*   } */
-   }
+ /*      u[p]='\0'; */
-      u[p]='\0';
-    for(j=0; j<= lg; j++) {
+ /*    for(j=0; j<= lg; j++) { */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   }
+ /*   } */
- }
+ /* } */
  /********************** nrerror ********************/
- Line 569  double **matrix(long nrl, long nrh, long
+ Line 920  double **matrix(long nrl, long nrh, long
    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    return m;
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     */
  }
- Line 843  char *asc_diff_time(long time_sec, char
+ Line 1196  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 872  void powell(double p[], double **xi, int
+ Line 1225  void powell(double p[], double **xi, int
      last_time=curr_time;
      (void) gettimeofday(&curr_time,&tzp);
      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
-     /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
-     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
-     */
     for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12lf",i, p[i]);
- Line 996  void powell(double p[], double **xi, int
+ Line 1348  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 1005  double **prevalim(double **prlim, int nl
+ Line 1357  double **prevalim(double **prlim, int nl
    int i, ii,j,k;
    double min, max, maxmin, maxmax,sumnew=0.;
-   double **matprod2();
+   /* double **matprod2(); */ /* test */
-   double **out, cov[NCOVMAX], **pmij();
+   double **out, cov[NCOVMAX+1], **pmij();
    double **newm;
    double agefin, delaymax=50 ; /* Max number of years to converge */
- Line 1021  double **prevalim(double **prlim, int nl
+ Line 1373  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("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, 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++) /\* Useless *\/ */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
+     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 1046  double **prevalim(double **prlim, int nl
+ Line 1400  double **prevalim(double **prlim, int nl
          sumnew=0;
          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
          prlim[i][j]= newm[i][j]/(1-sumnew);
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
          max=FMAX(max,prlim[i][j]);
          min=FMIN(min,prlim[i][j]);
        }
- Line 1062  double **prevalim(double **prlim, int nl
+ Line 1417  double **prevalim(double **prlim, int nl
  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
  {
-   double s1, s2;
+   /* According to parameters values stored in x and the covariate's values stored in cov,
+      computes the probability to be observed in state j being in state i by appying the
+      model to the ncovmodel covariates (including constant and age).
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+      ncth covariate in the global vector x is given by the formula:
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+      Outputs ps[i][j] the probability to be observed in j being in j according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
+   double s1, lnpijopii;
    /*double t34;*/
    int i,j,j1, nc, ii, jj;
      for(i=1; i<= nlstate; i++){
        for(j=1; j<i;j++){
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           /*s2 += param[i][j][nc]*cov[nc];*/
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
          }
-         ps[i][j]=s2;
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
        }
        for(j=i+1; j<=nlstate+ndeath;j++){
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
          }
-         ps[i][j]=s2;
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
        }
      }
-     /*ps[3][2]=1;*/
      for(i=1; i<= nlstate; i++){
        s1=0;
-       for(j=1; j<i; j++)
+       for(j=1; j<i; j++){
-         s1+=exp(ps[i][j]);
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-       for(j=i+1; j<=nlstate+ndeath; j++)
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         s1+=exp(ps[i][j]);
+       }
+       for(j=i+1; j<=nlstate+ndeath; j++){
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       }
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
        ps[i][i]=1./(s1+1.);
+       /* Computing other pijs */
        for(j=1; j<i; j++)
          ps[i][j]= exp(ps[i][j])*ps[i][i];
        for(j=i+1; j<=nlstate+ndeath; j++)
- Line 1107  double **pmij(double **ps, double *cov,
+ Line 1481  double **pmij(double **ps, double *cov,
        }
      }
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
- /*         printf("ddd %lf ",ps[ii][jj]); */
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
- /*       } */
+     /*   } */
- /*       printf("\n "); */
+     /*   printf("\n "); */
- /*        } */
+     /* } */
- /*        printf("\n ");printf("%lf ",cov[2]); */
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-        /*
+     /*
        for(i=1; i<= npar; i++) printf("%f ",x[i]);
        goto end;*/
      return ps;
- Line 1123  double **pmij(double **ps, double *cov,
+ Line 1497  double **pmij(double **ps, double *cov,
  /**************** Product of 2 matrices ******************/
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
  {
    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
    /* in, b, out are matrice of pointers which should have been initialized
       before: only the contents of out is modified. The function returns
       a pointer to pointers identical to out */
-   long i, j, k;
+   int i, j, k;
    for(i=nrl; i<= nrh; i++)
-     for(k=ncolol; k<=ncoloh; k++)
+     for(k=ncolol; k<=ncoloh; k++){
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+       out[i][k]=0.;
-         out[i][k] +=in[i][j]*b[j][k];
+       for(j=ncl; j<=nch; j++)
+         out[i][k] +=in[i][j]*b[j][k];
+     }
    return out;
  }
- Line 1157  double ***hpxij(double ***po, int nhstep
+ Line 1532  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 1173  double ***hpxij(double ***po, int nhstep
+ Line 1548  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++)
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
- Line 1190  double ***hpxij(double ***po, int nhstep
+ Line 1566  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 1202  double ***hpxij(double ***po, int nhstep
+ Line 1579  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 1221  double func( double *x)
+ Line 1598  double func( double *x)
    if(mle==1){
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       /* 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++){ /* Simple and product covariates without age* products */
+         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 1232  double func( double *x)
+ Line 1619  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 1261  double func( double *x)
+ Line 1648  double func( double *x)
           */
          /* 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 equal to probability to die before dh
+              die between last step unit time and current  step unit time,
+              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
- Line 1284  double func( double *x)
+ Line 1672  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 1434  double funcone( double *x)
+ Line 1843  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 1464  double funcone( double *x)
+ Line 1873  double funcone( double *x)
          for (kk=1; kk<=cptcovage;kk++) {
            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          }
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
          savm=oldm;
          oldm=newm;
        } /* end mult */
- Line 1478  double funcone( double *x)
+ Line 1890  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 1486  double funcone( double *x)
+ Line 1902  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 1580  void mlikeli(FILE *ficres,double p[], in
+ Line 1997  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 1696  double hessii(double x[], double delta,
+ Line 2114  double hessii(double x[], double delta,
    int i;
    int l=1, lmax=20;
    double k1,k2;
-   double p2[NPARMAX+1];
+   double p2[MAXPARM+1]; /* identical to x */
    double res;
    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
    double fx;
- Line 1705  double hessii(double x[], double delta,
+ Line 2123  double hessii(double x[], double delta,
    fx=func(x);
    for (i=1;i<=npar;i++) p2[i]=x[i];
-   for(l=0 ; l <=lmax; l++){
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
      l1=pow(10,l);
      delts=delt;
      for(k=1 ; k <kmax; k=k+1){
        delt = delta*(l1*k);
        p2[theta]=x[theta] +delt;
-       k1=func(p2)-fx;
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
        p2[theta]=x[theta]-delt;
        k2=func(p2)-fx;
        /*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 1743  double hessij( double x[], double delti[
+ Line 2161  double hessij( double x[], double delti[
    int i;
    int l=1, l1, lmax=20;
    double k1,k2,k3,k4,res,fx;
-   double p2[NPARMAX+1];
+   double p2[MAXPARM+1];
    int k;
    fx=func(x);
- Line 1847  void lubksb(double **a, int n, int *indx
+ Line 2265  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 1868  void  freqsummary(char fileres[], int ia
+ Line 2290  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 1876  void  freqsummary(char fileres[], int ia
+ Line 2298  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++;
+   /*    j1++;
+ */
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); 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;
        for (i=1; i<=imx; i++) {
          bool=1;
-         if  (cptcovn>0) {
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
            for (z1=1; z1<=cptcoveff; z1++)
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-               bool=0;
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
+               bool=0;
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
+             }
          }
          if (bool==1){
            for(m=firstpass; m<=lastpass; m++){
              k2=anint[m][i]+(mint[m][i]/12.);
- Line 1918  void  freqsummary(char fileres[], int ia
+ Line 2349  void  freqsummary(char fileres[], int ia
                /*}*/
            }
          }
-       }
+       } /* end i */
        /*      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 1950  void  freqsummary(char fileres[], int ia
+ Line 2384  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 2002  void  freqsummary(char fileres[], int ia
+ Line 2436  void  freqsummary(char fileres[], int ia
            printf("Others in log...\n");
          fprintf(ficlog,"\n");
        }
-     }
+       /*}*/
    }
    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 2021  void prevalence(double ***probs, double
+ Line 2455  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;
    double  y2; /* in fractional years */
    int iagemin, iagemax;
+   int first; /** to stop verbosity which is redirected to log file */
    iagemin= (int) agemin;
    iagemax= (int) agemax;
- Line 2035  void prevalence(double ***probs, double
+ Line 2470  void prevalence(double ***probs, double
    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    j1=0;
-   j=cptcoveff;
+   /*j=cptcoveff;*/
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   for(k1=1; k1<=j;k1++){
+   first=1;
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-       j1++;
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
+       j1++;*/
        for (i=1; i<=nlstate; i++)
          for(m=iagemin; m <= iagemax+3; m++)
- Line 2070  void prevalence(double ***probs, double
+ Line 2506  void prevalence(double ***probs, double
          }
        }
        for(i=iagemin; i <= iagemax+3; i++){
          for(jk=1,posprop=0; jk <=nlstate ; jk++) {
            posprop += prop[jk][i];
          }
          for(jk=1; jk <=nlstate ; jk++){
            if( i <=  iagemax){
              if(posprop>=1.e-5){
                probs[i][jk][j1]= prop[jk][i]/posprop;
-             }
+             } else{
+               if(first==1){
+                 first=0;
+                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
+               }
+             }
            }
          }/* end jk */
        }/* end i */
-     } /* end i1 */
+     /*} *//* end i1 */
-   } /* end k1 */
+   } /* end j1 */
    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    /*free_vector(pp,1,nlstate);*/
- Line 2116  void  concatwav(int wav[], int **dh, int
+ Line 2556  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 2134  void  concatwav(int wav[], int **dh, int
+ Line 2574  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 2156  void  concatwav(int wav[], int **dh, int
+ Line 2596  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 2170  void  concatwav(int wav[], int **dh, int
+ Line 2616  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 2191  void  concatwav(int wav[], int **dh, int
+ Line 2644  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 2216  void  concatwav(int wav[], int **dh, int
+ Line 2669  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)
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
  {
+   /**< 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;
+   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
+   /* nbcode[Tvar[j]][1]=
+   */
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+   int modmaxcovj=0; /* Modality max of covariates j */
+   int cptcode=0; /* Modality max of covariates j */
+   int modmincovj=0; /* Modality min of covariates j */
    cptcoveff=0;
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+   /* Loop on covariates without age and products */
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
-                                modality*/
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+                                modality of this covariate Vj*/
-       Ndum[ij]++; /*store the modality */
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+                                     * If product of Vn*Vm, still boolean *:
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
+                                       modality of the nth covariate of individual i. */
+       if (ij > modmaxcovj)
+         modmaxcovj=ij;
+       else if (ij < modmincovj)
+         modmincovj=ij;
+       if ((ij < -1) && (ij > NCOVMAX)){
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
+         exit(1);
+       }else
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
        /*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
+       /* getting the maximum value of the modality of the covariate
-                                        Tvar[j]. If V=sex and male is 0 and
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-                                        female is 1, then  cptcode=1.*/
+          female is 1, then modmaxcovj=1.*/
      }
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-     for (i=0; i<=cptcode; i++) {
+     cptcode=modmaxcovj;
-       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 */
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-     }
+    /*for (i=0; i<=cptcode; i++) {*/
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
-     ij=1;
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
-     for (i=1; i<=ncodemax[j]; i++) {
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-       for (k=0; k<= maxncov; k++) {
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
-         if (Ndum[k] != 0) {
+       }
-           nbcode[Tvar[j]][ij]=k;
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-           /* 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; */
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+     } /* Ndum[-1] number of undefined modalities */
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
+        modmincovj=3; modmaxcovj = 7;
+        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
+        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
+        variables V1_1 and V1_2.
+        nbcode[Tvar[j]][ij]=k;
+        nbcode[Tvar[j]][1]=0;
+        nbcode[Tvar[j]][2]=1;
+        nbcode[Tvar[j]][3]=2;
+     */
+     ij=1; /* ij is similar to i but can jumps over null modalities */
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
+         /*recode from 0 */
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
+                                      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=-1; 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=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
     if((Ndum[i]!=0) && (i<=ncovcol)){
-      Tvaraff[ij]=i; /*For printing */
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+      Tvaraff[ij]=i; /*For printing (unclear) */
       ij++;
-    }
+    }else
+        Tvaraff[ij]=0;
   }
+  ij--;
-  cptcoveff=ij-1; /*Number of simple covariates*/
+  cptcoveff=ij; /*Number of total 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 2335  void evsij(char fileres[], double ***eij
+ Line 2971  void evsij(char fileres[], double ***eij
    */
    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   /* If stepm=6 months */
+   /* nhstepm age range expressed in number of stepm */
    agelim=AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-     /* nhstepm age range expressed in number of stepm */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm);
+   /* if (stepm >= YEARM) hstepm=1;*/
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+   for (age=bage; age<=fage; age ++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      /* Typically if 20 years nstepm = 20*12/6=40 stepm */
      /* if (stepm >= YEARM) hstepm=1;*/
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-     gp=matrix(0,nhstepm,1,nlstate*nlstate);
-     gm=matrix(0,nhstepm,1,nlstate*nlstate);
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
+     /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      /* Computing  Variances of health expectancies */
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-      for(theta=1; theta <=npar; theta++){
+        decrease memory allocation */
+     for(theta=1; theta <=npar; theta++){
        for(i=1; i<=npar; i++){
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-       cptj=0;
        for(j=1; j<= nlstate; j++){
          for(i=1; i<=nlstate; i++){
-           cptj=cptj+1;
+           for(h=0; h<=nhstepm-1; h++){
-           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
            }
          }
        }
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-       for(i=1; i<=npar; i++)
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       cptj=0;
-       for(j=1; j<= nlstate; j++){
-         for(i=1;i<=nlstate;i++){
-           cptj=cptj+1;
-           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
-             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
-           }
-         }
-       }
-       for(j=1; j<= nlstate*nlstate; j++)
          for(h=0; h<=nhstepm-1; h++){
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
          }
-      }
+     }/* End theta */
- /* End theta */
+     for(h=0; h<=nhstepm-1; h++)
-      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-      for(h=0; h<=nhstepm-1; h++)
        for(j=1; j<=nlstate*nlstate;j++)
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
-      for(i=1;i<=nlstate*nlstate;i++)
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-       for(j=1;j<=nlstate*nlstate;j++)
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-         varhe[i][j][(int)age] =0.;
+         varhe[ij][ji][(int)age] =0.;
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
- Line 2413  void evsij(char fileres[], double ***eij
+ Line 3041  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 2453  void evsij(char fileres[], double ***eij
+ Line 3103  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 2504  void varevsij(char optionfilefiname[], d
+ Line 3154  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 2514  void varevsij(char optionfilefiname[], d
+ Line 3166  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 2545  void varevsij(char optionfilefiname[], d
+ Line 3202  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 2612  void varevsij(char optionfilefiname[], d
+ Line 3268  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 2722  void varevsij(char optionfilefiname[], d
+ Line 3378  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 size 320, 240");
    /* 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 1 ",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 2 ",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 2 ",subdirf(fileresprobmorprev));
    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
- Line 2751  void varevsij(char optionfilefiname[], d
+ Line 3407  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 2764  void varprevlim(char fileres[], double *
+ Line 3420  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 2834  void varprevlim(char fileres[], double *
+ Line 3491  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;
    int k=0,l, cptcode;
-   int first=1, first1;
+   int first=1, first1, first2;
    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
    double **dnewm,**doldm;
    double *xp;
    double *gp, *gm;
    double **gradg, **trgradg;
    double **mu;
-   double age,agelim, cov[NCOVMAX];
+   double age,agelim, cov[NCOVMAX+1];
    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
    int theta;
    char fileresprob[FILENAMELENGTH];
    char fileresprobcov[FILENAMELENGTH];
    char fileresprobcor[FILENAMELENGTH];
    double ***varpij;
    strcpy(fileresprob,"prob");
- Line 2879  void varprob(char optionfilefiname[], do
+ Line 3535  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 2898  void varprob(char optionfilefiname[], do
+ Line 3556  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 2923  standard deviations wide on each axis. <
+ Line 3581  standard deviations wide on each axis. <
  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
    cov[1]=1;
-   tj=cptcoveff;
+   /* tj=cptcoveff; */
+   tj = (int) pow(2,cptcoveff);
    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
    j1=0;
-   for(t=1; t<=tj;t++){
+   for(j1=1; j1<=tj;j1++){
-     for(i1=1; i1<=ncodemax[t];i1++){
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
-       j1++;
+     /*j1++;*/
        if  (cptcovn>0) {
          fprintf(ficresprob, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- Line 2951  To be simple, these graphs help to under
+ Line 3610  To be simple, these graphs help to under
          fprintf(ficresprobcor, "**********\n#");
        }
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
        for (age=bage; age<=fage; age ++){
          cov[2]=age;
          for (k=1; k<=cptcovn;k++) {
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
+                                                          * 1  1 1 1 1
+                                                          * 2  2 1 1 1
+                                                          * 3  1 2 1 1
+                                                          */
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
          }
          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          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]]];
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
          for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++)
- Line 3001  To be simple, these graphs help to under
+ Line 3665  To be simple, these graphs help to under
          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
          pmij(pmmij,cov,ncovmodel,x,nlstate);
- Line 3038  To be simple, these graphs help to under
+ Line 3698  To be simple, these graphs help to under
          i=0;
          for (k=1; k<=(nlstate);k++){
            for (l=1; l<=(nlstate+ndeath);l++){
-             i=i++;
+             i++;
              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
              for (j=1; j<=i;j++){
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
              }
            }
          }/* end of loop for state */
        } /* end of loop for age */
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
        /* 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 3061  To be simple, these graphs help to under
+ Line 3726  To be simple, these graphs help to under
        */
        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-       first1=1;
+       first1=1;first2=2;
        for (k2=1; k2<=(nlstate);k2++){
          for (l2=1; l2<=(nlstate+ndeath);l2++){
            if(l2==k2) continue;
- Line 3082  To be simple, these graphs help to under
+ Line 3747  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) ){
+                     if(first2==1){
+                       first1=0;
+                     printf("Strange: j1=%d 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. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+                     }
+                     fprintf(ficlog,"Strange: j1=%d 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. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
+                     /* lc2=fabs(lc2); */
+                   }
                    /* Eigen vectors */
                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                    /*v21=sqrt(1.-v11*v11); *//* error */
- Line 3101  To be simple, these graphs help to under
+ Line 3776  To be simple, these graphs help to under
                      first=0;
                      fprintf(ficgp,"\nset parametric;unset label");
                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
- Line 3132  To be simple, these graphs help to under
+ Line 3807  To be simple, these graphs help to under
            } /* k12 */
          } /*l1 */
        }/* k1 */
-     } /* loop covariates */
+       /* } /* loop covariates */
    }
    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 3154  void printinghtml(char fileres[], char t
+ Line 3831  void printinghtml(char fileres[], char t
                    double jprev2, double mprev2,double anprev2){
    int jj1, k1, i1, cpt;
-    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+ </ul>");
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
     fprintf(fichtm,"\
   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
     fprintf(fichtm,"\
-  - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
     fprintf(fichtm,"\
-  - Life expectancies by age and initial health status (estepm=%2d months): \
+  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
-    <a href=\"%s\">%s</a> <br>\n</li>",
+    <a href=\"%s\">%s</a> <br>\n",
             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+    fprintf(fichtm,"\
+  - Population projections by age and states: \
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-  m=cptcoveff;
+  m=pow(2,cptcoveff);
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   jj1=0;
- Line 3184  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3867  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%d_1.png\">%s%d_1.png</a><br> \
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ <img src=\"%s%d_1.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%d_2.png\">%s%d_2.png</a><br> \
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-        /* Stable prevalence in each health state */
+        /* Period (stable) prevalence in each health state */
         for(cpt=1; cpt<nlstate;cpt++){
-          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
+          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+ <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         }
       for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
+         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       }
     } /* end i1 */
   }/* End k1 */
- Line 3205  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3888  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   fprintf(fichtm,"\
- \n<br><li><h4> Result files (second order: variances)</h4>\n\
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
- Line 3218  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3901  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
   fprintf(fichtm,"\
-  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+  fprintf(fichtm,"\
+  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
   fprintf(fichtm,"\
-  - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   fprintf(fichtm,"\
-  - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
- Line 3236  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3927  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   fflush(fichtm);
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-  m=cptcoveff;
+  m=pow(2,cptcoveff);
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   jj1=0;
- Line 3251  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3942  fprintf(fichtm," \n<ul><li><b>Graphs</b>
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- prevalence (with 95%% confidence 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);
+ <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
       }
       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
- health expectancies in states (1) and (2): %s%d.png<br>\
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+ true period expectancies (those weighted with period prevalences are also\
+  drawn in addition to the population based expectancies computed using\
+  observed and cahotic prevalences: %s%d.png<br>\
  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     } /* end i1 */
   }/* End k1 */
- Line 3267  health expectancies in states (1) and (2
+ Line 3961  health expectancies in states (1) and (2
  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-   int ng;
+   int ng=0;
  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
- Line 3283  void printinggnuplot(char fileres[], cha
+ Line 3977  void printinggnuplot(char fileres[], cha
    strcpy(optfileres,"vpl");
   /* 1eme*/
    for (cpt=1; cpt<= nlstate ; cpt ++) {
-    for (k1=1; k1<= m ; k1 ++) {
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \n\
  set ylabel \"Probability\" \n\
- set ter png small\n\
+ set ter png small size 320, 240\n\
- set size 0.65,0.65\n\
  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+        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 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%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 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     }
    }
    /*2 eme*/
    for (k1=1; k1<= m ; k1 ++) {
      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
      for (i=1; i<= nlstate+1 ; i ++) {
        k=2*i;
- Line 3329  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 4022  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 0,");
        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
      }
    }
- Line 3344  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 4037  plot [%.f:%.f] \"%s\" every :::%d::%d u
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<= nlstate ; cpt ++) {
-       k=2+nlstate*(2*cpt-2);
+       /*       k=2+nlstate*(2*cpt-2); */
+       k=2+(nlstate+1)*(cpt-1);
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-       fprintf(ficgp,"set ter png small\n\
+       fprintf(ficgp,"set ter png small size 320, 240\n\
- set size 0.65,0.65\n\
  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
- Line 3358  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 4051  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 3368  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 4063  plot [%.f:%.f] \"%s\" every :::%d::%d u
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<=nlstate ; cpt ++) {
        k=3;
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- set ter png small\nset size 0.65,0.65\n\
+ set ter png small size 320, 240\n\
  unset log y\n\
  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
- Line 3400  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
+ Line 4095  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
        }
      }
     }
+   /*goto avoid;*/
     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       for(jk=1; jk <=m; jk++) {
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
         if (ng==2)
           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
         else
           fprintf(ficgp,"\nset title \"Probability\"\n");
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
         i=1;
         for(k2=1; k2<=nlstate; k2++) {
           k3=i;
- Line 3418  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
+ Line 4113  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]]]);
+                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
-                  ij++;
+                /*        ij++; */
-                }
+                /* } */
-                else
+                /* else */
                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
               }
               fprintf(ficgp,")/(1");
- Line 3433  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
+ Line 4128  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                 ij=1;
                 for(j=3; j <=ncovmodel; j++){
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
-                    ij++;
+                  /*   ij++; */
-                  }
+                  /* } */
-                  else
+                  /* else */
                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                 }
                 fprintf(ficgp,")");
- Line 3450  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
+ Line 4145  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
         } /* end k2 */
       } /* end jk */
     } /* end ng */
+  avoid:
     fflush(ficgp);
  }  /* end gnuplot */
- Line 3919  double gompertz(double x[])
+ Line 4615  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;
+     /*    sump=sump+1;*/
      num=num+1;
    }
-   /* for (i=1; i<=imx; i++)
+   /* 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=0;i<=imx-1 ; i++)
+   for (i=1;i<=imx ; i++)
      {
-       if (cens[i]==1 & wav[i]>1)
+       if (cens[i] == 1 && wav[i]>1)
-         A=-x[1]/(x[2])*
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-           (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
-       if (cens[i]==0 & wav[i]>1)
+       if (cens[i] == 0 && wav[i]>1)
-         A=-x[1]/(x[2])*
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-              (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-           +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM);
-       if (wav[i]>1 & agecens[i]>15) {
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
          L=L+A*weight[i];
          /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
        }
- Line 3951  double gompertz(double x[])
+ Line 4647  double gompertz(double x[])
    return -2*L*num/sump;
  }
+ #ifdef GSL
+ /******************* Gompertz_f Likelihood ******************************/
+ double gompertz_f(const gsl_vector *v, void *params)
+ {
+   double A,B,LL=0.0,sump=0.,num=0.;
+   double *x= (double *) v->data;
+   int i,n=0; /* n is the size of the sample */
+   for (i=0;i<=imx-1 ; i++) {
+     sump=sump+weight[i];
+     /*    sump=sump+1;*/
+     num=num+1;
+   }
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
+   for (i=1;i<=imx ; i++)
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
+       if (cens[i] == 0 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
+         LL=LL+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+       }
+     }
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
+   return -2*LL*num/sump;
+ }
+ #endif
  /******************* Printing html file ***********/
  void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
-                   int imx,  double p[],double **matcov){
+                   int imx,  double p[],double **matcov,double agemortsup){
-   int i;
+   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);
- Line 3963  void printinghtmlmort(char fileres[], ch
+ Line 4700  void printinghtmlmort(char fileres[], ch
      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);
  }
- Line 3983  void printinggnuplotmort(char fileres[],
+ Line 4729  void printinggnuplotmort(char fileres[],
    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 ter png small size 320, 240\n set log y\n");
-   fprintf(ficgp, "set size 0.65,0.65\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.",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 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.", 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 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);
+ }
+ void removespace(char *str) {
+   char *p1 = str, *p2 = str;
+   do
+     while (*p2 == ' ')
+       p2++;
+   while (*p1++ = *p2++);
+ }
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
+    * - cptcovn or number of covariates k of the models excluding age*products =6
+    * - cptcovage number of covariates with age*products =2
+    * - cptcovs number of simple covariates
+    * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
+    *     which is a new column after the 9 (ncovcol) variables.
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
+  */
+ {
+   int i, j, k, ks;
+   int i1, j1, k1, k2;
+   char modelsav[80];
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
+   /*removespace(model);*/
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
+     j=nbocc(model,'+'); /**< j=Number of '+' */
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
+                   /* including age products which are counted in cptcovage.
+                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
+     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;
+     }
+     /*   Design
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
+      *  <          ncovcol=8                >
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
+      *   k=  1    2      3       4     5       6      7        8
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
+      *  covar[k,i], value of kth covariate if not including age for individual i:
+      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
+      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
+      *  Tage[++cptcovage]=k
+      *       if products, new covar are created after ncovcol with k1
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
+      *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
+      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
+      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
+      *  <          ncovcol=8                >
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
+      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
+      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
+      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+      * p Tprod[1]@2={                         6, 5}
+      *p Tvard[1][1]@4= {7, 8, 5, 6}
+      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
+      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+      *How to reorganize?
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
+      * Struct []
+      */
+     /* 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]; */
+     /*
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
+         Tvar[k]=0;
+     cptcovage=0;
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+       cutl(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 */
+         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+           /* covar is not filled and then is empty */
+           cptcovprod--;
+           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; 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--;
+           cutl(stre,strb,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 */
+           cptcovn++;
+           cptcovprodnoage++;k1++;
+           cutl(stre,strb,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 */
+           cutl(strc,strb,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*/
+           k2=k2+2;
+           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
+           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=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 May not be defined */
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+           }
+         } /* 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);*/
+         cutl(strd,strc,strb,'V');
+         ks++; /**< Number of simple covariates */
+         cptcovn++;
+         Tvar[k]=atoi(strd);
+       }
+       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);
+ }
  /***********************************************/
  /**************** Main Program *****************/
- Line 3998  void printinggnuplotmort(char fileres[],
+ Line 5202  void printinggnuplotmort(char fileres[],
  int main(int argc, char *argv[])
  {
+ #ifdef GSL
+   const gsl_multimin_fminimizer_type *T;
+   size_t iteri = 0, it;
+   int rval = GSL_CONTINUE;
+   int status = GSL_SUCCESS;
+   double ssval;
+ #endif
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+   int linei, month, year,iout;
    int jj, ll, li, lj, lk, imk;
    int numlinepar=0; /* Current linenumber of parameter file */
    int itimes;
    int NDIM=2;
+   int vpopbased=0;
    char ca[32], cb[32], cc[32];
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
+   struct stat info;
    double agedeb, agefin,hf;
    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
- Line 4021  int main(int argc, char *argv[])
+ Line 5235  int main(int argc, char *argv[])
    char line[MAXLINE], linepar[MAXLINE];
    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
    char pathr[MAXLINE], pathimach[MAXLINE];
+   char **bp, *tok, *val; /* pathtot */
    int firstobs=1, lastobs=10;
    int sdeb, sfin; /* Status at beginning and end */
    int c,  h , cpt,l;
    int ju,jl, mi;
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   int i1,j1, jk,aa,bb, stepsize, ij;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
    int mobilav=0,popforecast=0;
    int hstepm, nhstepm;
+   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 4048  int main(int argc, char *argv[])
+ Line 5264  int main(int argc, char *argv[])
    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];
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
    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;
- Line 4096  int main(int argc, char *argv[])
+ Line 5310  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 4106  int main(int argc, char *argv[])
+ Line 5330  int main(int argc, char *argv[])
      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
    /* cutv(path,optionfile,pathtot,'\\');*/
+   /* Split argv[0], imach program to get pathimach */
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
    split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
   /*   strcpy(pathimach,argv[0]); */
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-   chdir(path);
+   chdir(path); /* Can be a relative path */
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+     printf("Current directory %s!\n",pathcd);
    strcpy(command,"mkdir ");
    strcat(command,optionfilefiname);
    if((outcmd=system(command)) != 0){
- Line 4178  int main(int argc, char *argv[])
+ Line 5408  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 4194  int main(int argc, char *argv[])
+ Line 5424  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);
    }
    ungetc(c,ficpar);
-   covar=matrix(0,NCOVMAX,1,n);
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-   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)
+     ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
+   else
+     ncovmodel=2;
    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
+     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fflush(stdout);
+     fclose (ficlog);
+     goto end;
+   }
    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
    delti=delti3[1][1];
    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
- Line 4219  int main(int argc, char *argv[])
+ Line 5461  int main(int argc, char *argv[])
      free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
      fclose (ficparo);
      fclose (ficlog);
+     goto end;
      exit(0);
    }
    else if(mle==-3) {
- Line 4229  int main(int argc, char *argv[])
+ Line 5472  int main(int argc, char *argv[])
      matcov=matrix(1,npar,1,npar);
    }
    else{
-     /* Read guess parameters */
+     /* Read guessed parameters */
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
        numlinepar++;
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
        fputs(line,ficlog);
      }
- Line 4249  int main(int argc, char *argv[])
+ Line 5492  int main(int argc, char *argv[])
          j++;
          fscanf(ficpar,"%1d%1d",&i1,&j1);
          if ((i1 != i) && (j1 != j)){
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+ It might be a problem of design; if ncovcol and the model are correct\n \
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
            exit(1);
          }
          fprintf(ficparo,"%1d%1d",i1,j1);
- Line 4276  int main(int argc, char *argv[])
+ Line 5521  int main(int argc, char *argv[])
      }
      fflush(ficlog);
+     /* Reads scales values */
      p=param[1][1];
      /* Reads comments: lines beginning with '#' */
- Line 4284  int main(int argc, char *argv[])
+ Line 5529  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 4315  int main(int argc, char *argv[])
+ Line 5560  int main(int argc, char *argv[])
      }
      fflush(ficlog);
+     /* Reads covariance matrix */
      delti=delti3[1][1];
- Line 4325  int main(int argc, char *argv[])
+ Line 5571  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);
      }
      ungetc(c,ficpar);
      matcov=matrix(1,npar,1,npar);
+     for(i=1; i <=npar; i++)
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
      for(i=1; i <=npar; i++){
-       fscanf(ficpar,"%s",&str);
+       fscanf(ficpar,"%s",str);
        if(mle==1)
          printf("%s",str);
        fprintf(ficlog,"%s",str);
- Line 4375  int main(int argc, char *argv[])
+ Line 5624  int main(int argc, char *argv[])
      fprintf(ficres,"#%s\n",version);
    }    /* End of mle != -3 */
-   /*-------- data file ----------*/
-   if((fic=fopen(datafile,"r"))==NULL)    {
-     printf("Problem with datafile: %s\n", datafile);goto end;
-     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
-   }
    n= lastobs;
-   severity = vector(1,maxwav);
-   outcome=imatrix(1,maxwav+1,1,n);
    num=lvector(1,n);
    moisnais=vector(1,n);
    annais=vector(1,n);
- Line 4395  int main(int argc, char *argv[])
+ Line 5637  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,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
-   i=1;
+   /* Reads data from file datafile */
-   while (fgets(line, MAXLINE, fic) != NULL)    {
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-     if ((i >= firstobs) && (i <=lastobs)) {
+     goto end;
-       for(j=0; line[j] != '\n';j++){  /* Untabifies line */
-         if(line[j] == '\t')
-           line[j] = ' ';
-       }
-       for (j=maxwav;j>=1;j--){
-         cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
-         strcpy(line,stra);
-         cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
-         cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
-       }
-       cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
+   /* Calculation of the number of parameters from char model */
-       cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
+         k=3 V4 Tvar[k=3]= 4 (from V4)
+         k=2 V1 Tvar[k=2]= 1 (from V1)
+         k=1 Tvar[1]=2 (from V2)
+     */
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+   */
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
+     Tvar[3=V1*V4]=4+1 etc */
+   Tprod=ivector(1,NCOVMAX); /* 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,NCOVMAX); /* Unclear */
+   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
+                             * 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) */
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+covariates (3 plus signs)
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+                       */
-       cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
+   if(decodemodel(model, lastobs) == 1)
-       for (j=ncovcol;j>=1;j--){
+     goto end;
-         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;
+   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. We can have weights different from 1 but want no weight*/
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
    }
-   /* printf("ii=%d", ij);
-      scanf("%d",i);*/
-   imx=i-1; /* Number of individuals */
-   /* for (i=1; i<=imx; i++){
+     /*-calculation of age at interview from date of interview and age at death -*/
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+   agev=matrix(1,maxwav,1,imx);
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
-     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*/
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
-   Tprod=ivector(1,15);
-   Tvaraff=ivector(1,15);
-   Tvard=imatrix(1,15,1,2);
-   Tage=ivector(1,15);
-   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;
-     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);
-   fclose(fic);*/
-     /*  if(mle==1){*/
-   if (weightopt != 1) { /* Maximisation without weights*/
-     for(i=1;i<=n;i++) weight[i]=1.0;
-   }
-     /*-calculation of age at interview from date of interview and age at death -*/
-   agev=matrix(1,maxwav,1,imx);
-   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){
-         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]);
- }
- }*/
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+     goto end;
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
    agegomp=(int)agemin;
-   free_vector(severity,1,maxwav);
-   free_imatrix(outcome,1,maxwav+1,1,n);
    free_vector(moisnais,1,n);
    free_vector(annais,1,n);
    /* free_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n);*/
    free_vector(moisdc,1,n);
    free_vector(andc,1,n);
+   /* */
    wav=ivector(1,imx);
    dh=imatrix(1,lastpass-firstpass+1,1,imx);
    bh=imatrix(1,lastpass-firstpass+1,1,imx);
- Line 4650  int main(int argc, char *argv[])
+ Line 5711  int main(int argc, char *argv[])
    /* Concatenates waves */
    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   /* */
    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-   Tcode=ivector(1,100);
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
    ncodemax[1]=1;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   Ndum =ivector(-1,NCOVMAX);
+   if (ncovmodel > 2)
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-                                  the estimations*/
+   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
    h=0;
+   /*if (cptcovn > 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   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
+            *     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 4678  int main(int argc, char *argv[])
+ Line 5769  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");
       }
       scanf("%d",i);*/
+  free_ivector(Ndum,-1,NCOVMAX);
    /*------------ gnuplot -------------*/
    strcpy(optionfilegnuplot,optionfilefiname);
- Line 4696  int main(int argc, char *argv[])
+ Line 5791  int main(int argc, char *argv[])
    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 --------*/
- Line 4706  int main(int argc, char *argv[])
+ Line 5802  int main(int argc, char *argv[])
      strcat(optionfilehtm,"-mort");
    strcat(optionfilehtm,".htm");
    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+     printf("Problem with %s \n",optionfilehtm);
+     exit(0);
    }
    strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
- Line 4715  int main(int argc, char *argv[])
+ Line 5812  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 4742  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5841  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 4761  Interval (in months) between two waves:
+ Line 5860  Interval (in months) between two waves:
    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
    if (mle==-3){
      ximort=matrix(1,NDIM,1,NDIM);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
      cens=ivector(1,n);
      ageexmed=vector(1,n);
      agecens=vector(1,n);
- Line 4770  Interval (in months) between two waves:
+ Line 5871  Interval (in months) between two waves:
      for (i=1; i<=imx; i++){
        dcwave[i]=-1;
-       for (j=1; j<=lastpass; j++)
+       for (m=firstpass; m<=lastpass; m++)
-         if (s[j][i]>nlstate) {
+         if (s[m][i]>nlstate) {
-           dcwave[i]=j;
+           dcwave[i]=m;
            /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
            break;
          }
- Line 4781  Interval (in months) between two waves:
+ Line 5882  Interval (in months) between two waves:
      for (i=1; i<=imx; i++) {
        if (wav[i]>0){
          ageexmed[i]=agev[mw[1][i]][i];
-         j=wav[i];agecens[i]=1.;
+         j=wav[i];
-         if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
+         agecens[i]=1.;
-         cens[i]=1;
+         if (ageexmed[i]> 1 && wav[i] > 0){
-         if (ageexmed[i]<1) cens[i]=-1;
+           agecens[i]=agev[mw[j][i]][i];
-         if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
+           cens[i]= 1;
+         }else if (ageexmed[i]< 1)
+           cens[i]= -1;
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+           cens[i]=0 ;
        }
        else cens[i]=-1;
      }
- Line 4795  Interval (in months) between two waves:
+ Line 5900  Interval (in months) between two waves:
        for (j=1;j<=NDIM;j++)
          ximort[i][j]=(i == j ? 1.0 : 0.0);
      }
-     p[1]=0.1; p[2]=0.1;
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
      /*printf("%lf %lf", p[1], p[2]);*/
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ #ifdef GSL
-   strcpy(filerespow,"pow-mort");
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
-   strcat(filerespow,fileres);
+ #elsedef
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-     printf("Problem with resultfile: %s\n", filerespow);
+ #endif
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+     strcpy(filerespow,"pow-mort");
-   }
+     strcat(filerespow,fileres);
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   /*  for (i=1;i<=nlstate;i++)
+       printf("Problem with resultfile: %s\n", filerespow);
-     for(j=1;j<=nlstate+ndeath;j++)
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     }
-   */
+ #ifdef GSL
-   fprintf(ficrespow,"\n");
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+ #elsedef
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
+     /*  for (i=1;i<=nlstate;i++)
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     */
+     fprintf(ficrespow,"\n");
+ #ifdef GSL
+     /* gsl starts here */
+     T = gsl_multimin_fminimizer_nmsimplex;
+     gsl_multimin_fminimizer *sfm = NULL;
+     gsl_vector *ss, *x;
+     gsl_multimin_function minex_func;
+     /* 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);
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+     /* Starting point */
+     x = gsl_vector_alloc (NDIM);
+     if (x == NULL){
+       gsl_vector_free(ss);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+     }
+     /* Initialize method and iterate */
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
+ /*     gsl_vector_set(x, 0, 0.0268); */
+ /*     gsl_vector_set(x, 1, 0.083); */
+     gsl_vector_set(x, 0, p[1]);
+     gsl_vector_set(x, 1, p[2]);
+     minex_func.f = &gompertz_f;
+     minex_func.n = NDIM;
+     minex_func.params = (void *)&p; /* ??? */
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+     printf("Iterations beginning .....\n\n");
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
+     iteri=0;
+     while (rval == GSL_CONTINUE){
+       iteri++;
+       status = gsl_multimin_fminimizer_iterate(sfm);
+       if (status) printf("error: %s\n", gsl_strerror (status));
+       fflush(0);
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+     gsl_vector_free(x); /* initial values */
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ #endif
      fclose(ficrespow);
-     hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
      for(i=1; i <=NDIM; i++)
        for(j=i+1;j<=NDIM;j++)
- Line 4834  Interval (in months) between two waves:
+ Line 6024  Interval (in months) between two waves:
      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]));
-     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+     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);
+                      model,imx,p,matcov,agemortsup);
+     free_vector(lsurv,1,AGESUP);
+     free_vector(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
    } /* Endof if mle==-3 */
-   else{ /* For mle >=1 */
+   else{ /* For mle >=1 */
+     globpr=0;/* debug */
      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
      printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
      for (k=1; k<=npar;k++)
- Line 4873  Interval (in months) between two waves:
+ Line 6104  Interval (in months) between two waves:
            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);
            for(j=1; j <=ncovmodel; j++){
-             printf("%f ",p[jk]);
+             printf("%lf ",p[jk]);
-             fprintf(ficlog,"%f ",p[jk]);
+             fprintf(ficlog,"%lf ",p[jk]);
-             fprintf(ficres,"%f ",p[jk]);
+             fprintf(ficres,"%lf ",p[jk]);
              jk++;
            }
            printf("\n");
- Line 5000  Interval (in months) between two waves:
+ Line 6231  Interval (in months) between two waves:
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
- Line 5020  Interval (in months) between two waves:
+ Line 6251  Interval (in months) between two waves:
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
- Line 5034  Interval (in months) between two waves:
+ Line 6265  Interval (in months) between two waves:
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
- Line 5050  Interval (in months) between two waves:
+ Line 6281  Interval (in months) between two waves:
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
- Line 5064  Interval (in months) between two waves:
+ Line 6295  Interval (in months) between two waves:
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
-     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
      printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
      printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
- Line 5089  Interval (in months) between two waves:
+ Line 6320  Interval (in months) between two waves:
      fclose(ficres);
-     /*--------------- Prevalence limit  (stable prevalence) --------------*/
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+ #include "prevlim.h"  /* Use ficrespl, ficlog */
-     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++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
-         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");
-         }
-       }
-     }
      fclose(ficrespl);
+ #ifdef FREEEXIT2
+ #include "freeexit2.h"
+ #endif
      /*------------- h Pij x at various ages ------------*/
+ #include "hpijx.h"
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     fclose(ficrespij);
-     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*/
-     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 */
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+   /*-------------- Variance of one-step probabilities---*/
+     k=1;
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-           for(i=1; i<=nlstate;i++)
-             for(j=1; j<=nlstate+ndeath;j++)
-               fprintf(ficrespij," %1d-%1d",i,j);
-           fprintf(ficrespij,"\n");
-           for (h=0; h<=nhstepm; h++){
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
-             for(i=1; i<=nlstate;i++)
-               for(j=1; j<=nlstate+ndeath;j++)
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-             fprintf(ficrespij,"\n");
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           fprintf(ficrespij,"\n");
-         }
-       }
-     }
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
-     fclose(ficrespij);
      probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
      for(i=1;i<=AGESUP;i++)
- Line 5221  Interval (in months) between two waves:
+ Line 6358  Interval (in months) between two waves:
      }
-     /*---------- Health expectancies and variances ------------*/
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
-     strcpy(filerest,"t");
+     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-     strcat(filerest,fileres);
+     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+     */
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     if (mobilav!=0) {
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
      }
-     printf("Computing Total LEs with variances: file '%s' \n", filerest);
-     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
+     /*---------- Health expectancies, no variances ------------*/
      strcpy(filerese,"e");
      strcat(filerese,fileres);
      if((ficreseij=fopen(filerese,"w"))==NULL) {
- Line 5241  Interval (in months) between two waves:
+ Line 6384  Interval (in months) between two waves:
      }
      printf("Computing Health Expectancies: result on file '%s' \n", filerese);
      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficreseij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficreseij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficreseij);
+     /*---------- Health expectancies and variances ------------*/
+     strcpy(filerest,"t");
+     strcat(filerest,fileres);
+     if((ficrest=fopen(filerest,"w"))==NULL) {
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     }
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     strcpy(fileresstde,"stde");
+     strcat(fileresstde,fileres);
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     }
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"cve");
+     strcat(filerescve,fileres);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
      strcpy(fileresv,"v");
      strcat(fileresv,fileres);
- Line 5251  Interval (in months) between two waves:
+ Line 6444  Interval (in months) between two waves:
      printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
      fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-     /*  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);
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
-     */
+         fprintf(ficrest,"\n#****** ");
-     if (mobilav!=0) {
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       }
-     }
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
-         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#****** ");
+         fprintf(ficresstdeij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrescveij,"\n#****** ");
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficreseij,"******\n");
+           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficresstdeij,"******\n");
+         fprintf(ficrescveij,"******\n");
          fprintf(ficresvij,"\n#****** ");
          for(j=1;j<=cptcoveff;j++)
- Line 5285  Interval (in months) between two waves:
+ Line 6469  Interval (in months) between two waves:
          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);
+         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+         /*
+          */
+         /* goto endfree; */
          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);
-         if(popbased==1){
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
-         }
-         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           oldm=oldms;savm=savms; /* Segmentation fault */
-         fprintf(ficrest,"\n");
+           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 ");
-         epj=vector(1,nlstate+1);
+           if(vpopbased==1)
-         for(age=bage; age <=fage ;age++){
+             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);
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           else
-           if (popbased==1) {
+             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
-             if(mobilav ==0){
+           fprintf(ficrest,"# Age e.. (std) ");
-               for(i=1; i<=nlstate;i++)
+           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-                 prlim[i][i]=probs[(int)age][i][k];
+           fprintf(ficrest,"\n");
-             }else{ /* mobilav */
-               for(i=1; i<=nlstate;i++)
+           epj=vector(1,nlstate+1);
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+           for(age=bage; age <=fage ;age++){
+             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+             if (vpopbased==1) {
+               if(mobilav ==0){
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=probs[(int)age][i][k];
+               }else{ /* mobilav */
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=mobaverage[(int)age][i][k];
+               }
              }
-           }
-           fprintf(ficrest," %4.0f",age);
+             fprintf(ficrest," %4.0f",age);
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+               for(i=1, epj[j]=0.;i <=nlstate;i++) {
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               }
+               epj[nlstate+1] +=epj[j];
              }
-             epj[nlstate+1] +=epj[j];
-           }
-           for(i=1, vepp=0.;i <=nlstate;i++)
+             for(i=1, vepp=0.;i <=nlstate;i++)
-             for(j=1;j <=nlstate;j++)
+               for(j=1;j <=nlstate;j++)
-               vepp += vareij[i][j][(int)age];
+                 vepp += vareij[i][j][(int)age];
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
-           for(j=1;j <=nlstate;j++){
+             for(j=1;j <=nlstate;j++){
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             }
+             fprintf(ficrest,"\n");
            }
-           fprintf(ficrest,"\n");
          }
          free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
          free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
          free_vector(epj,1,nlstate+1);
-       }
+       /*}*/
      }
      free_vector(weight,1,n);
-     free_imatrix(Tvard,1,15,1,2);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
      free_imatrix(s,1,maxwav+1,1,n);
      free_matrix(anint,1,maxwav,1,n);
      free_matrix(mint,1,maxwav,1,n);
      free_ivector(cod,1,n);
      free_ivector(tab,1,NCOVMAX);
-     fclose(ficreseij);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
      fclose(ficresvij);
      fclose(ficrest);
      fclose(ficpar);
-     /*------- Variance of stable prevalence------*/
+     /*------- Variance of period (stable) prevalence------*/
      strcpy(fileresvpl,"vpl");
      strcat(fileresvpl,fileres);
      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
        exit(0);
      }
-     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-         k=k+1;
-         fprintf(ficresvpl,"\n#****** ");
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         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);
          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);
-       }
+       /*}*/
      }
      fclose(ficresvpl);
- Line 5377  Interval (in months) between two waves:
+ Line 6571  Interval (in months) between two waves:
      /*---------- End : free ----------------*/
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
    }  /* mle==-3 arrives here for freeing */
+  endfree:
+     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);*/
- Line 5391  Interval (in months) between two waves:
+ Line 6585  Interval (in months) between two waves:
      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(ncodemax,1,NCOVMAX);
-     free_ivector(Tvar,1,15);
+     free_ivector(Tvar,1,NCOVMAX);
-     free_ivector(Tprod,1,15);
+     free_ivector(Tprod,1,NCOVMAX);
-     free_ivector(Tvaraff,1,15);
+     free_ivector(Tvaraff,1,NCOVMAX);
-     free_ivector(Tage,1,15);
+     free_ivector(Tage,1,NCOVMAX);
-     free_ivector(Tcode,1,100);
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     free_imatrix(codtab,1,100,1,10);
    fflush(fichtm);
    fflush(ficgp);
- Line 5416  Interval (in months) between two waves:
+ Line 6610  Interval (in months) between two waves:
    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,"\"");
+    printf("Before Current directory %s!\n",pathcd);
-   strcat(plotcmd,pathimach);
+    if(chdir(pathcd) != 0)
-   strcat(plotcmd,GNUPLOTPROGRAM);
+     printf("Can't move to directory %s!\n",path);
-   strcat(plotcmd,"\"");
+   if(getcwd(pathcd,MAXLINE) > 0)
-   strcat(plotcmd," ");
+     printf("Current directory %s!\n",pathcd);
-   strcat(plotcmd,optionfilegnuplot);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
-   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
+   sprintf(plotcmd,"gnuplot");
+ #ifndef UNIX
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef UNIX
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
    if((outcmd=system(plotcmd)) != 0){
-     printf(" Problem with gnuplot\n");
+     printf("\n Problem with gnuplot\n");
    }
    printf(" Wait...");
    while (z[0] != 'q') {

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Removed from v.1.102
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	Added in v.1.146