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Diff for /imach/src/imach.c between versions 1.43 and 1.125

-version 1.43, 2002/05/24 13:00:54
+version 1.125, 2006/04/04 15:20:31
  Line 1
  /* $Id$
+   $State$
+   $Log$
+   Revision 1.125  2006/04/04 15:20:31  lievre
+   Errors in calculation of health expectancies. Age was not initialized.
+   Forecasting file added.
+   Revision 1.124  2006/03/22 17:13:53  lievre
+   Parameters are printed with %lf instead of %f (more numbers after the comma).
+   The log-likelihood is printed in the log file
+   Revision 1.123  2006/03/20 10:52:43  brouard
+   * imach.c (Module): <title> changed, corresponds to .htm file
+   name. <head> headers where missing.
+   * imach.c (Module): Weights can have a decimal point as for
+   English (a comma might work with a correct LC_NUMERIC environment,
+   otherwise the weight is truncated).
+   Modification of warning when the covariates values are not 0 or
+.
+   Version 0.98g
+   Revision 1.122  2006/03/20 09:45:41  brouard
+   (Module): Weights can have a decimal point as for
+   English (a comma might work with a correct LC_NUMERIC environment,
+   otherwise the weight is truncated).
+   Modification of warning when the covariates values are not 0 or
+.
+   Version 0.98g
+   Revision 1.121  2006/03/16 17:45:01  lievre
+   * imach.c (Module): Comments concerning covariates added
+   * imach.c (Module): refinements in the computation of lli if
+   status=-2 in order to have more reliable computation if stepm is
+   not 1 month. Version 0.98f
+   Revision 1.120  2006/03/16 15:10:38  lievre
+   (Module): refinements in the computation of lli if
+   status=-2 in order to have more reliable computation if stepm is
+   not 1 month. Version 0.98f
+   Revision 1.119  2006/03/15 17:42:26  brouard
+   (Module): Bug if status = -2, the loglikelihood was
+   computed as likelihood omitting the logarithm. Version O.98e
+   Revision 1.118  2006/03/14 18:20:07  brouard
+   (Module): varevsij Comments added explaining the second
+   table of variances if popbased=1 .
+   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+   (Module): Function pstamp added
+   (Module): Version 0.98d
+   Revision 1.117  2006/03/14 17:16:22  brouard
+   (Module): varevsij Comments added explaining the second
+   table of variances if popbased=1 .
+   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+   (Module): Function pstamp added
+   (Module): Version 0.98d
+   Revision 1.116  2006/03/06 10:29:27  brouard
+   (Module): Variance-covariance wrong links and
+   varian-covariance of ej. is needed (Saito).
+   Revision 1.115  2006/02/27 12:17:45  brouard
+   (Module): One freematrix added in mlikeli! 0.98c
+   Revision 1.114  2006/02/26 12:57:58  brouard
+   (Module): Some improvements in processing parameter
+   filename with strsep.
+   Revision 1.113  2006/02/24 14:20:24  brouard
+   (Module): Memory leaks checks with valgrind and:
+   datafile was not closed, some imatrix were not freed and on matrix
+   allocation too.
+   Revision 1.112  2006/01/30 09:55:26  brouard
+   (Module): Back to gnuplot.exe instead of wgnuplot.exe
+   Revision 1.111  2006/01/25 20:38:18  brouard
+   (Module): Lots of cleaning and bugs added (Gompertz)
+   (Module): Comments can be added in data file. Missing date values
+   can be a simple dot '.'.
+   Revision 1.110  2006/01/25 00:51:50  brouard
+   (Module): Lots of cleaning and bugs added (Gompertz)
+   Revision 1.109  2006/01/24 19:37:15  brouard
+   (Module): Comments (lines starting with a #) are allowed in data.
+   Revision 1.108  2006/01/19 18:05:42  lievre
+   Gnuplot problem appeared...
+   To be fixed
+   Revision 1.107  2006/01/19 16:20:37  brouard
+   Test existence of gnuplot in imach path
+   Revision 1.106  2006/01/19 13:24:36  brouard
+   Some cleaning and links added in html output
+   Revision 1.105  2006/01/05 20:23:19  lievre
+   *** empty log message ***
+   Revision 1.104  2005/09/30 16:11:43  lievre
+   (Module): sump fixed, loop imx fixed, and simplifications.
+   (Module): If the status is missing at the last wave but we know
+   that the person is alive, then we can code his/her status as -2
+   (instead of missing=-1 in earlier versions) and his/her
+   contributions to the likelihood is 1 - Prob of dying from last
+   health status (= 1-p13= p11+p12 in the easiest case of somebody in
+   the healthy state at last known wave). Version is 0.98
+   Revision 1.103  2005/09/30 15:54:49  lievre
+   (Module): sump fixed, loop imx fixed, and simplifications.
+   Revision 1.102  2004/09/15 17:31:30  brouard
+   Add the possibility to read data file including tab characters.
+   Revision 1.101  2004/09/15 10:38:38  brouard
+   Fix on curr_time
+   Revision 1.100  2004/07/12 18:29:06  brouard
+   Add version for Mac OS X. Just define UNIX in Makefile
+   Revision 1.99  2004/06/05 08:57:40  brouard
+   *** empty log message ***
+   Revision 1.98  2004/05/16 15:05:56  brouard
+   New version 0.97 . First attempt to estimate force of mortality
+   directly from the data i.e. without the need of knowing the health
+   state at each age, but using a Gompertz model: log u =a + b*age .
+   This is the basic analysis of mortality and should be done before any
+   other analysis, in order to test if the mortality estimated from the
+   cross-longitudinal survey is different from the mortality estimated
+   from other sources like vital statistic data.
+   The same imach parameter file can be used but the option for mle should be -3.
+   Agn�s, who wrote this part of the code, tried to keep most of the
+   former routines in order to include the new code within the former code.
+   The output is very simple: only an estimate of the intercept and of
+   the slope with 95% confident intervals.
+   Current limitations:
+   A) Even if you enter covariates, i.e. with the
+   model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
+   B) There is no computation of Life Expectancy nor Life Table.
+   Revision 1.97  2004/02/20 13:25:42  lievre
+   Version 0.96d. Population forecasting command line is (temporarily)
+   suppressed.
+   Revision 1.96  2003/07/15 15:38:55  brouard
+   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
+   rewritten within the same printf. Workaround: many printfs.
+   Revision 1.95  2003/07/08 07:54:34  brouard
+   * imach.c (Repository):
+   (Repository): Using imachwizard code to output a more meaningful covariance
+   matrix (cov(a12,c31) instead of numbers.
+   Revision 1.94  2003/06/27 13:00:02  brouard
+   Just cleaning
+   Revision 1.93  2003/06/25 16:33:55  brouard
+   (Module): On windows (cygwin) function asctime_r doesn't
+   exist so I changed back to asctime which exists.
+   (Module): Version 0.96b
+   Revision 1.92  2003/06/25 16:30:45  brouard
+   (Module): On windows (cygwin) function asctime_r doesn't
+   exist so I changed back to asctime which exists.
+   Revision 1.91  2003/06/25 15:30:29  brouard
+   * imach.c (Repository): Duplicated warning errors corrected.
+   (Repository): Elapsed time after each iteration is now output. It
+   helps to forecast when convergence will be reached. Elapsed time
+   is stamped in powell.  We created a new html file for the graphs
+   concerning matrix of covariance. It has extension -cov.htm.
+   Revision 1.90  2003/06/24 12:34:15  brouard
+   (Module): Some bugs corrected for windows. Also, when
+   mle=-1 a template is output in file "or"mypar.txt with the design
+   of the covariance matrix to be input.
+   Revision 1.89  2003/06/24 12:30:52  brouard
+   (Module): Some bugs corrected for windows. Also, when
+   mle=-1 a template is output in file "or"mypar.txt with the design
+   of the covariance matrix to be input.
+   Revision 1.88  2003/06/23 17:54:56  brouard
+   * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
+   Revision 1.87  2003/06/18 12:26:01  brouard
+   Version 0.96
+   Revision 1.86  2003/06/17 20:04:08  brouard
+   (Module): Change position of html and gnuplot routines and added
+   routine fileappend.
+   Revision 1.85  2003/06/17 13:12:43  brouard
+   * imach.c (Repository): Check when date of death was earlier that
+   current date of interview. It may happen when the death was just
+   prior to the death. In this case, dh was negative and likelihood
+   was wrong (infinity). We still send an "Error" but patch by
+   assuming that the date of death was just one stepm after the
+   interview.
+   (Repository): Because some people have very long ID (first column)
+   we changed int to long in num[] and we added a new lvector for
+   memory allocation. But we also truncated to 8 characters (left
+   truncation)
+   (Repository): No more line truncation errors.
+   Revision 1.84  2003/06/13 21:44:43  brouard
+   * imach.c (Repository): Replace "freqsummary" at a correct
+   place. It differs from routine "prevalence" which may be called
+   many times. Probs is memory consuming and must be used with
+   parcimony.
+   Version 0.95a3 (should output exactly the same maximization than 0.8a2)
+   Revision 1.83  2003/06/10 13:39:11  lievre
+   *** empty log message ***
+   Revision 1.82  2003/06/05 15:57:20  brouard
+   Add log in  imach.c and  fullversion number is now printed.
+ */
+ /*
     Interpolated Markov Chain
    Short summary of the programme:
- Line 32
+ Line 260
    hPijx is the probability to be observed in state i at age x+h
    conditional to the observed state i at age x. The delay 'h' can be
    split into an exact number (nh*stepm) of unobserved intermediate
-   states. This elementary transition (by month or quarter trimester,
+   states. This elementary transition (by month, quarter,
-   semester or year) is model as a multinomial logistic.  The hPx
+   semester or year) is modelled as a multinomial logistic.  The hPx
    matrix is simply the matrix product of nh*stepm elementary matrices
    and the contribution of each individual to the likelihood is simply
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
-   of the life expectancies. It also computes the prevalence limits.
+   of the life expectancies. It also computes the period (stable) prevalence.
    Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
             Institut national d'�tudes d�mographiques, Paris.
- Line 48
+ Line 276
    It is copyrighted identically to a GNU software product, ie programme and
    software can be distributed freely for non commercial use. Latest version
    can be accessed at http://euroreves.ined.fr/imach .
+   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
+   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    **********************************************************************/
+ /*
+   main
+   read parameterfile
+   read datafile
+   concatwav
+   freqsummary
+   if (mle >= 1)
+     mlikeli
+   print results files
+   if mle==1
+      computes hessian
+   read end of parameter file: agemin, agemax, bage, fage, estepm
+       begin-prev-date,...
+   open gnuplot file
+   open html file
+   period (stable) prevalence
+    for age prevalim()
+   h Pij x
+   variance of p varprob
+   forecasting if prevfcast==1 prevforecast call prevalence()
+   health expectancies
+   Variance-covariance of DFLE
+   prevalence()
+    movingaverage()
+   varevsij()
+   if popbased==1 varevsij(,popbased)
+   total life expectancies
+   Variance of period (stable) prevalence
+  end
+ */
  #include <math.h>
  #include <stdio.h>
  #include <stdlib.h>
+ #include <string.h>
  #include <unistd.h>
+ #include <limits.h>
+ #include <sys/types.h>
+ #include <sys/stat.h>
+ #include <errno.h>
+ extern int errno;
+ /* #include <sys/time.h> */
+ #include <time.h>
+ #include "timeval.h"
+ /* #include <libintl.h> */
+ /* #define _(String) gettext (String) */
  #define MAXLINE 256
  #define GNUPLOTPROGRAM "gnuplot"
  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- #define FILENAMELENGTH 80
+ #define FILENAMELENGTH 132
- /*#define DEBUG*/
- #define windows
  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- Line 75
+ Line 354
  #define YEARM 12. /* Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
+ #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ #ifdef UNIX
+ #define DIRSEPARATOR '/'
+ #define CHARSEPARATOR "/"
+ #define ODIRSEPARATOR '\\'
+ #else
+ #define DIRSEPARATOR '\\'
+ #define CHARSEPARATOR "\\"
+ #define ODIRSEPARATOR '/'
+ #endif
+ /* $Id$ */
+ /* $State$ */
- int erreur; /* Error number */
+ char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ char fullversion[]="$Revision$ $Date$";
+ char strstart[80];
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
  int nvar;
- int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
+ int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
  int npar=NPARMAX;
  int nlstate=2; /* Number of live states */
  int ndeath=1; /* Number of dead states */
- Line 89  int popbased=0;
+ Line 384  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
  int maxwav; /* Maxim number of waves */
  int jmin, jmax; /* min, max spacing between 2 waves */
+ int ijmin, ijmax; /* Individuals having jmin and jmax */
+ int gipmx, gsw; /* Global variables on the number of contributions
+                    to the likelihood and the sum of weights (done by funcone)*/
  int mle, weightopt;
  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ 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 **oldm, **newm, **savm; /* Working pointers to matrices */
  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- FILE *ficgp,*ficresprob,*ficpop;
+ FILE *ficlog, *ficrespow;
+ int globpr; /* Global variable for printing or not */
+ double fretone; /* Only one call to likelihood */
+ long ipmx; /* Number of contributions */
+ double sw; /* Sum of weights */
+ char filerespow[FILENAMELENGTH];
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ FILE *ficresilk;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ FILE *ficresprobmorprev;
+ FILE *fichtm, *fichtmcov; /* Html File */
  FILE *ficreseij;
-   char filerese[FILENAMELENGTH];
+ char filerese[FILENAMELENGTH];
-  FILE  *ficresvij;
+ FILE *ficresstdeij;
-   char fileresv[FILENAMELENGTH];
+ char fileresstde[FILENAMELENGTH];
-  FILE  *ficresvpl;
+ FILE *ficrescveij;
-   char fileresvpl[FILENAMELENGTH];
+ char filerescve[FILENAMELENGTH];
+ FILE  *ficresvij;
+ char fileresv[FILENAMELENGTH];
+ FILE  *ficresvpl;
+ char fileresvpl[FILENAMELENGTH];
+ char title[MAXLINE];
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ char command[FILENAMELENGTH];
+ int  outcmd=0;
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char filelog[FILENAMELENGTH]; /* Log file */
+ char filerest[FILENAMELENGTH];
+ char fileregp[FILENAMELENGTH];
+ char popfile[FILENAMELENGTH];
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ struct timezone tzp;
+ extern int gettimeofday();
+ struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ long time_value;
+ extern long time();
+ char strcurr[80], strfor[80];
+ char *endptr;
+ long lval;
+ double dval;
  #define NR_END 1
  #define FREE_ARG char*
- Line 131  static double maxarg1,maxarg2;
+ Line 472  static double maxarg1,maxarg2;
  static double sqrarg;
  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ int agegomp= AGEGOMP;
  int imx;
- int stepm;
+ int stepm=1;
  /* Stepm, step in month: minimum step interpolation*/
  int estepm;
  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
  int m,nb;
- int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
+ long *num;
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- double **pmmij, ***probs, ***mobaverage;
+ double **pmmij, ***probs;
+ double *ageexmed,*agecens;
  double dateintmean=0;
  double *weight;
  int **s; /* Status */
  double *agedc, **covar, idx;
  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double *lsurv, *lpop, *tpop;
  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
  double ftolhess; /* Tolerance for computing hessian */
- Line 156  double ftolhess; /* Tolerance for comput
+ Line 501  double ftolhess; /* Tolerance for comput
  /**************** split *************************/
  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
  {
-    char *s;                             /* pointer */
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-    int  l1, l2;                         /* length counters */
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+   */
-    l1 = strlen( path );                 /* length of path */
+   char  *ss;                            /* pointer */
-    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+   int   l1, l2;                         /* length counters */
- #ifdef windows
-    s = strrchr( path, '\\' );           /* find last / */
+   l1 = strlen(path );                   /* length of path */
- #else
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-    s = strrchr( path, '/' );            /* find last / */
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
- #endif
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-    if ( s == NULL ) {                   /* no directory, so use current */
+     strcpy( name, path );               /* we got the fullname name because no directory */
- #if     defined(__bsd__)                /* get current working directory */
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-       extern char       *getwd( );
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+     /* get current working directory */
-       if ( getwd( dirc ) == NULL ) {
+     /*    extern  char* getcwd ( char *buf , int len);*/
- #else
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
-       extern char       *getcwd( );
+       return( GLOCK_ERROR_GETCWD );
+     }
+     /* 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 */
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+     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 */
+   if( dirc[l1-1] != DIRSEPARATOR ){
+     dirc[l1] =  DIRSEPARATOR;
+     dirc[l1+1] = 0;
+     printf(" DIRC3 = %s \n",dirc);
+   }
+   ss = strrchr( name, '.' );            /* find last / */
+   if (ss >0){
+     ss++;
+     strcpy(ext,ss);                     /* save extension */
+     l1= strlen( name);
+     l2= strlen(ss)+1;
+     strncpy( finame, name, l1-l2);
+     finame[l1-l2]= 0;
+   }
-       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+   return( 0 );                          /* we're done */
- #endif
-          return( GLOCK_ERROR_GETCWD );
-       }
-       strcpy( name, path );             /* we've got it */
-    } else {                             /* strip direcotry from path */
-       s++;                              /* after this, the filename */
-       l2 = strlen( s );                 /* length of filename */
-       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-       strcpy( name, s );                /* save file name */
-       strncpy( dirc, path, l1 - l2 );   /* now the directory */
-       dirc[l1-l2] = 0;                  /* add zero */
-    }
-    l1 = strlen( dirc );                 /* length of directory */
- #ifdef windows
-    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
- #else
-    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
- #endif
-    s = strrchr( name, '.' );            /* find last / */
-    s++;
-    strcpy(ext,s);                       /* save extension */
-    l1= strlen( name);
-    l2= strlen( s)+1;
-    strncpy( finame, name, l1-l2);
-    finame[l1-l2]= 0;
-    return( 0 );                         /* we're done */
  }
  /******************************************/
- void replace(char *s, char*t)
+ void replace_back_to_slash(char *s, char*t)
  {
    int i;
-   int lg=20;
+   int lg=0;
    i=0;
    lg=strlen(t);
    for(i=0; i<= lg; i++) {
- Line 232  int nbocc(char *s, char occ)
+ Line 579  int nbocc(char *s, char occ)
  void cutv(char *u,char *v, char*t, char occ)
  {
+   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+      gives u="abcedf" and v="ghi2j" */
    int i,lg,j,p=0;
    i=0;
    for(j=0; j<=strlen(t)-1; j++) {
- Line 255  void nrerror(char error_text[])
+ Line 605  void nrerror(char error_text[])
  {
    fprintf(stderr,"ERREUR ...\n");
    fprintf(stderr,"%s\n",error_text);
-   exit(1);
+   exit(EXIT_FAILURE);
  }
  /*********************** vector *******************/
  double *vector(int nl, int nh)
- Line 287  void free_ivector(int *v, long nl, long
+ Line 637  void free_ivector(int *v, long nl, long
    free((FREE_ARG)(v+nl-NR_END));
  }
+ /************************lvector *******************************/
+ long *lvector(long nl,long nh)
+ {
+   long *v;
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+   if (!v) nrerror("allocation failure in ivector");
+   return v-nl+NR_END;
+ }
+ /******************free lvector **************************/
+ void free_lvector(long *v, long nl, long nh)
+ {
+   free((FREE_ARG)(v+nl-NR_END));
+ }
  /******************* imatrix *******************************/
  int **imatrix(long nrl, long nrh, long ncl, long nch)
       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
- Line 341  double **matrix(long nrl, long nrh, long
+ Line 706  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])
+    */
  }
  /*************************free matrix ************************/
- Line 380  double ***ma3x(long nrl, long nrh, long
+ Line 747  double ***ma3x(long nrl, long nrh, long
      for (j=ncl+1; j<=nch; j++)
        m[i][j]=m[i][j-1]+nlay;
    }
    return m;
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   */
  }
  /*************************free ma3x ************************/
- Line 391  void free_ma3x(double ***m, long nrl, lo
+ Line 761  void free_ma3x(double ***m, long nrl, lo
    free((FREE_ARG)(m+nrl-NR_END));
  }
+ /*************** function subdirf ***********/
+ char *subdirf(char fileres[])
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/"); /* Add to the right */
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
+ /*************** function subdirf2 ***********/
+ char *subdirf2(char fileres[], char *preop)
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
+ /*************** function subdirf3 ***********/
+ char *subdirf3(char fileres[], char *preop, char *preop2)
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
+   strcat(tmpout,preop2);
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
  /***************** f1dim *************************/
  extern int ncom;
  extern double *pcom,*xicom;
- Line 428  double brent(double ax, double bx, doubl
+ Line 833  double brent(double ax, double bx, doubl
      tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
      printf(".");fflush(stdout);
+     fprintf(ficlog,".");fflush(ficlog);
  #ifdef DEBUG
      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
  #endif
      if (fabs(x-xm) <= (tol2-0.5*(b-a))){
- Line 554  void linmin(double p[], double xi[], int
+ Line 961  void linmin(double p[], double xi[], int
    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
  #ifdef DEBUG
    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
  #endif
    for (j=1;j<=n;j++) {
      xi[j] *= xmin;
- Line 563  void linmin(double p[], double xi[], int
+ Line 971  void linmin(double p[], double xi[], int
    free_vector(pcom,1,n);
  }
+ char *asc_diff_time(long time_sec, char ascdiff[])
+ {
+   long sec_left, days, hours, minutes;
+   days = (time_sec) / (60*60*24);
+   sec_left = (time_sec) % (60*60*24);
+   hours = (sec_left) / (60*60) ;
+   sec_left = (sec_left) %(60*60);
+   minutes = (sec_left) /60;
+   sec_left = (sec_left) % (60);
+   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+   return ascdiff;
+ }
  /*************** powell ************************/
  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
              double (*func)(double []))
- Line 573  void powell(double p[], double **xi, int
+ Line 994  void powell(double p[], double **xi, int
    double del,t,*pt,*ptt,*xit;
    double fp,fptt;
    double *xits;
+   int niterf, itmp;
    pt=vector(1,n);
    ptt=vector(1,n);
    xit=vector(1,n);
- Line 583  void powell(double p[], double **xi, int
+ Line 1006  void powell(double p[], double **xi, int
      fp=(*fret);
      ibig=0;
      del=0.0;
-     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+     last_time=curr_time;
-     for (i=1;i<=n;i++)
+     (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); fflush(ficlog);
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+    for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
+       fprintf(ficlog," %d %.12lf",i, p[i]);
+       fprintf(ficrespow," %.12lf", p[i]);
+     }
      printf("\n");
+     fprintf(ficlog,"\n");
+     fprintf(ficrespow,"\n");fflush(ficrespow);
+     if(*iter <=3){
+       tm = *localtime(&curr_time.tv_sec);
+       strcpy(strcurr,asctime(&tm));
+ /*       asctime_r(&tm,strcurr); */
+       forecast_time=curr_time;
+       itmp = strlen(strcurr);
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+         strcurr[itmp-1]='\0';
+       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       for(niterf=10;niterf<=30;niterf+=10){
+         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+         tmf = *localtime(&forecast_time.tv_sec);
+ /*      asctime_r(&tmf,strfor); */
+         strcpy(strfor,asctime(&tmf));
+         itmp = strlen(strfor);
+         if(strfor[itmp-1]=='\n')
+         strfor[itmp-1]='\0';
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+       }
+     }
      for (i=1;i<=n;i++) {
        for (j=1;j<=n;j++) xit[j]=xi[j][i];
        fptt=(*fret);
  #ifdef DEBUG
        printf("fret=%lf \n",*fret);
+       fprintf(ficlog,"fret=%lf \n",*fret);
  #endif
        printf("%d",i);fflush(stdout);
+       fprintf(ficlog,"%d",i);fflush(ficlog);
        linmin(p,xit,n,fret,func);
        if (fabs(fptt-(*fret)) > del) {
          del=fabs(fptt-(*fret));
- Line 601  void powell(double p[], double **xi, int
+ Line 1057  void powell(double p[], double **xi, int
        }
  #ifdef DEBUG
        printf("%d %.12e",i,(*fret));
+       fprintf(ficlog,"%d %.12e",i,(*fret));
        for (j=1;j<=n;j++) {
          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
          printf(" x(%d)=%.12e",j,xit[j]);
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
        }
-       for(j=1;j<=n;j++)
+       for(j=1;j<=n;j++) {
          printf(" p=%.12e",p[j]);
+         fprintf(ficlog," p=%.12e",p[j]);
+       }
        printf("\n");
+       fprintf(ficlog,"\n");
  #endif
      }
      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
- Line 616  void powell(double p[], double **xi, int
+ Line 1077  void powell(double p[], double **xi, int
        k[0]=1;
        k[1]=-1;
        printf("Max: %.12e",(*func)(p));
-       for (j=1;j<=n;j++)
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       for (j=1;j<=n;j++) {
          printf(" %.12e",p[j]);
+         fprintf(ficlog," %.12e",p[j]);
+       }
        printf("\n");
+       fprintf(ficlog,"\n");
        for(l=0;l<=1;l++) {
          for (j=1;j<=n;j++) {
            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
          }
          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
        }
  #endif
- Line 652  void powell(double p[], double **xi, int
+ Line 1119  void powell(double p[], double **xi, int
          }
  #ifdef DEBUG
          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         for(j=1;j<=n;j++)
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+         for(j=1;j<=n;j++){
            printf(" %.12e",xit[j]);
+           fprintf(ficlog," %.12e",xit[j]);
+         }
          printf("\n");
+         fprintf(ficlog,"\n");
  #endif
        }
      }
    }
  }
- /**** Prevalence limit ****************/
+ /**** 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 732  double **pmij(double **ps, double *cov,
+ Line 1203  double **pmij(double **ps, double *cov,
    int i,j,j1, nc, ii, jj;
      for(i=1; i<= nlstate; i++){
-     for(j=1; j<i;j++){
+       for(j=1; j<i;j++){
-       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-         /*s2 += param[i][j][nc]*cov[nc];*/
+           /*s2 += param[i][j][nc]*cov[nc];*/
-         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
+ /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
-       }
+         }
-       ps[i][j]=s2;
+         ps[i][j]=s2;
-       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
+ /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
-     }
+       }
-     for(j=i+1; j<=nlstate+ndeath;j++){
+       for(j=i+1; j<=nlstate+ndeath;j++){
-       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
+ /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+         }
+         ps[i][j]=s2;
        }
-       ps[i][j]=s2;
      }
-   }
      /*ps[3][2]=1;*/
-   for(i=1; i<= nlstate; i++){
+     for(i=1; i<= nlstate; i++){
-      s1=0;
+       s1=0;
-     for(j=1; j<i; j++)
+       for(j=1; j<i; j++)
-       s1+=exp(ps[i][j]);
+         s1+=exp(ps[i][j]);
-     for(j=i+1; j<=nlstate+ndeath; j++)
+       for(j=i+1; j<=nlstate+ndeath; j++)
-       s1+=exp(ps[i][j]);
+         s1+=exp(ps[i][j]);
-     ps[i][i]=1./(s1+1.);
+       ps[i][i]=1./(s1+1.);
-     for(j=1; j<i; j++)
+       for(j=1; j<i; j++)
-       ps[i][j]= exp(ps[i][j])*ps[i][i];
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-     for(j=i+1; j<=nlstate+ndeath; j++)
+       for(j=i+1; j<=nlstate+ndeath; j++)
-       ps[i][j]= exp(ps[i][j])*ps[i][i];
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-   } /* end i */
+     } /* end i */
-   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-     for(jj=1; jj<= nlstate+ndeath; jj++){
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-       ps[ii][jj]=0;
+         ps[ii][jj]=0;
-       ps[ii][ii]=1;
+         ps[ii][ii]=1;
+       }
      }
-   }
-   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
+ /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
-     for(jj=1; jj<= nlstate+ndeath; jj++){
+ /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
-      printf("%lf ",ps[ii][jj]);
+ /*         printf("ddd %lf ",ps[ii][jj]); */
-    }
+ /*       } */
-     printf("\n ");
+ /*       printf("\n "); */
-     }
+ /*        } */
-     printf("\n ");printf("%lf ",cov[2]);*/
+ /*        printf("\n ");printf("%lf ",cov[2]); */
- /*
+        /*
-   for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-   goto end;*/
+       goto end;*/
      return ps;
  }
- Line 809  double **matprod2(double **out, double *
+ Line 1280  double **matprod2(double **out, double *
  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
  {
-   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
+   /* Computes the transition matrix starting at age 'age' over
-      duration (i.e. until
+      'nhstepm*hstepm*stepm' months (i.e. until
-      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+      nhstepm*hstepm matrices.
       Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-      (typically every 2 years instead of every month which is too big).
+      (typically every 2 years instead of every month which is too big
+      for the memory).
       Model is determined by parameters x and covariates have to be
       included manually here.
- Line 869  double func( double *x)
+ Line 1342  double func( double *x)
    double **out;
    double sw; /* Sum of weights */
    double lli; /* Individual log likelihood */
+   int s1, s2;
+   double bbh, survp;
    long ipmx;
    /*extern weight */
    /* We are differentiating ll according to initial status */
- Line 879  double func( double *x)
+ Line 1354  double func( double *x)
    cov[1]=1.;
    for(k=1; k<=nlstate; k++) ll[k]=0.;
+   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];
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
+         } /* end mult */
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+         /* But now since version 0.9 we anticipate for bias at large stepm.
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
+          * (in months) between two waves is not a multiple of stepm, we rounded to
+          * the nearest (and in case of equal distance, to the lowest) interval but now
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+          * probability in order to take into account the bias as a fraction of the way
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+          * -stepm/2 to stepm/2 .
+          * For stepm=1 the results are the same as for previous versions of Imach.
+          * For stepm > 1 the results are less biased than in previous versions.
+          */
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
+         /* bias bh is positive if real duration
+          * is higher than the multiple of stepm and negative otherwise.
+          */
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+         if( s2 > nlstate){
+           /* i.e. if s2 is a death state and if the date of death is known
+              then the contribution to the likelihood is the probability to
+              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
+         health state: the date of the interview describes the actual state
+         and not the date of a change in health state. The former idea was
+         to consider that at each interview the state was recorded
+         (healthy, disable or death) and IMaCh was corrected; but when we
+         introduced the exact date of death then we should have modified
+         the contribution of an exact death to the likelihood. This new
+         contribution is smaller and very dependent of the step unit
+         stepm. It is no more the probability to die between last interview
+         and month of death but the probability to survive from last
+         interview up to one month before death multiplied by the
+         probability to die within a month. Thanks to Chris
+         Jackson for correcting this bug.  Former versions increased
+         mortality artificially. The bad side is that we add another loop
+         which slows down the processing. The difference can be up to 10%
+         lower mortality.
+           */
+           lli=log(out[s1][s2] - savm[s1][s2]);
+         } else if  (s2==-2) {
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           /*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 */
+         }
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+         /*if(lli ==000.0)*/
+         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
+         ipmx +=1;
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
+     } /* end of individual */
+   }  else if(mle==2){
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
+         for(d=0; d<=dh[mi][i]; d++){
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
+         } /* end mult */
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
+         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 */
+         ipmx +=1;
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
+     } /* end of individual */
+   }  else if(mle==3){  /* exponential inter-extrapolation */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
+         } /* end mult */
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
+         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+         ipmx +=1;
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
+     } /* end of individual */
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
+         } /* end mult */
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
+         if( s2 > nlstate){
+           lli=log(out[s1][s2] - savm[s1][s2]);
+         }else{
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         }
+         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]); */
+       } /* end of wave */
+     } /* end of individual */
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
+         } /* end mult */
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         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]);*/
+       } /* end of wave */
+     } /* end of individual */
+   } /* End of if */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   return -l;
+ }
+ /*************** log-likelihood *************/
+ double funcone( double *x)
+ {
+   /* Same as likeli but slower because of a lot of printf and if */
+   int i, ii, j, k, mi, d, kk;
+   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   double **out;
+   double lli; /* Individual log likelihood */
+   double llt;
+   int s1, s2;
+   double bbh, survp;
+   /*extern weight */
+   /* We are differentiating ll according to initial status */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   /*for(i=1;i<imx;i++)
+     printf(" %d\n",s[4][i]);
+   */
+   cov[1]=1.;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      for(mi=1; mi<= wav[i]-1; mi++){
        for (ii=1;ii<=nlstate+ndeath;ii++)
-         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         for (j=1;j<=nlstate+ndeath;j++){
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         }
        for(d=0; d<dh[mi][i]; d++){
          newm=savm;
          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
          for (kk=1; kk<=cptcovage;kk++) {
            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          }
          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          savm=oldm;
          oldm=newm;
        } /* end mult */
-       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
+       s1=s[mw[mi][i]][i];
-       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
+       s2=s[mw[mi+1][i]][i];
+       bbh=(double)bh[mi][i]/(double)stepm;
+       /* bias is positive if real duration
+        * is higher than the multiple of stepm and negative otherwise.
+        */
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         lli=log(out[s1][s2] - savm[s1][s2]);
+       } else if  (s2==-2) {
+         for (j=1,survp=0. ; j<=nlstate; j++)
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         lli= log(survp);
+       }else if (mle==1){
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+       } else if(mle==2){
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+       } else if(mle==3){  /* exponential inter-extrapolation */
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+         lli=log(out[s1][s2]); /* Original formula */
+       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+         lli=log(out[s1][s2]); /* Original formula */
+       } /* End of if */
        ipmx +=1;
        sw += weight[i];
        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       if(globpr){
+         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+  %11.6f %11.6f %11.6f ", \
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+           llt +=ll[k]*gipmx/gsw;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         }
+         fprintf(ficresilk," %10.6f\n", -llt);
+       }
      } /* end of wave */
    } /* end of individual */
    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   if(globpr==0){ /* First time we count the contributions and weights */
+     gipmx=ipmx;
+     gsw=sw;
+   }
    return -l;
  }
+ /*************** function likelione ***********/
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+ {
+   /* This routine should help understanding what is done with
+      the selection of individuals/waves and
+      to check the exact contribution to the likelihood.
+      Plotting could be done.
+    */
+   int k;
+   if(*globpri !=0){ /* Just counts and sums, no printings */
+     strcpy(fileresilk,"ilk");
+     strcat(fileresilk,fileres);
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", fileresilk);
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+     }
+     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+     for(k=1; k<=nlstate; k++)
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+   }
+   *fretone=(*funcone)(p);
+   if(*globpri !=0){
+     fclose(ficresilk);
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     fflush(fichtm);
+   }
+   return;
+ }
  /*********** Maximum Likelihood Estimation ***************/
  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
  {
    int i,j, iter;
-   double **xi,*delti;
+   double **xi;
    double fret;
+   double fretone; /* Only one call to likelihood */
+   /*  char filerespow[FILENAMELENGTH];*/
    xi=matrix(1,npar,1,npar);
    for (i=1;i<=npar;i++)
      for (j=1;j<=npar;j++)
        xi[i][j]=(i==j ? 1.0 : 0.0);
-   printf("Powell\n");
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+   strcpy(filerespow,"pow");
+   strcat(filerespow,fileres);
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", filerespow);
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+   }
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   for (i=1;i<=nlstate;i++)
+     for(j=1;j<=nlstate+ndeath;j++)
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   fprintf(ficrespow,"\n");
    powell(p,xi,npar,ftol,&iter,&fret,func);
-    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+   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));
    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
  }
- Line 941  void hesscov(double **matcov, double p[]
+ Line 1758  void hesscov(double **matcov, double p[]
    int i, j,jk;
    int *indx;
-   double hessii(double p[], double delta, int theta, double delti[]);
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-   double hessij(double p[], double delti[], int i, int j);
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
    void lubksb(double **a, int npar, int *indx, double b[]) ;
    void ludcmp(double **a, int npar, int *indx, double *d) ;
+   double gompertz(double p[]);
    hess=matrix(1,npar,1,npar);
    printf("\nCalculation of the hessian matrix. Wait...\n");
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
    for (i=1;i<=npar;i++){
      printf("%d",i);fflush(stdout);
-     hess[i][i]=hessii(p,ftolhess,i,delti);
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-     /*printf(" %f ",p[i]);*/
-     /*printf(" %lf ",hess[i][i]);*/
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+     /*  printf(" %f ",p[i]);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
    }
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++)  {
        if (j>i) {
          printf(".%d%d",i,j);fflush(stdout);
-         hess[i][j]=hessij(p,delti,i,j);
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
          hess[j][i]=hess[i][j];
          /*printf(" %lf ",hess[i][j]);*/
        }
      }
    }
    printf("\n");
+   fprintf(ficlog,"\n");
    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
    a=matrix(1,npar,1,npar);
    y=matrix(1,npar,1,npar);
- Line 988  void hesscov(double **matcov, double p[]
+ Line 1813  void hesscov(double **matcov, double p[]
    }
    printf("\n#Hessian matrix#\n");
+   fprintf(ficlog,"\n#Hessian matrix#\n");
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++) {
        printf("%.3e ",hess[i][j]);
+       fprintf(ficlog,"%.3e ",hess[i][j]);
      }
      printf("\n");
+     fprintf(ficlog,"\n");
    }
    /* Recompute Inverse */
- Line 1009  void hesscov(double **matcov, double p[]
+ Line 1837  void hesscov(double **matcov, double p[]
      for (i=1;i<=npar;i++){
        y[i][j]=x[i];
        printf("%.3e ",y[i][j]);
+       fprintf(ficlog,"%.3e ",y[i][j]);
      }
      printf("\n");
+     fprintf(ficlog,"\n");
    }
    */
- Line 1024  void hesscov(double **matcov, double p[]
+ Line 1854  void hesscov(double **matcov, double p[]
  }
  /*************** hessian matrix ****************/
- double hessii( double x[], double delta, int theta, double delti[])
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
  {
    int i;
    int l=1, lmax=20;
    double k1,k2;
    double p2[NPARMAX+1];
    double res;
-   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
    double fx;
    int k=0,kmax=10;
    double l1;
- Line 1052  double hessii( double x[], double delta,
+ Line 1882  double hessii( double x[], double delta,
  #ifdef DEBUG
        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
        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
- Line 1070  double hessii( double x[], double delta,
+ Line 1901  double hessii( double x[], double delta,
  }
- double hessij( double x[], double delti[], int thetai,int thetaj)
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
  {
    int i;
    int l=1, l1, lmax=20;
- Line 1099  double hessij( double x[], double delti[
+ Line 1930  double hessij( double x[], double delti[
      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
  #ifdef DEBUG
      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
  #endif
    }
    return res;
- Line 1178  void lubksb(double **a, int n, int *indx
+ Line 2010  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 agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
+ 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 first;
    double ***freq; /* Frequencies */
-   double *pp;
+   double *pp, **prop;
-   double pos, k2, dateintsum=0,k2cpt=0;
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   FILE *ficresp;
    char fileresp[FILENAMELENGTH];
    pp=vector(1,nlstate);
-   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
    strcpy(fileresp,"p");
    strcat(fileresp,fileres);
    if((ficresp=fopen(fileresp,"w"))==NULL) {
      printf("Problem with prevalence resultfile: %s\n", fileresp);
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      exit(0);
    }
-   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
    j1=0;
    j=cptcoveff;
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   first=1;
    for(k1=1; k1<=j;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        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=agemin; m <= agemax+3; m++)
+           for(m=iagemin; m <= iagemax+3; m++)
              freq[i][jk][m]=0;
+     for (i=1; i<=nlstate; i++)
+       for(m=iagemin; m <= iagemax+3; m++)
+         prop[i][m]=0;
        dateintsum=0;
        k2cpt=0;
- Line 1222  void  freqsummary(char fileres[], int ag
+ Line 2066  void  freqsummary(char fileres[], int ag
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
                bool=0;
          }
-         if (bool==1) {
+         if (bool==1){
            for(m=firstpass; m<=lastpass; m++){
              k2=anint[m][i]+(mint[m][i]/12.);
-             if ((k2>=dateprev1) && (k2<=dateprev2)) {
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-               if(agev[m][i]==0) agev[m][i]=agemax+1;
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-               if(agev[m][i]==1) agev[m][i]=agemax+2;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                if (m<lastpass) {
                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                }
-               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                  dateintsum=dateintsum+k2;
                  k2cpt++;
                }
-             }
+               /*}*/
            }
          }
        }
-       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+       pstamp(ficresp);
        if  (cptcovn>0) {
          fprintf(ficresp, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- Line 1253  void  freqsummary(char fileres[], int ag
+ Line 2098  void  freqsummary(char fileres[], int ag
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        fprintf(ficresp, "\n");
-       for(i=(int)agemin; i <= (int)agemax+3; i++){
+       for(i=iagemin; i <= iagemax+3; i++){
-         if(i==(int)agemax+3)
+         if(i==iagemax+3){
-           printf("Total");
+           fprintf(ficlog,"Total");
-         else
+         }else{
-           printf("Age %d", i);
+           if(first==1){
+             first=0;
+             printf("See log file for details...\n");
+           }
+           fprintf(ficlog,"Age %d", i);
+         }
          for(jk=1; jk <=nlstate ; jk++){
            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
              pp[jk] += freq[jk][m][i];
- Line 1265  void  freqsummary(char fileres[], int ag
+ Line 2115  void  freqsummary(char fileres[], int ag
          for(jk=1; jk <=nlstate ; jk++){
            for(m=-1, pos=0; m <=0 ; m++)
              pos += freq[jk][m][i];
-           if(pp[jk]>=1.e-10)
+           if(pp[jk]>=1.e-10){
+             if(first==1){
              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-           else
+             }
-             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           }else{
+             if(first==1)
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+           }
          }
          for(jk=1; jk <=nlstate ; jk++){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
              pp[jk] += freq[jk][m][i];
          }
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-         for(jk=1,pos=0; jk <=nlstate ; jk++)
            pos += pp[jk];
+           posprop += prop[jk][i];
+         }
          for(jk=1; jk <=nlstate ; jk++){
-           if(pos>=1.e-5)
+           if(pos>=1.e-5){
-             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+             if(first==1)
-           else
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-           if( i <= (int) agemax){
+           }else{
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+           }
+           if( i <= iagemax){
              if(pos>=1.e-5){
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-               probs[i][jk][j1]= pp[jk]/pos;
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
              }
              else
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
            }
          }
          for(jk=-1; jk <=nlstate+ndeath; jk++)
            for(m=-1; m <=nlstate+ndeath; m++)
-             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+             if(freq[jk][m][i] !=0 ) {
-         if(i <= (int) agemax)
+             if(first==1)
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+             }
+         if(i <= iagemax)
            fprintf(ficresp,"\n");
-         printf("\n");
+         if(first==1)
+           printf("Others in log...\n");
+         fprintf(ficlog,"\n");
        }
      }
    }
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
-   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+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 */
  }
  /************ Prevalence ********************/
- void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
+ void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
- {  /* Some frequencies */
+ {
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
+      We still use firstpass and lastpass as another selection.
+   */
    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
    double ***freq; /* Frequencies */
-   double *pp;
+   double *pp, **prop;
-   double pos, k2;
+   double pos,posprop;
+   double  y2; /* in fractional years */
-   pp=vector(1,nlstate);
+   int iagemin, iagemax;
-   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   iagemin= (int) agemin;
-   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
+   iagemax= (int) agemax;
+   /*pp=vector(1,nlstate);*/
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    j1=0;
    j=cptcoveff;
- Line 1334  void prevalence(int agemin, float agemax
+ Line 2209  void prevalence(int agemin, float agemax
      for(i1=1; i1<=ncodemax[k1];i1++){
        j1++;
-       for (i=-1; i<=nlstate+ndeath; i++)
+       for (i=1; i<=nlstate; i++)
-         for (jk=-1; jk<=nlstate+ndeath; jk++)
+         for(m=iagemin; m <= iagemax+3; m++)
-           for(m=agemin; m <= agemax+3; m++)
+           prop[i][m]=0.0;
-             freq[i][jk][m]=0;
-       for (i=1; i<=imx; i++) {
+       for (i=1; i<=imx; i++) { /* Each individual */
          bool=1;
          if  (cptcovn>0) {
            for (z1=1; z1<=cptcoveff; z1++)
- Line 1347  void prevalence(int agemin, float agemax
+ Line 2221  void prevalence(int agemin, float agemax
                bool=0;
          }
          if (bool==1) {
-           for(m=firstpass; m<=lastpass; m++){
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-             k2=anint[m][i]+(mint[m][i]/12.);
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-             if ((k2>=dateprev1) && (k2<=dateprev2)) {
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-               if(agev[m][i]==0) agev[m][i]=agemax+1;
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-               if(agev[m][i]==1) agev[m][i]=agemax+2;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-               if (m<lastpass) {
+               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
-                 if (calagedate>0)
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
+                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
-                 else
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+                 prop[s[m][i]][iagemax+3] += weight[i];
-                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
+               }
-               }
              }
-           }
+           } /* end selection of waves */
          }
        }
-       for(i=(int)agemin; i <= (int)agemax+3; i++){
+       for(i=iagemin; i <= iagemax+3; i++){
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-             pp[jk] += freq[jk][m][i];
-         }
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=-1, pos=0; m <=0 ; m++)
-             pos += freq[jk][m][i];
-         }
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-             pp[jk] += freq[jk][m][i];
-         }
-         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
-         for(jk=1; jk <=nlstate ; jk++){
-           if( i <= (int) agemax){
-             if(pos>=1.e-5){
-               probs[i][jk][j1]= pp[jk]/pos;
-             }
-           }
-         }
-       }
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-     }
+           posprop += prop[jk][i];
-   }
+         }
+         for(jk=1; jk <=nlstate ; jk++){
-   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
+           if( i <=  iagemax){
-   free_vector(pp,1,nlstate);
+             if(posprop>=1.e-5){
+               probs[i][jk][j1]= prop[jk][i]/posprop;
- }  /* End of Freq */
+             }
+           }
+         }/* end jk */
+       }/* end i */
+     } /* end i1 */
+   } /* end k1 */
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+   /*free_vector(pp,1,nlstate);*/
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+ }  /* End of prevalence */
  /************* Waves Concatenation ***************/
- void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
+ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
  {
    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       Death is a valid wave (if date is known).
       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       and mw[mi+1][i]. dh depends on stepm.
       */
    int i, mi, m;
    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       double sum=0., jmean=0.;*/
+   int first;
    int j, k=0,jk, ju, jl;
    double sum=0.;
+   first=0;
    jmin=1e+5;
    jmax=-1;
    jmean=0.;
- Line 1422  void  concatwav(int wav[], int **dh, int
+ Line 2283  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 1437  void  concatwav(int wav[], int **dh, int
+ Line 2298  void  concatwav(int wav[], int **dh, int
      }
      wav[i]=mi;
-     if(mi==0)
+     if(mi==0){
-       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
+       nbwarn++;
-   }
+       if(first==0){
+         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! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+       }
+     } /* end mi==0 */
+   } /* End individuals */
    for(i=1; i<=imx; i++){
      for(mi=1; mi<wav[i];mi++){
        if (stepm <=0)
          dh[mi][i]=1;
        else{
-         if (s[mw[mi+1][i]][i] > nlstate) {
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
            if (agedc[i] < 2*AGESUP) {
-           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-           if(j==0) j=1;  /* Survives at least one month after exam */
+             if(j==0) j=1;  /* Survives at least one month after exam */
-           k=k+1;
+             else if(j<0){
-           if (j >= jmax) jmax=j;
+               nberr++;
-           if (j <= jmin) jmin=j;
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-           sum=sum+j;
+               j=1; /* Temporary Dangerous patch */
-           /*if (j<0) printf("j=%d num=%d \n",j,i); */
+               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+               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. You MUST fix the contradiction between dates.\n",stepm);
+             }
+             k=k+1;
+             if (j >= jmax){
+               jmax=j;
+               ijmax=i;
+             }
+             if (j <= jmin){
+               jmin=j;
+               ijmin=i;
+             }
+             sum=sum+j;
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
            }
          }
          else{
            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+ /*        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){
+             nberr++;
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+           }
            sum=sum+j;
          }
          jk= j/stepm;
          jl= j -jk*stepm;
          ju= j -(jk+1)*stepm;
-         if(jl <= -ju)
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-           dh[mi][i]=jk;
+           if(jl==0){
-         else
+             dh[mi][i]=jk;
-           dh[mi][i]=jk+1;
+             bh[mi][i]=0;
-         if(dh[mi][i]==0)
+           }else{ /* We want a negative bias in order to only have interpolation ie
-           dh[mi][i]=1; /* At least one step */
+                   * at the price of an extra matrix product in likelihood */
+             dh[mi][i]=jk+1;
+             bh[mi][i]=ju;
+           }
+         }else{
+           if(jl <= -ju){
+             dh[mi][i]=jk;
+             bh[mi][i]=jl;       /* bias is positive if real duration
+                                  * is higher than the multiple of stepm and negative otherwise.
+                                  */
+           }
+           else{
+             dh[mi][i]=jk+1;
+             bh[mi][i]=ju;
+           }
+           if(dh[mi][i]==0){
+             dh[mi][i]=1; /* At least one step */
+             bh[mi][i]=ju; /* At least one step */
+             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+           }
+         } /* end if mle */
        }
-     }
+     } /* end 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 (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   }
  /*********** Tricode ****************************/
  void tricode(int *Tvar, int **nbcode, int imx)
  {
-   int Ndum[20],ij=1, k, j, i;
+   int Ndum[20],ij=1, k, j, i, maxncov=19;
    int cptcode=0;
    cptcoveff=0;
-   for (k=0; k<19; k++) Ndum[k]=0;
+   for (k=0; k<maxncov; k++) Ndum[k]=0;
    for (k=1; k<=7; k++) ncodemax[k]=0;
    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
-     for (i=1; i<=imx; i++) {
+     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
-       ij=(int)(covar[Tvar[j]][i]);
+                                modality*/
-       Ndum[ij]++;
+       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+       Ndum[ij]++; /*store the modality */
        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-       if (ij > cptcode) cptcode=ij;
+       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+                                        Tvar[j]. If V=sex and male is 0 and
+                                        female is 1, then  cptcode=1.*/
      }
      for (i=0; i<=cptcode; i++) {
-       if(Ndum[i]!=0) ncodemax[j]++;
+       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 */
      }
-     ij=1;
+     ij=1;
      for (i=1; i<=ncodemax[j]; i++) {
-       for (k=0; k<=19; k++) {
+       for (k=0; k<= maxncov; k++) {
          if (Ndum[k] != 0) {
            nbcode[Tvar[j]][ij]=k;
+           /* 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; */
            ij++;
          }
- Line 1516  void tricode(int *Tvar, int **nbcode, in
+ Line 2440  void tricode(int *Tvar, int **nbcode, in
      }
    }
-  for (k=0; k<19; k++) Ndum[k]=0;
+  for (k=0; k< maxncov; k++) Ndum[k]=0;
   for (i=1; i<=ncovmodel-2; i++) {
-       ij=Tvar[i];
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-       Ndum[ij]++;
+    ij=Tvar[i];
-     }
+    Ndum[ij]++;
+  }
   ij=1;
-  for (i=1; i<=10; i++) {
+  for (i=1; i<= maxncov; i++) {
     if((Ndum[i]!=0) && (i<=ncovcol)){
-      Tvaraff[ij]=i;
+      Tvaraff[ij]=i; /*For printing */
       ij++;
     }
   }
-     cptcoveff=ij-1;
+  cptcoveff=ij-1; /*Number of simple covariates*/
  }
  /*********** Health Expectancies ****************/
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
+ void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
  {
-   /* Health expectancies */
+   /* Health expectancies, no variances */
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
    double age, agelim, hf;
-   double ***p3mat,***varhe;
+   double ***p3mat;
-   double **dnewm,**doldm;
+   double eip;
-   double *xp;
-   double **gp, **gm;
-   double ***gradg, ***trgradg;
-   int theta;
-   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
+   pstamp(ficreseij);
-   xp=vector(1,npar);
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-   dnewm=matrix(1,nlstate*2,1,npar);
-   doldm=matrix(1,nlstate*2,1,nlstate*2);
-   fprintf(ficreseij,"# Health expectancies\n");
    fprintf(ficreseij,"# Age");
-   for(i=1; i<=nlstate;i++)
+   for(i=1; i<=nlstate;i++){
-     for(j=1; j<=nlstate;j++)
+     for(j=1; j<=nlstate;j++){
-       fprintf(ficreseij," %1d-%1d (SE)",i,j);
+       fprintf(ficreseij," e%1d%1d ",i,j);
+     }
+     fprintf(ficreseij," e%1d. ",i);
+   }
    fprintf(ficreseij,"\n");
    if(estepm < stepm){
      printf ("Problem %d lower than %d\n",estepm, stepm);
    }
- Line 1569  void evsij(char fileres[], double ***eij
+ Line 2490  void evsij(char fileres[], double ***eij
     * 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 inbetween and thus overestimating or underestimating according
+    * 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
- Line 1591  void evsij(char fileres[], double ***eij
+ Line 2512  void evsij(char fileres[], double ***eij
    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
    agelim=AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   /* If stepm=6 months */
-     /* nhstepm age range expressed in number of stepm */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm);
-     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     /* if (stepm >= YEARM) hstepm=1;*/
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
-     gp=matrix(0,nhstepm,1,nlstate*2);
-     gm=matrix(0,nhstepm,1,nlstate*2);
      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
+ /* nhstepm age range expressed in number of stepm */
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   /* 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);
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   for (age=bage; age<=fage; age ++){
-     /* Computing Variances of health expectancies */
-      for(theta=1; theta <=npar; theta++){
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-       for(i=1; i<=npar; i++){
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+     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] );
        }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       fprintf(ficreseij,"%9.4f", eip );
+     }
+     fprintf(ficreseij,"\n");
+   }
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   printf("\n");
+   fprintf(ficlog,"\n");
-       cptj=0;
+ }
-       for(j=1; j<= nlstate; j++){
-         for(i=1; i<=nlstate; i++){
+ void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
-           cptj=cptj+1;
-           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
+ {
-             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+   /* Covariances of health expectancies eij and of total life expectancies according
-           }
+    to initial status i, ei. .
+   */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+   double age, agelim, hf;
+   double ***p3matp, ***p3matm, ***varhe;
+   double **dnewm,**doldm;
+   double *xp, *xm;
+   double **gp, **gm;
+   double ***gradg, ***trgradg;
+   int theta;
+   double eip, vip;
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+   xp=vector(1,npar);
+   xm=vector(1,npar);
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+   pstamp(ficresstdeij);
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+   fprintf(ficresstdeij,"# Age");
+   for(i=1; i<=nlstate;i++){
+     for(j=1; j<=nlstate;j++)
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+     fprintf(ficresstdeij," e%1d. ",i);
+   }
+   fprintf(ficresstdeij,"\n");
+   pstamp(ficrescveij);
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   fprintf(ficrescveij,"# Age");
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++){
+       cptj= (j-1)*nlstate+i;
+       for(i2=1; i2<=nlstate;i2++)
+         for(j2=1; j2<=nlstate;j2++){
+           cptj2= (j2-1)*nlstate+i2;
+           if(cptj2 <= cptj)
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
          }
+     }
+   fprintf(ficrescveij,"\n");
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else  hstepm=estepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
+    * if stepm=24 months pijx are given only every 2 years and by summing them
+    * we are calculating an estimate of the Life Expectancy assuming a linear
+    * progression in between and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+    * to compare the new estimate of Life expectancy with the same linear
+    * hypothesis. A more precise result, taking into account a more precise
+    * curvature will be obtained if estepm is as small as stepm. */
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like estepm months */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed only each two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+      results. So we changed our mind and took the option of the best precision.
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   /* If stepm=6 months */
+   /* nhstepm age range expressed in number of stepm */
+   agelim=AGESUP;
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   /* if (stepm >= YEARM) hstepm=1;*/
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+   for (age=bage; age<=fage; age ++){
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     /* Computing  Variances of health expectancies */
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+        decrease memory allocation */
+     for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-       for(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++){
+         for(i=1; i<=nlstate; i++){
-           cptj=cptj+1;
+           for(h=0; h<=nhstepm-1; h++){
-           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-             gm[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(j=1; j<= nlstate*2; 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++)
+       for(j=1; j<=nlstate*nlstate;j++)
-      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
-      for(h=0; h<=nhstepm-1; h++)
-       for(j=1; j<=nlstate*2;j++)
          for(theta=1; theta <=npar; theta++)
-         trgradg[h][j][theta]=gradg[h][theta][j];
+           trgradg[h][j][theta]=gradg[h][theta][j];
-      for(i=1;i<=nlstate*2;i++)
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-       for(j=1;j<=nlstate*2;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);
-     for(h=0;h<=nhstepm-1;h++){
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+      for(h=0;h<=nhstepm-1;h++){
        for(k=0;k<=nhstepm-1;k++){
-         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-         for(i=1;i<=nlstate*2;i++)
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-           for(j=1;j<=nlstate*2;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*2);
-     free_matrix(gp,0,nhstepm,1,nlstate*2);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,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*2,1,npar);
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-   free_matrix(doldm,1,nlstate*2,1,nlstate*2);
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  }
  /************ Variance ******************/
- void varevsij(char fileres[], 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)
+ 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);*/
-   double **newm;
+   /* double **newm;*/
    double **dnewm,**doldm;
+   double **dnewmp,**doldmp;
    int i, j, nhstepm, hstepm, h, nstepm ;
    int k, cptcode;
    double *xp;
-   double **gp, **gm;
+   double **gp, **gm;  /* for var eij */
-   double ***gradg, ***trgradg;
+   double ***gradg, ***trgradg; /*for var eij */
+   double **gradgp, **trgradgp; /* for var p point j */
+   double *gpp, *gmp; /* for var p point j */
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
    double ***p3mat;
    double age,agelim, hf;
+   double ***mobaverage;
    int theta;
+   char digit[4];
+   char digitp[25];
+   char fileresprobmorprev[FILENAMELENGTH];
-   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");
+   if(popbased==1){
+     if(mobilav!=0)
+       strcpy(digitp,"-populbased-mobilav-");
+     else strcpy(digitp,"-populbased-nomobil-");
+   }
+   else
+     strcpy(digitp,"-stablbased-");
+   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);
+     }
+   }
+   strcpy(fileresprobmorprev,"prmorprev");
+   sprintf(digit,"%-d",ij);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+   strcat(fileresprobmorprev,fileres);
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+     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++){
+     fprintf(ficresprobmorprev," p.%-d SE",j);
+     for(i=1; i<=nlstate;i++)
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+   }
+   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 ");
+   if(popbased==1)
+     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+   else
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
    fprintf(ficresvij,"# Age");
    for(i=1; i<=nlstate;i++)
      for(j=1; j<=nlstate;j++)
-       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
    fprintf(ficresvij,"\n");
    xp=vector(1,npar);
    dnewm=matrix(1,nlstate,1,npar);
    doldm=matrix(1,nlstate,1,nlstate);
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   gpp=vector(nlstate+1,nlstate+ndeath);
+   gmp=vector(nlstate+1,nlstate+ndeath);
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    if(estepm < stepm){
      printf ("Problem %d lower than %d\n",estepm, stepm);
- Line 1747  void varevsij(char fileres[], double ***
+ Line 2869  void varevsij(char fileres[], double ***
       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 only each two years of age and if
+      means that if the survival funtion is printed every 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.
    */
- Line 1761  void varevsij(char fileres[], double ***
+ Line 2883  void varevsij(char fileres[], double ***
      gp=matrix(0,nhstepm,1,nlstate);
      gm=matrix(0,nhstepm,1,nlstate);
      for(theta=1; theta <=npar; theta++){
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        if (popbased==1) {
-         for(i=1; i<=nlstate;i++)
+         if(mobilav ==0){
-           prlim[i][i]=probs[(int)age][i][ij];
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=probs[(int)age][i][ij];
+         }else{ /* mobilav */
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=mobaverage[(int)age][i][ij];
+         }
        }
        for(j=1; j<= nlstate; j++){
- Line 1779  void varevsij(char fileres[], double ***
+ Line 2907  void varevsij(char fileres[], double ***
              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
          }
        }
+       /* This for computing probability of death (h=1 means
-       for(i=1; i<=npar; i++) /* Computes gradient */
+          computed over hstepm matrices product = hstepm*stepm months)
+          as a weighted average of prlim.
+       */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+       }
+       /* end probability of death */
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        if (popbased==1) {
-         for(i=1; i<=nlstate;i++)
+         if(mobilav ==0){
-           prlim[i][i]=probs[(int)age][i][ij];
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=probs[(int)age][i][ij];
+         }else{ /* mobilav */
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=mobaverage[(int)age][i][ij];
+         }
        }
        for(j=1; j<= nlstate; j++){
- Line 1796  void varevsij(char fileres[], double ***
+ Line 2938  void varevsij(char fileres[], double ***
              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
          }
        }
+       /* This for computing probability of death (h=1 means
+          computed over hstepm matrices product = hstepm*stepm months)
+          as a weighted average of prlim.
+       */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+       }
+       /* end probability of death */
-       for(j=1; j<= nlstate; j++)
+       for(j=1; j<= nlstate; j++) /* vareij */
          for(h=0; h<=nhstepm; h++){
            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
          }
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+       }
      } /* End theta */
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-     for(h=0; h<=nhstepm; h++)
+     for(h=0; h<=nhstepm; h++) /* veij */
        for(j=1; j<=nlstate;j++)
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+       for(theta=1; theta <=npar; theta++)
+         trgradgp[j][theta]=gradgp[theta][j];
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate;j++)
- Line 1824  void varevsij(char fileres[], double ***
+ Line 2985  void varevsij(char fileres[], double ***
              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
        }
      }
+     /* pptj */
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+         varppt[j][i]=doldmp[j][i];
+     /* end ppptj */
+     /*  x centered again */
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+     if (popbased==1) {
+       if(mobilav ==0){
+         for(i=1; i<=nlstate;i++)
+           prlim[i][i]=probs[(int)age][i][ij];
+       }else{ /* mobilav */
+         for(i=1; i<=nlstate;i++)
+           prlim[i][i]=mobaverage[(int)age][i][ij];
+       }
+     }
+     /* This for computing probability of death (h=1 means
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+        as a weighted average of prlim.
+     */
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+     }
+     /* end probability of death */
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+       for(i=1; i<=nlstate;i++){
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+       }
+     }
+     fprintf(ficresprobmorprev,"\n");
      fprintf(ficresvij,"%.0f ",age );
      for(i=1; i<=nlstate;i++)
- Line 1837  void varevsij(char fileres[], double ***
+ Line 3038  void varevsij(char fileres[], double ***
      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    } /* End age */
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-   free_vector(xp,1,npar);
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-   free_matrix(doldm,1,nlstate,1,npar);
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   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");
+   /* 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 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 replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",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);
+ */
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
- }
+   free_vector(xp,1,npar);
+   free_matrix(doldm,1,nlstate,1,nlstate);
+   free_matrix(dnewm,1,nlstate,1,npar);
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficresprobmorprev);
+   fflush(ficgp);
+   fflush(fichtm);
+ }  /* end varevsij */
  /************ Variance of prevlim ******************/
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
+ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
  {
    /* Variance of prevalence limit */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
    double **newm;
    double **dnewm,**doldm;
    int i, j, nhstepm, hstepm;
- Line 1858  void varprevlim(char fileres[], double *
+ Line 3084  void varprevlim(char fileres[], double *
    double **gradg, **trgradg;
    double age,agelim;
    int theta;
-   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\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 1928  void varprevlim(char fileres[], double *
+ Line 3155  void varprevlim(char fileres[], double *
  }
  /************ Variance of one-step probabilities  ******************/
- void varprob(char fileres[], 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, i1, k1, j1, z1;
+   int i, j=0,  i1, k1, l1, t, tj;
-   int k=0, cptcode;
+   int k2, l2, j1,  z1;
+   int k=0,l, cptcode;
+   int first=1, first1;
+   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 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");
    strcat(fileresprob,fileres);
    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", fileresprob);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+   }
+   strcpy(fileresprobcov,"probcov");
+   strcat(fileresprobcov,fileres);
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcov);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   }
+   strcpy(fileresprobcor,"probcor");
+   strcat(fileresprobcor,fileres);
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcor);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
    }
    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
- fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   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");
-   for(i=1; i<=nlstate;i++)
+   pstamp(ficresprobcov);
-     for(j=1; j<=(nlstate+ndeath);j++)
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+   fprintf(ficresprobcov,"# Age");
+   pstamp(ficresprobcor);
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   fprintf(ficresprobcor,"# Age");
-   fprintf(ficresprob,"\n");
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=(nlstate+ndeath);j++){
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+     }
+  /* fprintf(ficresprob,"\n");
+   fprintf(ficresprobcov,"\n");
+   fprintf(ficresprobcor,"\n");
+  */
+  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);
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   first=1;
+   fprintf(ficgp,"\n# Routine varprob");
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+   fprintf(fichtm,"\n");
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+   file %s<br>\n",optionfilehtmcov);
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+ and drawn. It helps understanding how is the covariance between two incidences.\
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+ standard deviations wide on each axis. <br>\
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-   xp=vector(1,npar);
-   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
    cov[1]=1;
-   j=cptcoveff;
+   tj=cptcoveff;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
    j1=0;
-   for(k1=1; k1<=1;k1++){
+   for(t=1; t<=tj;t++){
-     for(i1=1; i1<=ncodemax[k1];i1++){
+     for(i1=1; i1<=ncodemax[t];i1++){
-     j1++;
+       j1++;
+       if  (cptcovn>0) {
-     if  (cptcovn>0) {
+         fprintf(ficresprob, "\n#********** Variable ");
-       fprintf(ficresprob, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprob, "**********\n#\n");
-       fprintf(ficresprob, "**********\n#");
+         fprintf(ficresprobcov, "\n#********** Variable ");
-     }
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprobcov, "**********\n#\n");
+         fprintf(ficgp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficgp, "**********\n#\n");
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+         fprintf(ficresprobcor, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprobcor, "**********\n#");
+       }
        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]]];
          }
          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,1,9);
+         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-         trgradg=matrix(1,9,1,npar);
+         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+         gp=vector(1,(nlstate)*(nlstate+ndeath));
-         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+         gm=vector(1,(nlstate)*(nlstate+ndeath));
          for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++)
-             xp[i] = x[i] + (i==theta ?delti[theta]:0);
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
            pmij(pmmij,cov,ncovmodel,xp,nlstate);
            k=0;
-           for(i=1; i<= (nlstate+ndeath); i++){
+           for(i=1; i<= (nlstate); i++){
              for(j=1; j<=(nlstate+ndeath);j++){
                k=k+1;
                gp[k]=pmmij[i][j];
- Line 2005  fprintf(ficresprob,"#One-step probabilit
+ Line 3303  fprintf(ficresprob,"#One-step probabilit
            }
            for(i=1; i<=npar; i++)
-             xp[i] = x[i] - (i==theta ?delti[theta]:0);
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
            pmij(pmmij,cov,ncovmodel,xp,nlstate);
            k=0;
-           for(i=1; i<=(nlstate+ndeath); i++){
+           for(i=1; i<=(nlstate); i++){
              for(j=1; j<=(nlstate+ndeath);j++){
                k=k+1;
                gm[k]=pmmij[i][j];
              }
            }
-           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
          }
-         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
            for(theta=1; theta <=npar; theta++)
              trgradg[j][theta]=gradg[theta][j];
-         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
+         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);
          k=0;
-         for(i=1; i<=(nlstate+ndeath); i++){
+         for(i=1; i<=(nlstate); i++){
            for(j=1; j<=(nlstate+ndeath);j++){
              k=k+1;
-             gm[k]=pmmij[i][j];
+             mu[k][(int) age]=pmmij[i][j];
            }
          }
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-      /*printf("\n%d ",(int)age);
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
+             varpij[i][j][(int)age] = doldm[i][j];
-        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-      }*/
+         /*printf("\n%d ",(int)age);
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+           }*/
          fprintf(ficresprob,"\n%d ",(int)age);
+         fprintf(ficresprobcov,"\n%d ",(int)age);
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-       }
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-     }
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+         }
-     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+         i=0;
-     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+         for (k=1; k<=(nlstate);k++){
-     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+           for (l=1; l<=(nlstate+ndeath);l++){
-   }
+             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++){
+               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 */
+       /* Confidence intervalle of pij  */
+       /*
+         fprintf(ficgp,"\nset noparametric;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);
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+       */
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+       first1=1;
+       for (k2=1; k2<=(nlstate);k2++){
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
+           if(l2==k2) continue;
+           j=(k2-1)*(nlstate+ndeath)+l2;
+           for (k1=1; k1<=(nlstate);k1++){
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
+               if(l1==k1) continue;
+               i=(k1-1)*(nlstate+ndeath)+l1;
+               if(i<=j) continue;
+               for (age=bage; age<=fage; age ++){
+                 if ((int)age %5==0){
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
+                   mu2=mu[j][(int) age]/stepm*YEARM;
+                   c12=cv12/sqrt(v1*v2);
+                   /* 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.;
+                   /* Eigen vectors */
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                   /*v21=sqrt(1.-v11*v11); *//* error */
+                   v21=(lc1-v1)/cv12*v11;
+                   v12=-v21;
+                   v22=v11;
+                   tnalp=v21/v11;
+                   if(first1==1){
+                     first1=0;
+                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                   }
+                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                   /*printf(fignu*/
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+                   if(first==1){
+                     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(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,\
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                   }else{
+                     first=0;
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                   }/* if first */
+                 } /* age mod 5 */
+               } /* end loop age */
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+               first=1;
+             } /*l12 */
+           } /* k12 */
+         } /*l1 */
+       }/* k1 */
+     } /* 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);
+   fclose(ficresprobcor);
+   fflush(ficgp);
+   fflush(fichtmcov);
  }
  /******************* Printing html file ***********/
  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
-                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
+                   int popforecast, int estepm ,\
-                   char version[], int popforecast, int estepm ,/* \ */
                    double jprev1, double mprev1,double anprev1, \
                    double jprev2, double mprev2,double anprev2){
    int jj1, k1, i1, cpt;
-   FILE *fichtm;
-   /*char optionfilehtm[FILENAMELENGTH];*/
-   strcpy(optionfilehtm,optionfile);
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-   strcat(optionfilehtm,".htm");
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+ </ul>");
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+    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,"\
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+    fprintf(fichtm,"\
+  - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n",
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+    fprintf(fichtm,"\
+  - Population projections by age and states: \
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
- \n
- Total number of observations=%d <br>\n
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
- <hr  size=\"2\" color=\"#EC5E5E\">
-  <ul><li>Parameter files<br>\n
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
-  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
-    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
-  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
-  - Life expectancies by age and initial health status (estepm=%2d months):
-    <a href=\"e%s\">e%s</a> <br>\n</li>", \
-   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
-  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
-  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
-  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
-  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
-  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
-  if(popforecast==1) fprintf(fichtm,"\n
-  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
-  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
-         <br>",fileres,fileres,fileres,fileres);
-  else
-    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
- fprintf(fichtm," <li>Graphs</li><p>");
   m=cptcoveff;
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- Line 2116  fprintf(fichtm," <li>Graphs</li><p>");
+ Line 3507  fprintf(fichtm," <li>Graphs</li><p>");
   jj1=0;
   for(k1=1; k1<=m;k1++){
     for(i1=1; i1<=ncodemax[k1];i1++){
-        jj1++;
+      jj1++;
-        if (cptcovn > 0) {
+      if (cptcovn > 0) {
-          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-          for (cpt=1; cpt<=cptcoveff;cpt++)
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-        }
+      }
-        /* Pij */
+      /* Pij */
-        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
- <img src=\"pe%s%d1.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);
+ <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-        /* Quasi-incidences */
+      /* Quasi-incidences */
-        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- <img src=\"pe%s%d2.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
-        /* Stable prevalence in each health state */
+ <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+        /* Period (stable) prevalence in each health state */
         for(cpt=1; cpt<nlstate;cpt++){
-          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
+          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
- <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         }
-     for(cpt=1; cpt<=nlstate;cpt++) {
+      for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
+         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> \
- interval) in state (%d): v%s%d%d.png <br>
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
- <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+      }
+    } /* end i1 */
+  }/* End k1 */
+  fprintf(fichtm,"</ul>");
+  fprintf(fichtm,"\
+ \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",
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+  fprintf(fichtm,"\
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+  fprintf(fichtm,"\
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+  fprintf(fichtm,"\
+  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+  fprintf(fichtm,"\
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+  fprintf(fichtm,"\
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+ /*      <br>",fileres,fileres,fileres,fileres); */
+ /*  else  */
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+  fflush(fichtm);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+  m=cptcoveff;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+  jj1=0;
+  for(k1=1; k1<=m;k1++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
+      jj1++;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
       }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
- health expectancies in states (1) and (2): e%s%d.png<br>
+ health expectancies in states (1) and (2): %s%d.png<br>\
- <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
- fprintf(fichtm,"\n</body>");
+    } /* end i1 */
-    }
+  }/* End k1 */
-    }
+  fprintf(fichtm,"</ul>");
- fclose(fichtm);
+  fflush(fichtm);
  }
  /******************* Gnuplot file **************/
- void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   char dirfileres[132],optfileres[132];
    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
    int ng;
-   strcpy(optionfilegnuplot,optionfilefiname);
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-   strcat(optionfilegnuplot,".gp.txt");
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-     printf("Problem with file %s",optionfilegnuplot);
+ /*   } */
-   }
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     /*#endif */
+   m=pow(2,cptcoveff);
- #ifdef windows
+   strcpy(dirfileres,optionfilefiname);
-     fprintf(ficgp,"cd \"%s\" \n",pathc);
+   strcpy(optfileres,"vpl");
- #endif
- m=pow(2,cptcoveff);
   /* 1eme*/
    for (cpt=1; cpt<= nlstate ; cpt ++) {
     for (k1=1; k1<= m ; 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,"set xlabel \"Age\" \n\
+ set ylabel \"Probability\" \n\
+ set ter png small\n\
+ set size 0.65,0.65\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
- #ifdef windows
-      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
-      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
- #endif
- #ifdef unix
- fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
- fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
- #endif
- for (i=1; i<= nlstate ; i ++) {
-   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
-     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
-     for (i=1; i<= nlstate ; i ++) {
-   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
-   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
-   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   else fprintf(ficgp," \%%*lf (\%%*lf)");
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
+      }
-      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
+      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
- #ifdef unix
+      for (i=1; i<= nlstate ; i ++) {
- fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
- #endif
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
+      }
+      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+      for (i=1; i<= nlstate ; i ++) {
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
+      }
+      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     }
    }
    /*2 eme*/
    for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
      for (i=1; i<= nlstate+1 ; i ++) {
        k=2*i;
-       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
-   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-   else fprintf(ficgp," \%%*lf (\%%*lf)");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
+       }
        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
+       }
        fprintf(ficgp,"\" t\"\" w l 0,");
-      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
-   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-   else fprintf(ficgp," \%%*lf (\%%*lf)");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
+       }
        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
        else fprintf(ficgp,"\" t\"\" w l 0,");
      }
    }
    /*3eme*/
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<= nlstate ; cpt ++) {
-       k=2+nlstate*(2*cpt-2);
+       /*       k=2+nlstate*(2*cpt-2); */
-       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       k=2+(nlstate+1)*(cpt-1);
-       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+       fprintf(ficgp,"set ter png small\n\
+ set size 0.65,0.65\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
- fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
- fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
- fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
- */
+       */
        for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
        }
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
      }
    }
-   /* CV preval stat */
+   /* CV preval stable (period) */
-     for (k1=1; k1<= m ; k1 ++) {
+   for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<nlstate ; cpt ++) {
+     for (cpt=1; cpt<=nlstate ; cpt ++) {
        k=3;
-       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter png small\nset size 0.65,0.65\n\
+ unset log y\n\
+ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
        for (i=1; i< nlstate ; i ++)
          fprintf(ficgp,"+$%d",k+i+1);
        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
        l=3+(nlstate+ndeath)*cpt;
-       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
+       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
        for (i=1; i< nlstate ; i ++) {
          l=3+(nlstate+ndeath)*cpt;
          fprintf(ficgp,"+$%d",l+i+1);
- Line 2276  fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ Line 3731  fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
    }
    /* proba elementaires */
-    for(i=1,jk=1; i <=nlstate; i++){
+   for(i=1,jk=1; i <=nlstate; i++){
      for(k=1; k <=(nlstate+ndeath); k++){
        if (k != i) {
          for(j=1; j <=ncovmodel; j++){
            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
            jk++;
            fprintf(ficgp,"\n");
- Line 2291  fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ Line 3745  fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       for(jk=1; jk <=m; jk++) {
-        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
+        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
         if (ng==2)
           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
         else
- Line 2303  fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ Line 3757  fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           for(k=1; k<=(nlstate+ndeath); k++) {
             if (k != k2){
               if(ng==2)
-                fprintf(ficgp," %f*exp(p%d+p%d*x",stepm/YEARM,i,i+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;
- Line 2334  fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ Line 3788  fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
               i=i+ncovmodel;
             }
-          }
+          } /* end k */
-        }
+        } /* end k2 */
-      }
+      } /* end jk */
-    }
+    } /* end ng */
-    fclose(ficgp);
+    fflush(ficgp);
  }  /* end gnuplot */
  /*************** Moving average **************/
- void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
    int i, cpt, cptcod;
-     for (agedeb=ageminpar; agedeb<=fage; agedeb++)
+   int modcovmax =1;
+   int mobilavrange, mob;
+   double age;
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+                            a covariate has 2 modalities */
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+     if(mobilav==1) mobilavrange=5; /* default */
+     else mobilavrange=mobilav;
+     for (age=bage; age<=fage; age++)
        for (i=1; i<=nlstate;i++)
-         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-           mobaverage[(int)agedeb][i][cptcod]=0.;
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+     /* We keep the original values on the extreme ages bage, fage and for
-     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-       for (i=1; i<=nlstate;i++){
+        we use a 5 terms etc. until the borders are no more concerned.
-         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+     */
-           for (cpt=0;cpt<=4;cpt++){
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+         for (i=1; i<=nlstate;i++){
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+               }
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
            }
-           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
          }
-       }
+       }/* end age */
-     }
+     }/* end mob */
+   }else return -1;
- }
+   return 0;
+ }/* End movingaverage */
  /************** Forecasting ******************/
- prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
+ prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+   /* proj1, year, month, day of starting projection
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+      agemin, agemax range of age
+      dateprev1 dateprev2 range of dates during which prevalence is computed
+      anproj2 year of en of projection (same day and month as proj1).
+   */
+   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
    int *popage;
-   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double agec; /* generic age */
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
    double *popeffectif,*popcount;
    double ***p3mat;
+   double ***mobaverage;
    char fileresf[FILENAMELENGTH];
-  agelim=AGESUP;
+   agelim=AGESUP;
- calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
    strcpy(fileresf,"f");
    strcat(fileresf,fileres);
    if((ficresf=fopen(fileresf,"w"))==NULL) {
      printf("Problem with forecast resultfile: %s\n", fileresf);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
    }
    printf("Computing forecasting: result on file '%s' \n", fileresf);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
    if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   if (mobilav==1) {
+   if (mobilav!=0) {
      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     movingaverage(agedeb, fage, ageminpar, mobaverage);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
    }
    stepsize=(int) (stepm+YEARM-1)/YEARM;
    if (stepm<=12) stepsize=1;
+   if(estepm < stepm){
-   agelim=AGESUP;
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
-   hstepm=1;
+   else  hstepm=estepm;
    hstepm=hstepm/stepm;
-   yp1=modf(dateintmean,&yp);
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+                                fractional in yp1 */
    anprojmean=yp;
    yp2=modf((yp1*12),&yp);
    mprojmean=yp;
- Line 2410  calagedate=(anproj1+mproj1/12.+jproj1/36
+ Line 3893  calagedate=(anproj1+mproj1/12.+jproj1/36
    jprojmean=yp;
    if(jprojmean==0) jprojmean=1;
    if(mprojmean==0) jprojmean=1;
+   i1=cptcoveff;
+   if (cptcovn < 1){i1=1;}
-   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-   for(cptcov=1;cptcov<=i2;cptcov++){
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
+ /*            if (h==(int)(YEARM*yearp)){ */
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
        k=k+1;
        fprintf(ficresf,"\n#******");
        for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        }
        fprintf(ficresf,"******\n");
-       fprintf(ficresf,"# StartingAge FinalAge");
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
+       for(j=1; j<=nlstate+ndeath;j++){
+         for(i=1; i<=nlstate;i++)
+           fprintf(ficresf," p%d%d",i,j);
-       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
+         fprintf(ficresf," p.%d",j);
+       }
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
          fprintf(ficresf,"\n");
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+         for (agec=fage; agec>=(ageminpar-1); agec--){
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
            nhstepm = nhstepm/hstepm;
            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);
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
            for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedate+YEARM*cpt)) {
+             if (h*hstepm/YEARM*stepm ==yearp) {
-               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
+               fprintf(ficresf,"\n");
+               for(j=1;j<=cptcoveff;j++)
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
              }
              for(j=1; j<=nlstate+ndeath;j++) {
-               kk1=0.;kk2=0;
+               ppij=0.;
                for(i=1; i<=nlstate;i++) {
                  if (mobilav==1)
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                  else {
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                  }
+                 if (h*hstepm/YEARM*stepm== yearp) {
-               }
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-               if (h==(int)(calagedate+12*cpt)){
+                 }
-                 fprintf(ficresf," %.3f", kk1);
+               } /* end i */
+               if (h*hstepm/YEARM*stepm==yearp) {
+                 fprintf(ficresf," %.3f", ppij);
                }
-             }
+             }/* end j */
-           }
+           } /* end h */
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
+         } /* end agec */
-       }
+       } /* end yearp */
-     }
+     } /* end cptcod */
-   }
+   } /* end  cptcov */
-   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    fclose(ficresf);
  }
- /************** Forecasting ******************/
+ /************** Forecasting *****not tested NB*************/
  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
    int *popage;
-   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double calagedatem, agelim, kk1, kk2;
    double *popeffectif,*popcount;
    double ***p3mat,***tabpop,***tabpopprev;
+   double ***mobaverage;
    char filerespop[FILENAMELENGTH];
    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    agelim=AGESUP;
-   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    strcpy(filerespop,"pop");
    strcat(filerespop,fileres);
    if((ficrespop=fopen(filerespop,"w"))==NULL) {
      printf("Problem with forecast resultfile: %s\n", filerespop);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
    }
    printf("Computing forecasting: result on file '%s' \n", filerespop);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
    if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   if (mobilav==1) {
+   if (mobilav!=0) {
      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     movingaverage(agedeb, fage, ageminpar, mobaverage);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
    }
    stepsize=(int) (stepm+YEARM-1)/YEARM;
- Line 2510  populforecast(char fileres[], double anp
+ Line 4011  populforecast(char fileres[], double anp
    if (popforecast==1) {
      if((ficpop=fopen(popfile,"r"))==NULL) {
        printf("Problem with population file : %s\n",popfile);exit(0);
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
      }
      popage=ivector(0,AGESUP);
      popeffectif=vector(0,AGESUP);
- Line 2522  populforecast(char fileres[], double anp
+ Line 4024  populforecast(char fileres[], double anp
      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
    }
-   for(cptcov=1;cptcov<=i2;cptcov++){
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
        k=k+1;
        fprintf(ficrespop,"\n#******");
- Line 2537  populforecast(char fileres[], double anp
+ Line 4039  populforecast(char fileres[], double anp
        for (cpt=0; cpt<=0;cpt++) {
          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
            nhstepm = nhstepm/hstepm;
- Line 2546  populforecast(char fileres[], double anp
+ Line 4048  populforecast(char fileres[], double anp
            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
            for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedate+YEARM*cpt)) {
+             if (h==(int) (calagedatem+YEARM*cpt)) {
                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
              }
              for(j=1; j<=nlstate+ndeath;j++) {
- Line 2558  populforecast(char fileres[], double anp
+ Line 4060  populforecast(char fileres[], double anp
                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                  }
                }
-               if (h==(int)(calagedate+12*cpt)){
+               if (h==(int)(calagedatem+12*cpt)){
                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                    /*fprintf(ficrespop," %.3f", kk1);
                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
- Line 2569  populforecast(char fileres[], double anp
+ Line 4071  populforecast(char fileres[], double anp
                  for(j=1; j<=nlstate;j++){
                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
                  }
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
              }
-             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
            }
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- Line 2583  populforecast(char fileres[], double anp
+ Line 4085  populforecast(char fileres[], double anp
        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
            nhstepm = nhstepm/hstepm;
- Line 2591  populforecast(char fileres[], double anp
+ Line 4093  populforecast(char fileres[], double anp
            oldm=oldms;savm=savms;
            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
            for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedate+YEARM*cpt)) {
+             if (h==(int) (calagedatem+YEARM*cpt)) {
                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
              }
              for(j=1; j<=nlstate+ndeath;j++) {
- Line 2599  populforecast(char fileres[], double anp
+ Line 4101  populforecast(char fileres[], double anp
                for(i=1; i<=nlstate;i++) {
                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
                }
-               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
              }
            }
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- Line 2608  populforecast(char fileres[], double anp
+ Line 4110  populforecast(char fileres[], double anp
     }
    }
-   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    if (popforecast==1) {
      free_ivector(popage,0,AGESUP);
- Line 2618  populforecast(char fileres[], double anp
+ Line 4120  populforecast(char fileres[], double anp
    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    fclose(ficrespop);
+ } /* End of popforecast */
+ int fileappend(FILE *fichier, char *optionfich)
+ {
+   if((fichier=fopen(optionfich,"a"))==NULL) {
+     printf("Problem with file: %s\n", optionfich);
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+     return (0);
+   }
+   fflush(fichier);
+   return (1);
+ }
+ /**************** function prwizard **********************/
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+ {
+   /* Wizard to print covariance matrix template */
+   char ca[32], cb[32], cc[32];
+   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+   int numlinepar;
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   for(i=1; i <=nlstate; i++){
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
+       jj++;
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+       printf("%1d%1d",i,j);
+       fprintf(ficparo,"%1d%1d",i,j);
+       for(k=1; k<=ncovmodel;k++){
+         /*        printf(" %lf",param[i][j][k]); */
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+         printf(" 0.");
+         fprintf(ficparo," 0.");
+       }
+       printf("\n");
+       fprintf(ficparo,"\n");
+     }
+   }
+   printf("# Scales (for hessian or gradient estimation)\n");
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   for(i=1; i <=nlstate; i++){
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
+       jj++;
+       fprintf(ficparo,"%1d%1d",i,j);
+       printf("%1d%1d",i,j);
+       fflush(stdout);
+       for(k=1; k<=ncovmodel;k++){
+         /*      printf(" %le",delti3[i][j][k]); */
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+         printf(" 0.");
+         fprintf(ficparo," 0.");
+       }
+       numlinepar++;
+       printf("\n");
+       fprintf(ficparo,"\n");
+     }
+   }
+   printf("# Covariance matrix\n");
+ /* # 121 Var(a12)\n\ */
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   fflush(stdout);
+   fprintf(ficparo,"# Covariance matrix\n");
+   /* # 121 Var(a12)\n\ */
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   /* #   ...\n\ */
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+   for(itimes=1;itimes<=2;itimes++){
+     jj=0;
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j==i) continue;
+         for(k=1; k<=ncovmodel;k++){
+           jj++;
+           ca[0]= k+'a'-1;ca[1]='\0';
+           if(itimes==1){
+             printf("#%1d%1d%d",i,j,k);
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+           }else{
+             printf("%1d%1d%d",i,j,k);
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
+             /*  printf(" %.5le",matcov[i][j]); */
+           }
+           ll=0;
+           for(li=1;li <=nlstate; li++){
+             for(lj=1;lj <=nlstate+ndeath; lj++){
+               if(lj==li) continue;
+               for(lk=1;lk<=ncovmodel;lk++){
+                 ll++;
+                 if(ll<=jj){
+                   cb[0]= lk +'a'-1;cb[1]='\0';
+                   if(ll<jj){
+                     if(itimes==1){
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                     }else{
+                       printf(" 0.");
+                       fprintf(ficparo," 0.");
+                     }
+                   }else{
+                     if(itimes==1){
+                       printf(" Var(%s%1d%1d)",ca,i,j);
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+                     }else{
+                       printf(" 0.");
+                       fprintf(ficparo," 0.");
+                     }
+                   }
+                 }
+               } /* end lk */
+             } /* end lj */
+           } /* end li */
+           printf("\n");
+           fprintf(ficparo,"\n");
+           numlinepar++;
+         } /* end k*/
+       } /*end j */
+     } /* end i */
+   } /* end itimes */
+ } /* end of prwizard */
+ /******************* Gompertz Likelihood ******************************/
+ double gompertz(double x[])
+ {
+   double A,B,L=0.0,sump=0.,num=0.;
+   int i,n=0; /* n is the size of the sample */
+   for (i=0;i<=imx-1 ; i++) {
+     sump=sump+weight[i];
+     /*    sump=sump+1;*/
+     num=num+1;
+   }
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+   for (i=1;i<=imx ; i++)
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+       if (cens[i] == 0 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
+         L=L+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+       }
+     }
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   return -2*L*num/sump;
+ }
+ /******************* Printing html file ***********/
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   int imx,  double p[],double **matcov,double agemortsup){
+   int i,k;
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   for (i=1;i<=2;i++)
+     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+   fprintf(fichtm,"</ul>");
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+  for (k=agegomp;k<(agemortsup-2);k++)
+    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+   fflush(fichtm);
  }
+ /******************* Gnuplot file **************/
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   char dirfileres[132],optfileres[132];
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   int ng;
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     /*#endif */
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+   fprintf(ficgp, "set ter png small\n set log y\n");
+   fprintf(ficgp, "set size 0.65,0.65\n");
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+ }
  /***********************************************/
  /**************** Main Program *****************/
  /***********************************************/
  int main(int argc, char *argv[])
  {
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+   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;
+   char ca[32], cb[32], cc[32];
+   char dummy[]="                         ";
+   /*  FILE *fichtm; *//* Html File */
+   /* FILE *ficgp;*/ /*Gnuplot File */
+   struct stat info;
    double agedeb, agefin,hf;
    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
- Line 2636  int main(int argc, char *argv[])
+ Line 4371  int main(int argc, char *argv[])
    double dum; /* Dummy variable */
    double ***p3mat;
+   double ***mobaverage;
    int *indx;
    char line[MAXLINE], linepar[MAXLINE];
-   char title[MAXLINE];
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+   char pathr[MAXLINE], pathimach[MAXLINE];
-   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+   char **bp, *tok, *val; /* pathtot */
-   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
-   char filerest[FILENAMELENGTH];
-   char fileregp[FILENAMELENGTH];
-   char popfile[FILENAMELENGTH];
-   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
    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 jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
+   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
    int mobilav=0,popforecast=0;
    int hstepm, nhstepm;
-   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
+   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;
- Line 2671  int main(int argc, char *argv[])
+ Line 4404  int main(int argc, char *argv[])
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
    double kk1, kk2;
-   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double **ximort;
-   char version[80]="Imach version 0.8d, May 2002, INED-EUROREVES ";
    char *alph[]={"a","a","b","c","d","e"}, str[4];
+   int *dcwave;
    char z[1]="c", occ;
- #include <sys/time.h>
- #include <time.h>
    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+   char  *strt, strtend[80];
+   char *stratrunc;
+   int lstra;
+   long total_usecs;
-   /* long total_usecs;
+ /*   setlocale (LC_ALL, ""); */
-   struct timeval start_time, end_time;
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
-   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   (void) gettimeofday(&start_time,&tzp);
+   curr_time=start_time;
+   tm = *localtime(&start_time.tv_sec);
+   tmg = *gmtime(&start_time.tv_sec);
+   strcpy(strstart,asctime(&tm));
+ /*  printf("Localtime (at start)=%s",strstart); */
+ /*  tp.tv_sec = tp.tv_sec +86400; */
+ /*  tm = *localtime(&start_time.tv_sec); */
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ /*   tp.tv_sec = mktime(&tmg); */
+ /*   strt=asctime(&tmg); */
+ /*   printf("Time(after) =%s",strstart);  */
+ /*  (void) time (&time_value);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+ *  tm = *localtime(&time_value);
+ *  strstart=asctime(&tm);
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+ */
+   nberr=0; /* Number of errors and warnings */
+   nbwarn=0;
    getcwd(pathcd, size);
-   printf("\n%s",version);
+   printf("\n%s\n%s",version,fullversion);
    if(argc <=1){
      printf("\nEnter the parameter file name: ");
-     scanf("%s",pathtot);
+     fgets(pathr,FILENAMELENGTH,stdin);
+     i=strlen(pathr);
+     if(pathr[i-1]=='\n')
+       pathr[i-1]='\0';
+    for (tok = pathr; tok != NULL; ){
+       printf("Pathr |%s|\n",pathr);
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+       printf("val= |%s| pathr=%s\n",val,pathr);
+       strcpy (pathtot, val);
+       if(pathr[0] == '\0') break; /* Dirty */
+     }
    }
    else{
      strcpy(pathtot,argv[1]);
    }
-   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
    /*cygwin_split_path(pathtot,path,optionfile);
      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
    /* cutv(path,optionfile,pathtot,'\\');*/
+   /* Split argv[0], imach program to get pathimach */
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+  /*   strcpy(pathimach,argv[0]); */
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-   chdir(path);
+   chdir(path); /* Can be a relative path */
-   replace(pathc,path);
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+     printf("Current directory %s!\n",pathcd);
- /*-------- arguments in the command line --------*/
+   strcpy(command,"mkdir ");
+   strcat(command,optionfilefiname);
+   if((outcmd=system(command)) != 0){
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+     /* fclose(ficlog); */
+ /*     exit(1); */
+   }
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
+ /*     perror("mkdir"); */
+ /*   } */
+   /*-------- arguments in the command line --------*/
+   /* Log file */
+   strcat(filelog, optionfilefiname);
+   strcat(filelog,".log");    /* */
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
+     printf("Problem with logfile %s\n",filelog);
+     goto end;
+   }
+   fprintf(ficlog,"Log filename:%s\n",filelog);
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+  path=%s \n\
+  optionfile=%s\n\
+  optionfilext=%s\n\
+  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("Local time (at start):%s",strstart);
+   fprintf(ficlog,"Local time (at start): %s",strstart);
+   fflush(ficlog);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+   /* */
    strcpy(fileres,"r");
    strcat(fileres, optionfilefiname);
    strcat(fileres,".txt");    /* Other files have txt extension */
- Line 2717  int main(int argc, char *argv[])
+ Line 4530  int main(int argc, char *argv[])
    if((ficpar=fopen(optionfile,"r"))==NULL)    {
      printf("Problem with optionfile %s\n",optionfile);
+     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+     fflush(ficlog);
      goto end;
    }
    strcpy(filereso,"o");
    strcat(filereso,fileres);
-   if((ficparo=fopen(filereso,"w"))==NULL) {
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-     printf("Problem with Output resultfile: %s\n", filereso);goto end;
+     printf("Problem with Output resultfile: %s\n", filereso);
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     fflush(ficlog);
+     goto end;
    }
    /* Reads comments: lines beginning with '#' */
+   numlinepar=0;
    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
+     numlinepar++;
      puts(line);
      fputs(line,ficparo);
+     fputs(line,ficlog);
    }
    ungetc(c,ficpar);
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   numlinepar++;
    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
- while((c=getc(ficpar))=='#' && c!= EOF){
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fflush(ficlog);
+   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
+     numlinepar++;
      puts(line);
      fputs(line,ficparo);
+     fputs(line,ficlog);
    }
    ungetc(c,ficpar);
    covar=matrix(0,NCOVMAX,1,n);
-   cptcovn=0;
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
-   ncovmodel=2+cptcovn;
+   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-   /* Read guess parameters */
-   /* Reads comments: lines beginning with '#' */
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+   delti=delti3[1][1];
-     ungetc(c,ficpar);
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-     fgets(line, MAXLINE, ficpar);
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-     puts(line);
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     fputs(line,ficparo);
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     fclose (ficparo);
+     fclose (ficlog);
+     goto end;
+     exit(0);
    }
-   ungetc(c,ficpar);
+   else if(mle==-3) {
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     for(i=1; i <=nlstate; i++)
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     for(j=1; j <=nlstate+ndeath-1; j++){
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
+     matcov=matrix(1,npar,1,npar);
-       fprintf(ficparo,"%1d%1d",i1,j1);
+   }
-       printf("%1d%1d",i,j);
+   else{
-       for(k=1; k<=ncovmodel;k++){
+     /* Read guess parameters */
-         fscanf(ficpar," %lf",&param[i][j][k]);
+     /* Reads comments: lines beginning with '#' */
-         printf(" %lf",param[i][j][k]);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-         fprintf(ficparo," %lf",param[i][j][k]);
+       ungetc(c,ficpar);
-       }
+       fgets(line, MAXLINE, ficpar);
-       fscanf(ficpar,"\n");
+       numlinepar++;
-       printf("\n");
+       puts(line);
-       fprintf(ficparo,"\n");
+       fputs(line,ficparo);
+       fputs(line,ficlog);
      }
+     ungetc(c,ficpar);
-     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     for(i=1; i <=nlstate; i++){
+       j=0;
+       for(jj=1; jj <=nlstate+ndeath; jj++){
+         if(jj==i) continue;
+         j++;
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ((i1 != i) && (j1 != j)){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+ It might be a problem of design; if ncovcol and the model are correct\n \
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+           exit(1);
+         }
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         if(mle==1)
+           printf("%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i,j);
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar," %lf",&param[i][j][k]);
+           if(mle==1){
+             printf(" %lf",param[i][j][k]);
+             fprintf(ficlog," %lf",param[i][j][k]);
+           }
+           else
+             fprintf(ficlog," %lf",param[i][j][k]);
+           fprintf(ficparo," %lf",param[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         if(mle==1)
+           printf("\n");
+         fprintf(ficlog,"\n");
+         fprintf(ficparo,"\n");
+       }
+     }
+     fflush(ficlog);
-   p=param[1][1];
+     p=param[1][1];
-   /* Reads comments: lines beginning with '#' */
+     /* Reads comments: lines beginning with '#' */
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       puts(line);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     for(i=1; i <=nlstate; i++){
-   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
+       for(j=1; j <=nlstate+ndeath-1; j++){
-   for(i=1; i <=nlstate; i++){
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     for(j=1; j <=nlstate+ndeath-1; j++){
+         if ((i1-i)*(j1-j)!=0){
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-       printf("%1d%1d",i,j);
+           exit(1);
-       fprintf(ficparo,"%1d%1d",i1,j1);
+         }
-       for(k=1; k<=ncovmodel;k++){
+         printf("%1d%1d",i,j);
-         fscanf(ficpar,"%le",&delti3[i][j][k]);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-         printf(" %le",delti3[i][j][k]);
+         fprintf(ficlog,"%1d%1d",i1,j1);
-         fprintf(ficparo," %le",delti3[i][j][k]);
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
+           printf(" %le",delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
+           fprintf(ficlog," %le",delti3[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         printf("\n");
+         fprintf(ficparo,"\n");
+         fprintf(ficlog,"\n");
        }
-       fscanf(ficpar,"\n");
-       printf("\n");
-       fprintf(ficparo,"\n");
      }
-   }
+     fflush(ficlog);
-   delti=delti3[1][1];
+     delti=delti3[1][1];
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-   /* Reads comments: lines beginning with '#' */
+     /* Reads comments: lines beginning with '#' */
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       puts(line);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   matcov=matrix(1,npar,1,npar);
+     matcov=matrix(1,npar,1,npar);
-   for(i=1; i <=npar; i++){
+     for(i=1; i <=npar; i++){
-     fscanf(ficpar,"%s",&str);
+       fscanf(ficpar,"%s",&str);
-     printf("%s",str);
+       if(mle==1)
-     fprintf(ficparo,"%s",str);
+         printf("%s",str);
-     for(j=1; j <=i; j++){
+       fprintf(ficlog,"%s",str);
-       fscanf(ficpar," %le",&matcov[i][j]);
+       fprintf(ficparo,"%s",str);
-       printf(" %.5le",matcov[i][j]);
+       for(j=1; j <=i; j++){
-       fprintf(ficparo," %.5le",matcov[i][j]);
+         fscanf(ficpar," %le",&matcov[i][j]);
+         if(mle==1){
+           printf(" %.5le",matcov[i][j]);
+         }
+         fprintf(ficlog," %.5le",matcov[i][j]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
+       }
+       fscanf(ficpar,"\n");
+       numlinepar++;
+       if(mle==1)
+         printf("\n");
+       fprintf(ficlog,"\n");
+       fprintf(ficparo,"\n");
      }
-     fscanf(ficpar,"\n");
+     for(i=1; i <=npar; i++)
-     printf("\n");
+       for(j=i+1;j<=npar;j++)
-     fprintf(ficparo,"\n");
+         matcov[i][j]=matcov[j][i];
-   }
-   for(i=1; i <=npar; i++)
+     if(mle==1)
-     for(j=i+1;j<=npar;j++)
+       printf("\n");
-       matcov[i][j]=matcov[j][i];
+     fprintf(ficlog,"\n");
-   printf("\n");
+     fflush(ficlog);
+     /*-------- Rewriting parameter file ----------*/
-     /*-------- Rewriting paramater file ----------*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
-      strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     strcat(rfileres,".");    /* */
-      strcat(rfileres,".");    /* */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-      strcat(rfileres,optionfilext);    /* Other files have txt extension */
      if((ficres =fopen(rfileres,"w"))==NULL) {
        printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
      }
      fprintf(ficres,"#%s\n",version);
+   }    /* End of mle != -3 */
-     /*-------- data file ----------*/
-     if((fic=fopen(datafile,"r"))==NULL)    {
-       printf("Problem with datafile: %s\n", datafile);goto end;
-     }
-     n= lastobs;
-     severity = vector(1,maxwav);
-     outcome=imatrix(1,maxwav+1,1,n);
-     num=ivector(1,n);
-     moisnais=vector(1,n);
-     annais=vector(1,n);
-     moisdc=vector(1,n);
-     andc=vector(1,n);
-     agedc=vector(1,n);
-     cod=ivector(1,n);
-     weight=vector(1,n);
-     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);
-     adl=imatrix(1,maxwav+1,1,n);
-     tab=ivector(1,NCOVMAX);
-     ncodemax=ivector(1,8);
-     i=1;
-     while (fgets(line, MAXLINE, fic) != NULL)    {
-       if ((i >= firstobs) && (i <=lastobs)) {
-         for (j=maxwav;j>=1;j--){
-           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
-           strcpy(line,stra);
-           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
-           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
-         }
-         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
-         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
-         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
-         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
-         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
-         for (j=ncovcol;j>=1;j--){
-           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
-         }
-         num[i]=atol(stra);
-         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
-         i=i+1;
+   /*-------- data file ----------*/
+   if((fic=fopen(datafile,"r"))==NULL)    {
+     printf("Problem while opening datafile: %s\n", datafile);goto end;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+   }
+   n= lastobs;
+   severity = vector(1,maxwav);
+   outcome=imatrix(1,maxwav+1,1,n);
+   num=lvector(1,n);
+   moisnais=vector(1,n);
+   annais=vector(1,n);
+   moisdc=vector(1,n);
+   andc=vector(1,n);
+   agedc=vector(1,n);
+   cod=ivector(1,n);
+   weight=vector(1,n);
+   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);
+   tab=ivector(1,NCOVMAX);
+   ncodemax=ivector(1,8);
+   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;
+     }
+     for (j=maxwav;j>=1;j--){
+       cutv(stra, strb,line,' ');
+       errno=0;
+       lval=strtol(strb,&endptr,10);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+       if( strb[0]=='\0' || (*endptr != '\0')){
+         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+         exit(1);
        }
+       s[j][i]=lval;
+       strcpy(line,stra);
+       cutv(stra, strb,line,' ');
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       }
+       else  if(iout=sscanf(strb,"%s.") != 0){
+         month=99;
+         year=9999;
+       }else{
+         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+         exit(1);
+       }
+       anint[j][i]= (double) year;
+       mint[j][i]= (double)month;
+       strcpy(line,stra);
+     } /* ENd Waves */
+     cutv(stra, strb,line,' ');
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+       exit(1);
+     }
+     andc[i]=(double) year;
+     moisdc[i]=(double) month;
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
+     else  if(iout=sscanf(strb,"%s.") != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
+       exit(1);
+     }
+     annais[i]=(double)(year);
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     errno=0;
+     dval=strtod(strb,&endptr);
+     if( strb[0]=='\0' || (*endptr != '\0')){
+       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       exit(1);
+     }
+     weight[i]=dval;
+     strcpy(line,stra);
+     for (j=ncovcol;j>=1;j--){
+       cutv(stra, strb,line,' ');
+       errno=0;
+       lval=strtol(strb,&endptr,10);
+       if( strb[0]=='\0' || (*endptr != '\0')){
+         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
+         exit(1);
+       }
+       if(lval <-1 || lval >1){
+         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n \
+  Exiting.\n",lval,linei, i,line,j);
+         exit(1);
+       }
+       covar[j][i]=(double)(lval);
+       strcpy(line,stra);
      }
-     /* printf("ii=%d", ij);
+     lstra=strlen(stra);
-        scanf("%d",i);*/
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       stratrunc = &(stra[lstra-9]);
+       num[i]=atol(stratrunc);
+     }
+     else
+       num[i]=atol(stra);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+     i=i+1;
+   } /* End loop reading  data */
+   fclose(fic);
+   /* printf("ii=%d", ij);
+      scanf("%d",i);*/
    imx=i-1; /* Number of individuals */
    /* for (i=1; i<=imx; i++){
- Line 2916  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4906  while((c=getc(ficpar))=='#' && c!= EOF){
      }*/
     /*  for (i=1; i<=imx; i++){
       if (s[4][i]==9)  s[4][i]=-1;
-      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+   /* for (i=1; i<=imx; i++) */
-   /* Calculation of the number of parameter from char model*/
+    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
-   Tvar=ivector(1,15);
+      else weight[i]=1;*/
+   /* Calculation of the number of parameters from char model */
+   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
    Tprod=ivector(1,15);
    Tvaraff=ivector(1,15);
    Tvard=imatrix(1,15,1,2);
    Tage=ivector(1,15);
-   if (strlen(model) >1){
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
      j=0, j1=0, k1=1, k2=1;
-     j=nbocc(model,'+');
+     j=nbocc(model,'+'); /* j=Number of '+' */
-     j1=nbocc(model,'*');
+     j1=nbocc(model,'*'); /* j1=Number of '*' */
      cptcovn=j+1;
-     cptcovprod=j1;
+     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,'+');
+       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
+       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,'*')) {
+       if (strchr(strb,'*')) {  /* Model includes a product */
-         cutv(strd,strc,strb,'*');
+         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
-         if (strcmp(strc,"age")==0) {
+         if (strcmp(strc,"age")==0) { /* Vn*age */
            cptcovprod--;
            cutv(strb,stre,strd,'V');
-           Tvar[i]=atoi(stre);
+           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) {
+         else if (strcmp(strd,"age")==0) { /* or age*Vn */
            cptcovprod--;
            cutv(strb,stre,strc,'V');
            Tvar[i]=atoi(stre);
            cptcovage++;
            Tage[cptcovage]=i;
          }
-         else {
+         else {  /* Age is not in the model */
-           cutv(strb,stre,strc,'V');
+           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
            Tvar[i]=ncovcol+k1;
-           cutv(strb,strc,strd,'V');
+           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
            Tprod[k1]=i;
-           Tvard[k1][1]=atoi(strc);
+           Tvard[k1][1]=atoi(strc); /* m*/
-           Tvard[k1][2]=atoi(stre);
+           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++)
- Line 2976  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4973  while((c=getc(ficpar))=='#' && c!= EOF){
            k2=k2+2;
          }
        }
-       else {
+       else { /* no more sum */
          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
         /*  scanf("%d",i);*/
        cutv(strd,strc,strb,'V');
- Line 2985  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 4982  while((c=getc(ficpar))=='#' && c!= EOF){
        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*/
+   if (weightopt != 1) { /* Maximisation without weights*/
-       for(i=1;i<=n;i++) weight[i]=1.0;
+     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);
+   agev=matrix(1,maxwav,1,imx);
-     for (i=1; i<=imx; i++) {
+   for (i=1; i<=imx; i++) {
-       for(m=2; (m<= maxwav); m++) {
+     for(m=2; (m<= maxwav); m++) {
-        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-          anint[m][i]=9999;
+         anint[m][i]=9999;
-          s[m][i]=-1;
+         s[m][i]=-1;
-        }
+       }
-      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) 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++)  {
+   for (i=1; i<=imx; i++)  {
-       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-       for(m=1; (m<= maxwav); m++){
+     for(m=firstpass; (m<= lastpass); m++){
-         if(s[m][i] >0){
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-           if (s[m][i] >= nlstate+1) {
+         if (s[m][i] >= nlstate+1) {
-             if(agedc[i]>0)
+           if(agedc[i]>0)
-               if(moisdc[i]!=99 && andc[i]!=9999)
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-                 agev[m][i]=agedc[i];
+               agev[m][i]=agedc[i];
-             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-            else {
+             else {
-               if (andc[i]!=9999){
+               if ((int)andc[i]!=9999){
-               printf("Warning negative age at death: %d line:%d\n",num[i],i);
+                 nbwarn++;
-               agev[m][i]=-1;
+                 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){ /* Should no more exist */
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+                                  years but with the precision of a month */
-             if(mint[m][i]==99 || anint[m][i]==9999)
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-               agev[m][i]=1;
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-             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 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 /*= 0 Unknown */
+         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=1; (m<= maxwav); m++){
+   }
-         if (s[m][i] > (nlstate+ndeath)) {
+   for (i=1; i<=imx; i++)  {
-           printf("Error: Wrong value in nlstate or ndeath\n");
+     for(m=firstpass; (m<=lastpass); m++){
-           goto end;
+       if (s[m][i] > (nlstate+ndeath)) {
-         }
+         nberr++;
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         goto end;
        }
      }
+   }
+   /*for (i=1; i<=imx; i++){
+   for (m=firstpass; (m<lastpass); m++){
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+ }
+ }*/
- printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-     free_vector(severity,1,maxwav);
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-     free_imatrix(outcome,1,maxwav+1,1,n);
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-     free_vector(moisnais,1,n);
-     free_vector(annais,1,n);
+   agegomp=(int)agemin;
-     /* free_matrix(mint,1,maxwav,1,n);
+   free_vector(severity,1,maxwav);
-        free_matrix(anint,1,maxwav,1,n);*/
+   free_imatrix(outcome,1,maxwav+1,1,n);
-     free_vector(moisdc,1,n);
+   free_vector(moisnais,1,n);
-     free_vector(andc,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);
+   wav=ivector(1,imx);
-     dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-     mw=imatrix(1,lastpass-firstpass+1,1,imx);
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-     /* Concatenates waves */
+   /* Concatenates waves */
-       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   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);
+   Tcode=ivector(1,100);
-       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-       ncodemax[1]=1;
+   ncodemax[1]=1;
-       if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
-    codtab=imatrix(1,100,1,10);
+   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
-    h=0;
+                                  the estimations*/
-    m=pow(2,cptcoveff);
+   h=0;
+   m=pow(2,cptcoveff);
-    for(k=1;k<=cptcoveff; k++){
-      for(i=1; i <=(m/pow(2,k));i++){
+   for(k=1;k<=cptcoveff; k++){
-        for(j=1; j <= ncodemax[k]; j++){
+     for(i=1; i <=(m/pow(2,k));i++){
-          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+       for(j=1; j <= ncodemax[k]; j++){
-            h++;
+         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
-            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+           h++;
-            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
-          }
+           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
-        }
+         }
-      }
-    }
-    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-       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("\n");
        }
-       scanf("%d",i);*/
+     }
+   }
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+      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("\n");
+      }
+      scanf("%d",i);*/
-    /* Calculates basic frequencies. Computes observed prevalence at single age
+   /*------------ gnuplot -------------*/
-        and prints on file fileres'p'. */
+   strcpy(optionfilegnuplot,optionfilefiname);
+   if(mle==-3)
+     strcat(optionfilegnuplot,"-mort");
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
-     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   }
+   else{
+     fprintf(ficgp,"\n# %s\n", version);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     fprintf(ficgp,"set missing 'NaNq'\n");
+   }
+   /*  fclose(ficgp);*/
+   /*--------- index.htm --------*/
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   if(mle==-3)
+     strcat(optionfilehtm,"-mort");
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm), exit(0);
+   }
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   strcat(optionfilehtmcov,"-cov.htm");
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   }
+   else{
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+ \n\
+ <hr  size=\"2\" color=\"#EC5E5E\">\
+  <ul><li><h4>Parameter files</h4>\n\
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+  - Date and time at start: %s</ul>\n",\
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+           fileres,fileres,\
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+   fflush(fichtm);
+   strcpy(pathr,path);
+   strcat(pathr,optionfilefiname);
+   chdir(optionfilefiname); /* Move to directory named optionfile */
+   /* Calculates basic frequencies. Computes observed prevalence at single age
+      and prints on file fileres'p'. */
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+   fprintf(fichtm,"\n");
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+           imx,agemin,agemax,jmin,jmax,jmean);
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-     /* For Powell, parameters are in a vector p[] starting at p[1]
-        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+   /* For Powell, parameters are in a vector p[] starting at p[1]
-     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   if (mle==-3){
+     ximort=matrix(1,NDIM,1,NDIM);
+     cens=ivector(1,n);
+     ageexmed=vector(1,n);
+     agecens=vector(1,n);
+     dcwave=ivector(1,n);
+     for (i=1; i<=imx; i++){
+       dcwave[i]=-1;
+       for (m=firstpass; m<=lastpass; m++)
+         if (s[m][i]>nlstate) {
+           dcwave[i]=m;
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+           break;
+         }
+     }
+     for (i=1; i<=imx; i++) {
+       if (wav[i]>0){
+         ageexmed[i]=agev[mw[1][i]][i];
+         j=wav[i];
+         agecens[i]=1.;
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
+           cens[i]= 1;
+         }else if (ageexmed[i]< 1)
+           cens[i]= -1;
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+           cens[i]=0 ;
+       }
+       else cens[i]=-1;
+     }
+     for (i=1;i<=NDIM;i++) {
+       for (j=1;j<=NDIM;j++)
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     }
+     p[1]=0.0268; p[NDIM]=0.083;
+     /*printf("%lf %lf", p[1], p[2]);*/
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+     strcpy(filerespow,"pow-mort");
+     strcat(filerespow,fileres);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", filerespow);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+     }
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+     /*  for (i=1;i<=nlstate;i++)
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     */
+     fprintf(ficrespow,"\n");
+     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+     fclose(ficrespow);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
-     if(mle==1){
+     for(i=1; i <=NDIM; i++)
-     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+       for(j=i+1;j<=NDIM;j++)
+         matcov[i][j]=matcov[j][i];
+     printf("\nCovariance matrix\n ");
+     for(i=1; i <=NDIM; i++) {
+       for(j=1;j<=NDIM;j++){
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\n ");
+     }
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     for (i=1;i<=NDIM;i++)
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     lsurv=vector(1,AGESUP);
+     lpop=vector(1,AGESUP);
+     tpop=vector(1,AGESUP);
+     lsurv[agegomp]=100000;
+     for (k=agegomp;k<=AGESUP;k++) {
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
+     }
+     tpop[agegomp]=sumlpop;
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+                      stepm, weightopt,\
+                      model,imx,p,matcov,agemortsup);
+     free_vector(lsurv,1,AGESUP);
+     free_vector(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+   } /* Endof if mle==-3 */
+   else{ /* For mle >=1 */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     globpr=1; /* to print the contributions */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     if(mle>=1){ /* Could be 1 or 2 */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
      }
      /*--------- results files --------------*/
      fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
-    jk=1;
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-    for(i=1,jk=1; i <=nlstate; i++){
+     for(i=1,jk=1; i <=nlstate; i++){
-      for(k=1; k <=(nlstate+ndeath); k++){
+       for(k=1; k <=(nlstate+ndeath); k++){
-        if (k != i)
+         if (k != i) {
-          {
+           printf("%d%d ",i,k);
-            printf("%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
-            fprintf(ficres,"%1d%1d ",i,k);
+           fprintf(ficres,"%1d%1d ",i,k);
-            for(j=1; j <=ncovmodel; j++){
+           for(j=1; j <=ncovmodel; j++){
-              printf("%f ",p[jk]);
+             printf("%lf ",p[jk]);
-              fprintf(ficres,"%f ",p[jk]);
+             fprintf(ficlog,"%lf ",p[jk]);
-              jk++;
+             fprintf(ficres,"%lf ",p[jk]);
-            }
+             jk++;
-            printf("\n");
+           }
-            fprintf(ficres,"\n");
+           printf("\n");
-          }
+           fprintf(ficlog,"\n");
-      }
+           fprintf(ficres,"\n");
-    }
+         }
-  if(mle==1){
+       }
-     /* Computing hessian and covariance matrix */
+     }
-     ftolhess=ftol; /* Usually correct */
+     if(mle!=0){
-     hesscov(matcov, p, npar, delti, ftolhess, func);
+       /* Computing hessian and covariance matrix */
-  }
+       ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, p, npar, delti, ftolhess, func);
+     }
      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
      printf("# Scales (for hessian or gradient estimation)\n");
-      for(i=1,jk=1; i <=nlstate; i++){
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath; j++){
          if (j!=i) {
            fprintf(ficres,"%1d%1d",i,j);
            printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
            for(k=1; k<=ncovmodel;k++){
              printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
              fprintf(ficres," %.5e",delti[jk]);
              jk++;
            }
            printf("\n");
+           fprintf(ficlog,"\n");
            fprintf(ficres,"\n");
          }
        }
-      }
+     }
-     k=1;
      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     if(mle>=1)
-     for(i=1;i<=npar;i++){
+       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-       /*  if (k>nlstate) k=1;
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-       i1=(i-1)/(ncovmodel*nlstate)+1;
+     /* # 121 Var(a12)\n\ */
-       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
-       printf("%s%d%d",alph[k],i1,tab[i]);*/
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-       fprintf(ficres,"%3d",i);
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-       printf("%3d",i);
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-       for(j=1; j<=i;j++){
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-         fprintf(ficres," %.5e",matcov[i][j]);
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-         printf(" %.5e",matcov[i][j]);
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-       }
-       fprintf(ficres,"\n");
-       printf("\n");
+     /* Just to have a covariance matrix which will be more understandable
-       k++;
+        even is we still don't want to manage dictionary of variables
-     }
+     */
+     for(itimes=1;itimes<=2;itimes++){
+       jj=0;
+       for(i=1; i <=nlstate; i++){
+         for(j=1; j <=nlstate+ndeath; j++){
+           if(j==i) continue;
+           for(k=1; k<=ncovmodel;k++){
+             jj++;
+             ca[0]= k+'a'-1;ca[1]='\0';
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
- Line 3201  printf("Total number of individuals= %d,
+ Line 5502  printf("Total number of individuals= %d,
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
      estepm=0;
      fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
      if (estepm==0 || estepm < stepm) estepm=stepm;
- Line 3212  printf("Total number of individuals= %d,
+ Line 5514  printf("Total number of individuals= %d,
      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       puts(line);
+       fputs(line,ficparo);
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
+     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
-     fputs(line,ficparo);
+     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   }
+     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   ungetc(c,ficpar);
+     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
-   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       puts(line);
-     ungetc(c,ficpar);
+       fputs(line,ficparo);
-     fgets(line, MAXLINE, ficpar);
+     }
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-    dateprev1=anprev1+mprev1/12.+jprev1/365.;
-    dateprev2=anprev2+mprev2/12.+jprev2/365.;
-   fscanf(ficpar,"pop_based=%d\n",&popbased);
-   fprintf(ficparo,"pop_based=%d\n",popbased);
-   fprintf(ficres,"pop_based=%d\n",popbased);
-   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-   }
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-   ungetc(c,ficpar);
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
-   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
+     fprintf(ficparo,"pop_based=%d\n",popbased);
- fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+     fprintf(ficres,"pop_based=%d\n",popbased);
- fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
- while((c=getc(ficpar))=='#' && c!= EOF){
+       fgets(line, MAXLINE, ficpar);
+       puts(line);
+       fputs(line,ficparo);
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
+     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
-     fputs(line,ficparo);
+     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   }
+     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   ungetc(c,ficpar);
+     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
+     /* day and month of proj2 are not used but only year anproj2.*/
-   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
- /*------------ gnuplot -------------*/
-  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
- /*------------ free_vector  -------------*/
-  chdir(path);
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+    /*------------ free_vector  -------------*/
+    /*  chdir(path); */
-  free_ivector(wav,1,imx);
+     free_ivector(wav,1,imx);
-  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
-  free_ivector(num,1,n);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-  free_vector(agedc,1,n);
+     free_lvector(num,1,n);
-  /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     free_vector(agedc,1,n);
-  fclose(ficparo);
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
-  fclose(ficres);
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     fclose(ficparo);
- /*--------- index.htm --------*/
+     fclose(ficres);
-   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-   /*--------------- Prevalence limit --------------*/
+     strcpy(filerespl,"pl");
+     strcat(filerespl,fileres);
-   strcpy(filerespl,"pl");
+     if((ficrespl=fopen(filerespl,"w"))==NULL) {
-   strcat(filerespl,fileres);
+       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-   if((ficrespl=fopen(filerespl,"w"))==NULL) {
+       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
+     }
-   }
+     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-   printf("Computing prevalence limit: result on file '%s' \n", filerespl);
+     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficrespl,"#Prevalence limit\n");
+     pstamp(ficrespl);
-   fprintf(ficrespl,"#Age ");
+     fprintf(ficrespl,"# Period (stable) prevalence \n");
-   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     fprintf(ficrespl,"#Age ");
-   fprintf(ficrespl,"\n");
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     fprintf(ficrespl,"\n");
-   prlim=matrix(1,nlstate,1,nlstate);
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     prlim=matrix(1,nlstate,1,nlstate);
-   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     agebase=ageminpar;
-   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     agelim=agemaxpar;
-   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+     ftolpl=1.e-10;
-   k=0;
+     i1=cptcoveff;
-   agebase=ageminpar;
+     if (cptcovn < 1){i1=1;}
-   agelim=agemaxpar;
-   ftolpl=1.e-10;
-   i1=cptcoveff;
-   if (cptcovn < 1){i1=1;}
-   for(cptcov=1;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;
          /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
          fprintf(ficrespl,"\n#******");
-         for(j=1;j<=cptcoveff;j++)
+         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 );
+           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," %.5f", prlim[i][i]);
            fprintf(ficrespl,"\n");
          }
        }
      }
-   fclose(ficrespl);
+     fclose(ficrespl);
-   /*------------- h Pij x at various ages ------------*/
-   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-   if((ficrespij=fopen(filerespij,"w"))==NULL) {
-     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-   }
-   printf("Computing pij: result on file '%s' \n", filerespij);
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   /*if (stepm<=24) stepsize=2;*/
-   agelim=AGESUP;
+     /*------------- h Pij x at various ages ------------*/
-   hstepm=stepsize*YEARM; /* Every year of age */
-   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-   k=0;
+     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-   for(cptcov=1;cptcov<=i1;cptcov++){
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-       k=k+1;
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+     }
+     printf("Computing pij: result on file '%s' \n", filerespij);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     /*if (stepm<=24) stepsize=2;*/
+     agelim=AGESUP;
+     hstepm=stepsize*YEARM; /* Every year of age */
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     /* hstepm=1;   aff par mois*/
+     pstamp(ficrespij);
+     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
          fprintf(ficrespij,"\n#****** ");
          for(j=1;j<=cptcoveff;j++)
            fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- Line 3361  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 5671  while((c=getc(ficpar))=='#' && c!= EOF){
          for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
            nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+           /*      nhstepm=nhstepm*YEARM; aff par mois*/
            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            oldm=oldms;savm=savms;
            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-           fprintf(ficrespij,"# Age");
+           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++){
+           for (h=0; h<=nhstepm; h++){
-             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+             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(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
-   fclose(ficrespij);
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     fclose(ficrespij);
-   /*---------- Forecasting ------------------*/
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   if((stepm == 1) && (strcmp(model,".")==0)){
+     for(i=1;i<=AGESUP;i++)
-     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
+       for(j=1;j<=NCOVMAX;j++)
-     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
+         for(k=1;k<=NCOVMAX;k++)
-   }
+           probs[i][j][k]=0.;
-   else{
-     erreur=108;
+     /*---------- Forecasting ------------------*/
-     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
-   }
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
+       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
-   /*---------- Health expectancies and variances ------------*/
+       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+       /*      }  */
-   strcpy(filerest,"t");
+       /*      else{ */
-   strcat(filerest,fileres);
+       /*        erreur=108; */
-   if((ficrest=fopen(filerest,"w"))==NULL) {
+       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
-     printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
-   }
+       /*      } */
-   printf("Computing Total LEs with variances: file '%s' \n", filerest);
+     }
-   strcpy(filerese,"e");
+     /*---------- Health expectancies and variances ------------*/
-   strcat(filerese,fileres);
-   if((ficreseij=fopen(filerese,"w"))==NULL) {
+     strcpy(filerest,"t");
-     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     strcat(filerest,fileres);
-   }
+     if((ficrest=fopen(filerest,"w"))==NULL) {
-   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+       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(filerese,"e");
+     strcat(filerese,fileres);
+     if((ficreseij=fopen(filerese,"w"))==NULL) {
+       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     }
+     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     strcpy(fileresstde,"stde");
+     strcat(fileresstde,fileres);
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     }
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"cve");
+     strcat(filerescve,fileres);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     strcpy(fileresv,"v");
+     strcat(fileresv,fileres);
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     }
+     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+     */
+     if (mobilav!=0) {
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
+     }
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
+         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");
-  strcpy(fileresv,"v");
+         fprintf(ficreseij,"\n#****** ");
-   strcat(fileresv,fileres);
+         fprintf(ficresstdeij,"\n#****** ");
-   if((ficresvij=fopen(fileresv,"w"))==NULL) {
+         fprintf(ficrescveij,"\n#****** ");
-     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+         for(j=1;j<=cptcoveff;j++) {
-   }
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   calagedate=-1;
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+         }
+         fprintf(ficreseij,"******\n");
+         fprintf(ficresstdeij,"******\n");
+         fprintf(ficrescveij,"******\n");
-   k=0;
+         fprintf(ficresvij,"\n#****** ");
-   for(cptcov=1;cptcov<=i1;cptcov++){
+         for(j=1;j<=cptcoveff;j++)
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       k=k+1;
+         fprintf(ficresvij,"******\n");
-       fprintf(ficrest,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficrest,"******\n");
-       fprintf(ficreseij,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficreseij,"******\n");
-       fprintf(ficresvij,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficresvij,"******\n");
-       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
-       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
-       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
-        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
-       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         oldm=oldms;savm=savms;
-       fprintf(ficrest,"\n");
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+         if(popbased==1){
-       epj=vector(1,nlstate+1);
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
-       for(age=bage; age <=fage ;age++){
-         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-         if (popbased==1) {
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][k];
          }
+         pstamp(ficrest);
+         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         fprintf(ficrest,"\n");
+         epj=vector(1,nlstate+1);
+         for(age=bage; age <=fage ;age++){
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           if (popbased==1) {
+             if(mobilav ==0){
+               for(i=1; i<=nlstate;i++)
+                 prlim[i][i]=probs[(int)age][i][k];
+             }else{ /* mobilav */
+               for(i=1; i<=nlstate;i++)
+                 prlim[i][i]=mobaverage[(int)age][i][k];
+             }
+           }
-         fprintf(ficrest," %4.0f",age);
+           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_matrix(mint,1,maxwav,1,n);
-     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
      free_vector(weight,1,n);
-   fclose(ficreseij);
+     free_imatrix(Tvard,1,15,1,2);
-   fclose(ficresvij);
+     free_imatrix(s,1,maxwav+1,1,n);
-   fclose(ficrest);
+     free_matrix(anint,1,maxwav,1,n);
-   fclose(ficpar);
+     free_matrix(mint,1,maxwav,1,n);
-   free_vector(epj,1,nlstate+1);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
-   /*------- Variance limit prevalence------*/
+     fclose(ficreseij);
+     fclose(ficresstdeij);
-   strcpy(fileresvpl,"vpl");
+     fclose(ficrescveij);
-   strcat(fileresvpl,fileres);
+     fclose(ficresvij);
-   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+     fclose(ficrest);
-     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
+     fclose(ficpar);
-     exit(0);
-   }
+     /*------- Variance of period (stable) prevalence------*/
-   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
+     strcpy(fileresvpl,"vpl");
+     strcat(fileresvpl,fileres);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
-   k=0;
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-   for(cptcov=1;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
-       k=k+1;
+         fprintf(ficresvpl,"\n#****** ");
-       fprintf(ficresvpl,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
-       for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvpl,"******\n");
-       fprintf(ficresvpl,"******\n");
-       varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         varpl=matrix(1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
+         oldm=oldms;savm=savms;
-      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
+         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       }
      }
-  }
-   fclose(ficresvpl);
-   /*---------- End : free ----------------*/
+     fclose(ficresvpl);
-   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+     /*---------- End : free ----------------*/
-   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }  /* mle==-3 arrives here for freeing */
-   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(prlim,1,nlstate,1,nlstate);
-   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(savms, 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(matcov,1,npar,1,npar);
+     free_matrix(covar,0,NCOVMAX,1,n);
-   free_vector(delti,1,npar);
+     free_matrix(matcov,1,npar,1,npar);
-   free_matrix(agev,1,maxwav,1,imx);
+     /*free_vector(delti,1,npar);*/
-   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
-   if(erreur >0)
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     printf("End of Imach with error or warning %d\n",erreur);
-   else   printf("End of Imach\n");
+     free_ivector(ncodemax,1,8);
+     free_ivector(Tvar,1,15);
+     free_ivector(Tprod,1,15);
+     free_ivector(Tvaraff,1,15);
+     free_ivector(Tage,1,15);
+     free_ivector(Tcode,1,100);
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     free_imatrix(codtab,1,100,1,10);
+   fflush(fichtm);
+   fflush(ficgp);
+   if((nberr >0) || (nbwarn>0)){
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+   }else{
+     printf("End of Imach\n");
+     fprintf(ficlog,"End of Imach\n");
+   }
+   printf("See log file on %s\n",filelog);
    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   (void) gettimeofday(&end_time,&tzp);
-   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
+   tm = *localtime(&end_time.tv_sec);
-   /*printf("Total time was %d uSec.\n", total_usecs);*/
+   tmg = *gmtime(&end_time.tv_sec);
+   strcpy(strtend,asctime(&tm));
+   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ /*   if(fileappend(fichtm,optionfilehtm)){ */
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtm);
+   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtmcov);
+   fclose(ficgp);
+   fclose(ficlog);
    /*------ End -----------*/
-  end:
+    printf("Before Current directory %s!\n",pathcd);
- #ifdef windows
+    if(chdir(pathcd) != 0)
-   /* chdir(pathcd);*/
+     printf("Can't move to directory %s!\n",path);
- #endif
+   if(getcwd(pathcd,MAXLINE) > 0)
-  /*system("wgnuplot graph.plt");*/
+     printf("Current directory %s!\n",pathcd);
-  /*system("../gp37mgw/wgnuplot graph.plt");*/
+   /*strcat(plotcmd,CHARSEPARATOR);*/
-  /*system("cd ../gp37mgw");*/
+   sprintf(plotcmd,"gnuplot");
-  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
+ #ifndef UNIX
-  strcpy(plotcmd,GNUPLOTPROGRAM);
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
-  strcat(plotcmd," ");
+ #endif
-  strcat(plotcmd,optionfilegnuplot);
+   if(!stat(plotcmd,&info)){
-  system(plotcmd);
+     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);
- #ifdef windows
+   if((outcmd=system(plotcmd)) != 0){
+     printf("\n Problem with gnuplot\n");
+   }
+   printf(" Wait...");
    while (z[0] != 'q') {
      /* chdir(path); */
-     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
+     printf("\nType e to edit output files, g to graph again and q for exiting: ");
      scanf("%s",z);
-     if (z[0] == 'c') system("./imach");
+ /*     if (z[0] == 'c') system("./imach"); */
-     else if (z[0] == 'e') system(optionfilehtm);
+     if (z[0] == 'e') {
+       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+       system(optionfilehtm);
+     }
      else if (z[0] == 'g') system(plotcmd);
      else if (z[0] == 'q') exit(0);
    }
- #endif
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: ");
+     scanf("%s",z);
+   }
  }

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