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Diff for /imach/src/imach.c between versions 1.78 and 1.147

-version 1.78, 2003/05/27 17:26:53
+version 1.147, 2014/06/16 10:33:11
  Line 1
  /* $Id$
+   $State$
+   $Log$
+   Revision 1.147  2014/06/16 10:33:11  brouard
+   *** empty log message ***
+   Revision 1.146  2014/06/16 10:20:28  brouard
+   Summary: Merge
+   Author: Brouard
+   Merge, before building revised version.
+   Revision 1.145  2014/06/10 21:23:15  brouard
+   Summary: Debugging with valgrind
+   Author: Nicolas Brouard
+   Lot of changes in order to output the results with some covariates
+   After the Edimburgh REVES conference 2014, it seems mandatory to
+   improve the code.
+   No more memory valgrind error but a lot has to be done in order to
+   continue the work of splitting the code into subroutines.
+   Also, decodemodel has been improved. Tricode is still not
+   optimal. nbcode should be improved. Documentation has been added in
+   the source code.
+   Revision 1.143  2014/01/26 09:45:38  brouard
+   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
+   Revision 1.142  2014/01/26 03:57:36  brouard
+   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.141  2014/01/26 02:42:01  brouard
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.140  2011/09/02 10:37:54  brouard
+   Summary: times.h is ok with mingw32 now.
+   Revision 1.139  2010/06/14 07:50:17  brouard
+   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
+   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
+   Revision 1.138  2010/04/30 18:19:40  brouard
+   *** empty log message ***
+   Revision 1.137  2010/04/29 18:11:38  brouard
+   (Module): Checking covariates for more complex models
+   than V1+V2. A lot of change to be done. Unstable.
+   Revision 1.136  2010/04/26 20:30:53  brouard
+   (Module): merging some libgsl code. Fixing computation
+   of likelione (using inter/intrapolation if mle = 0) in order to
+   get same likelihood as if mle=1.
+   Some cleaning of code and comments added.
+   Revision 1.135  2009/10/29 15:33:14  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.134  2009/10/29 13:18:53  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.133  2009/07/06 10:21:25  brouard
+   just nforces
+   Revision 1.132  2009/07/06 08:22:05  brouard
+   Many tings
+   Revision 1.131  2009/06/20 16:22:47  brouard
+   Some dimensions resccaled
+   Revision 1.130  2009/05/26 06:44:34  brouard
+   (Module): Max Covariate is now set to 20 instead of 8. A
+   lot of cleaning with variables initialized to 0. Trying to make
+   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
+   Revision 1.129  2007/08/31 13:49:27  lievre
+   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
+   Revision 1.128  2006/06/30 13:02:05  brouard
+   (Module): Clarifications on computing e.j
+   Revision 1.127  2006/04/28 18:11:50  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   (Module): In order to speed up (in case of numerous covariates) we
+   compute health expectancies (without variances) in a first step
+   and then all the health expectancies with variances or standard
+   deviation (needs data from the Hessian matrices) which slows the
+   computation.
+   In the future we should be able to stop the program is only health
+   expectancies and graph are needed without standard deviations.
+   Revision 1.126  2006/04/28 17:23:28  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   Version 0.98h
+   Revision 1.125  2006/04/04 15:20:31  lievre
+   Errors in calculation of health expectancies. Age was not initialized.
+   Forecasting file added.
+   Revision 1.124  2006/03/22 17:13:53  lievre
+   Parameters are printed with %lf instead of %f (more numbers after the comma).
+   The log-likelihood is printed in the log file
+   Revision 1.123  2006/03/20 10:52:43  brouard
+   * imach.c (Module): <title> changed, corresponds to .htm file
+   name. <head> headers where missing.
+   * imach.c (Module): Weights can have a decimal point as for
+   English (a comma might work with a correct LC_NUMERIC environment,
+   otherwise the weight is truncated).
+   Modification of warning when the covariates values are not 0 or
+.
+   Version 0.98g
+   Revision 1.122  2006/03/20 09:45:41  brouard
+   (Module): Weights can have a decimal point as for
+   English (a comma might work with a correct LC_NUMERIC environment,
+   otherwise the weight is truncated).
+   Modification of warning when the covariates values are not 0 or
+.
+   Version 0.98g
+   Revision 1.121  2006/03/16 17:45:01  lievre
+   * imach.c (Module): Comments concerning covariates added
+   * imach.c (Module): refinements in the computation of lli if
+   status=-2 in order to have more reliable computation if stepm is
+   not 1 month. Version 0.98f
+   Revision 1.120  2006/03/16 15:10:38  lievre
+   (Module): refinements in the computation of lli if
+   status=-2 in order to have more reliable computation if stepm is
+   not 1 month. Version 0.98f
+   Revision 1.119  2006/03/15 17:42:26  brouard
+   (Module): Bug if status = -2, the loglikelihood was
+   computed as likelihood omitting the logarithm. Version O.98e
+   Revision 1.118  2006/03/14 18:20:07  brouard
+   (Module): varevsij Comments added explaining the second
+   table of variances if popbased=1 .
+   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+   (Module): Function pstamp added
+   (Module): Version 0.98d
+   Revision 1.117  2006/03/14 17:16:22  brouard
+   (Module): varevsij Comments added explaining the second
+   table of variances if popbased=1 .
+   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+   (Module): Function pstamp added
+   (Module): Version 0.98d
+   Revision 1.116  2006/03/06 10:29:27  brouard
+   (Module): Variance-covariance wrong links and
+   varian-covariance of ej. is needed (Saito).
+   Revision 1.115  2006/02/27 12:17:45  brouard
+   (Module): One freematrix added in mlikeli! 0.98c
+   Revision 1.114  2006/02/26 12:57:58  brouard
+   (Module): Some improvements in processing parameter
+   filename with strsep.
+   Revision 1.113  2006/02/24 14:20:24  brouard
+   (Module): Memory leaks checks with valgrind and:
+   datafile was not closed, some imatrix were not freed and on matrix
+   allocation too.
+   Revision 1.112  2006/01/30 09:55:26  brouard
+   (Module): Back to gnuplot.exe instead of wgnuplot.exe
+   Revision 1.111  2006/01/25 20:38:18  brouard
+   (Module): Lots of cleaning and bugs added (Gompertz)
+   (Module): Comments can be added in data file. Missing date values
+   can be a simple dot '.'.
+   Revision 1.110  2006/01/25 00:51:50  brouard
+   (Module): Lots of cleaning and bugs added (Gompertz)
+   Revision 1.109  2006/01/24 19:37:15  brouard
+   (Module): Comments (lines starting with a #) are allowed in data.
+   Revision 1.108  2006/01/19 18:05:42  lievre
+   Gnuplot problem appeared...
+   To be fixed
+   Revision 1.107  2006/01/19 16:20:37  brouard
+   Test existence of gnuplot in imach path
+   Revision 1.106  2006/01/19 13:24:36  brouard
+   Some cleaning and links added in html output
+   Revision 1.105  2006/01/05 20:23:19  lievre
+   *** empty log message ***
+   Revision 1.104  2005/09/30 16:11:43  lievre
+   (Module): sump fixed, loop imx fixed, and simplifications.
+   (Module): If the status is missing at the last wave but we know
+   that the person is alive, then we can code his/her status as -2
+   (instead of missing=-1 in earlier versions) and his/her
+   contributions to the likelihood is 1 - Prob of dying from last
+   health status (= 1-p13= p11+p12 in the easiest case of somebody in
+   the healthy state at last known wave). Version is 0.98
+   Revision 1.103  2005/09/30 15:54:49  lievre
+   (Module): sump fixed, loop imx fixed, and simplifications.
+   Revision 1.102  2004/09/15 17:31:30  brouard
+   Add the possibility to read data file including tab characters.
+   Revision 1.101  2004/09/15 10:38:38  brouard
+   Fix on curr_time
+   Revision 1.100  2004/07/12 18:29:06  brouard
+   Add version for Mac OS X. Just define UNIX in Makefile
+   Revision 1.99  2004/06/05 08:57:40  brouard
+   *** empty log message ***
+   Revision 1.98  2004/05/16 15:05:56  brouard
+   New version 0.97 . First attempt to estimate force of mortality
+   directly from the data i.e. without the need of knowing the health
+   state at each age, but using a Gompertz model: log u =a + b*age .
+   This is the basic analysis of mortality and should be done before any
+   other analysis, in order to test if the mortality estimated from the
+   cross-longitudinal survey is different from the mortality estimated
+   from other sources like vital statistic data.
+   The same imach parameter file can be used but the option for mle should be -3.
+   Agnès, who wrote this part of the code, tried to keep most of the
+   former routines in order to include the new code within the former code.
+   The output is very simple: only an estimate of the intercept and of
+   the slope with 95% confident intervals.
+   Current limitations:
+   A) Even if you enter covariates, i.e. with the
+   model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
+   B) There is no computation of Life Expectancy nor Life Table.
+   Revision 1.97  2004/02/20 13:25:42  lievre
+   Version 0.96d. Population forecasting command line is (temporarily)
+   suppressed.
+   Revision 1.96  2003/07/15 15:38:55  brouard
+   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
+   rewritten within the same printf. Workaround: many printfs.
+   Revision 1.95  2003/07/08 07:54:34  brouard
+   * imach.c (Repository):
+   (Repository): Using imachwizard code to output a more meaningful covariance
+   matrix (cov(a12,c31) instead of numbers.
+   Revision 1.94  2003/06/27 13:00:02  brouard
+   Just cleaning
+   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 39
+ Line 367
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
-   of the life expectancies. It also computes the stable prevalence.
+   of the life expectancies. It also computes the period (stable) prevalence.
-   Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
-            Institut national d'�tudes d�mographiques, Paris.
+            Institut national d'études démographiques, Paris.
    This software have been partly granted by Euro-REVES, a concerted action
    from the European Union.
    It is copyrighted identically to a GNU software product, ie programme and
- Line 58
+ Line 386
    read parameterfile
    read datafile
    concatwav
+   freqsummary
    if (mle >= 1)
      mlikeli
    print results files
- Line 67
+ Line 396
        begin-prev-date,...
    open gnuplot file
    open html file
-   stable prevalence
+   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
-    for age prevalim()
+    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
-   h Pij x
+                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
-   variance of p varprob
+     freexexit2 possible for memory heap.
+   h Pij x                         | pij_nom  ficrestpij
+    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
+ 85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
+ 85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
+ 65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
+ 65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
+   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
+    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
+    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
    forecasting if prevfcast==1 prevforecast call prevalence()
    health expectancies
    Variance-covariance of DFLE
- Line 79
+ Line 420
    varevsij()
    if popbased==1 varevsij(,popbased)
    total life expectancies
-   Variance of stable prevalence
+   Variance of period (stable) prevalence
   end
  */
- Line 89
+ Line 430
  #include <math.h>
  #include <stdio.h>
  #include <stdlib.h>
+ #include <string.h>
  #include <unistd.h>
- #define MAXLINE 256
+ #include <limits.h>
+ #include <sys/types.h>
+ #include <sys/stat.h>
+ #include <errno.h>
+ extern int errno;
+ #ifdef LINUX
+ #include <time.h>
+ #include "timeval.h"
+ #else
+ #include <sys/time.h>
+ #endif
+ #ifdef GSL
+ #include <gsl/gsl_errno.h>
+ #include <gsl/gsl_multimin.h>
+ #endif
+ /* #include <libintl.h> */
+ /* #define _(String) gettext (String) */
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
  #define 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 */
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
  #define NINTERVMAX 8
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- #define NCOVMAX 8 /* Maximum number of covariates */
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
  #define MAXN 20000
- #define YEARM 12. /* Number of months per year */
+ #define YEARM 12. /**< Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
- #ifdef windows
+ #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
- #define DIRSEPARATOR '\\'
+ #ifdef UNIX
- #define ODIRSEPARATOR '/'
- #else
  #define DIRSEPARATOR '/'
+ #define CHARSEPARATOR "/"
  #define ODIRSEPARATOR '\\'
+ #else
+ #define DIRSEPARATOR '\\'
+ #define CHARSEPARATOR "\\"
+ #define ODIRSEPARATOR '/'
  #endif
- char version[80]="Imach version 0.95a, May 2003, INED-EUROREVES ";
+ /* $Id$ */
- int erreur; /* Error number */
+ /* $State$ */
- int nvar;
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
+ char fullversion[]="$Revision$ $Date$";
+ char strstart[80];
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
+ int cptcov=0; /* Working variable */
  int npar=NPARMAX;
  int nlstate=2; /* Number of live states */
  int ndeath=1; /* Number of dead states */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
- int maxwav; /* Maxim number of waves */
+ int maxwav=0; /* Maxim number of waves */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- int mle, weightopt;
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
+                    to the likelihood and the sum of weights (done by funcone)*/
+ int mle=1, weightopt=0;
  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
             * wave mi and wave mi+1 is not an exact multiple of stepm. */
- double jmean; /* Mean space between 2 waves */
+ double jmean=1; /* Mean space between 2 waves */
+ double **matprod2(); /* test */
  double **oldm, **newm, **savm; /* Working pointers to matrices */
  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ /*FILE *fic ; */ /* Used in readdata only */
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
  FILE *ficlog, *ficrespow;
+ int globpr=0; /* Global variable for printing or not */
+ double fretone; /* Only one call to likelihood */
+ long ipmx=0; /* Number of contributions */
+ double sw; /* Sum of weights */
+ char filerespow[FILENAMELENGTH];
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ FILE *ficresilk;
  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
  FILE *ficresprobmorprev;
- FILE *fichtm; /* Html File */
+ FILE *fichtm, *fichtmcov; /* Html File */
  FILE *ficreseij;
  char filerese[FILENAMELENGTH];
+ FILE *ficresstdeij;
+ char fileresstde[FILENAMELENGTH];
+ FILE *ficrescveij;
+ char filerescve[FILENAMELENGTH];
  FILE  *ficresvij;
  char fileresv[FILENAMELENGTH];
  FILE  *ficresvpl;
  char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ char command[FILENAMELENGTH];
+ int  outcmd=0;
  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
  char filelog[FILENAMELENGTH]; /* Log file */
  char filerest[FILENAMELENGTH];
  char fileregp[FILENAMELENGTH];
  char popfile[FILENAMELENGTH];
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ struct timezone tzp;
+ extern int gettimeofday();
+ struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ long time_value;
+ extern long time();
+ char strcurr[80], strfor[80];
+ char *endptr;
+ long lval;
+ double dval;
  #define NR_END 1
  #define FREE_ARG char*
- Line 190  static double maxarg1,maxarg2;
+ Line 602  static double maxarg1,maxarg2;
  static double sqrarg;
  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ int agegomp= AGEGOMP;
  int imx;
- int stepm;
+ int stepm=1;
  /* Stepm, step in month: minimum step interpolation*/
  int estepm;
  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
  int m,nb;
- int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
+ long *num;
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  double **pmmij, ***probs;
+ double *ageexmed,*agecens;
  double dateintmean=0;
  double *weight;
  int **s; /* Status */
- double *agedc, **covar, idx;
+ double *agedc;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
+                   * covar=matrix(0,NCOVMAX,1,n);
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
+ double  idx;
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+ int *Ndum; /** Freq of modality (tricode */
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double *lsurv, *lpop, *tpop;
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
- double ftolhess; /* Tolerance for computing hessian */
+ double ftolhess; /**< Tolerance for computing hessian */
  /**************** split *************************/
  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
  {
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+   */
    char  *ss;                            /* pointer */
    int   l1, l2;                         /* length counters */
    l1 = strlen(path );                   /* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   if ( ss == NULL ) {                   /* no directory, so use current */
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+     strcpy( name, path );               /* we got the fullname name because no directory */
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      /* get current working directory */
- Line 229  static int split( char *path, char *dirc
+ Line 656  static int split( char *path, char *dirc
      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
        return( GLOCK_ERROR_GETCWD );
      }
-     strcpy( name, path );               /* we've got it */
+     /* got dirc from getcwd*/
+     printf(" DIRC = %s \n",dirc);
    } else {                              /* strip direcotry from path */
      ss++;                               /* after this, the filename */
      l2 = strlen( ss );                  /* length of filename */
- Line 237  static int split( char *path, char *dirc
+ Line 665  static int split( char *path, char *dirc
      strcpy( name, ss );         /* save file name */
      strncpy( dirc, path, l1 - l2 );     /* now the directory */
      dirc[l1-l2] = 0;                    /* add zero */
+     printf(" DIRC2 = %s \n",dirc);
    }
+   /* We add a separator at the end of dirc if not exists */
    l1 = strlen( dirc );                  /* length of directory */
- #ifdef windows
+   if( dirc[l1-1] != DIRSEPARATOR ){
-   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
+     dirc[l1] =  DIRSEPARATOR;
- #else
+     dirc[l1+1] = 0;
-   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
+     printf(" DIRC3 = %s \n",dirc);
- #endif
+   }
    ss = strrchr( name, '.' );            /* find last / */
-   ss++;
+   if (ss >0){
-   strcpy(ext,ss);                       /* save extension */
+     ss++;
-   l1= strlen( name);
+     strcpy(ext,ss);                     /* save extension */
-   l2= strlen(ss)+1;
+     l1= strlen( name);
-   strncpy( finame, name, l1-l2);
+     l2= strlen(ss)+1;
-   finame[l1-l2]= 0;
+     strncpy( finame, name, l1-l2);
+     finame[l1-l2]= 0;
+   }
    return( 0 );                          /* we're done */
  }
  /******************************************/
- void replace(char *s, char*t)
+ void replace_back_to_slash(char *s, char*t)
  {
    int i;
-   int lg=20;
+   int lg=0;
    i=0;
    lg=strlen(t);
    for(i=0; i<= lg; i++) {
- Line 269  void replace(char *s, char*t)
+ Line 702  void replace(char *s, char*t)
    }
  }
+ char *trimbb(char *out, char *in)
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
+   char *s;
+   s=out;
+   while (*in != '\0'){
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
+       in++;
+     }
+     *out++ = *in++;
+   }
+   *out='\0';
+   return s;
+ }
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
+ {
+   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+      gives blocc="abcdef2ghi" and alocc="j".
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
+   */
+   char *s, *t, *bl;
+   t=in;s=in;
+   while ((*in != occ) && (*in != '\0')){
+     *alocc++ = *in++;
+   }
+   if( *in == occ){
+     *(alocc)='\0';
+     s=++in;
+   }
+   if (s == t) {/* occ not found */
+     *(alocc-(in-s))='\0';
+     in=s;
+   }
+   while ( *in != '\0'){
+     *blocc++ = *in++;
+   }
+   *blocc='\0';
+   return t;
+ }
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
+ {
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+      gives blocc="abcdef2ghi" and alocc="j".
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
+   */
+   char *s, *t;
+   t=in;s=in;
+   while (*in != '\0'){
+     while( *in == occ){
+       *blocc++ = *in++;
+       s=in;
+     }
+     *blocc++ = *in++;
+   }
+   if (s == t) /* occ not found */
+     *(blocc-(in-s))='\0';
+   else
+     *(blocc-(in-s)-1)='\0';
+   in=s;
+   while ( *in != '\0'){
+     *alocc++ = *in++;
+   }
+   *alocc='\0';
+   return s;
+ }
  int nbocc(char *s, char occ)
  {
    int i,j=0;
- Line 281  int nbocc(char *s, char occ)
+ Line 785  int nbocc(char *s, char occ)
    return j;
  }
- void cutv(char *u,char *v, char*t, char occ)
+ /* void cutv(char *u,char *v, char*t, char occ) */
- {
+ /* { */
-   /* cuts string t into u and v where u is ended by char occ excluding it
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-      gives u="abcedf" and v="ghi2j" */
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   int i,lg,j,p=0;
+ /*   int i,lg,j,p=0; */
-   i=0;
+ /*   i=0; */
-   for(j=0; j<=strlen(t)-1; j++) {
+ /*   lg=strlen(t); */
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+ /*   for(j=0; j<=lg-1; j++) { */
-   }
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
+ /*   } */
-   lg=strlen(t);
-   for(j=0; j<p; j++) {
+ /*   for(j=0; j<p; j++) { */
-     (u[j] = t[j]);
+ /*     (u[j] = t[j]); */
-   }
+ /*   } */
-      u[p]='\0';
+ /*      u[p]='\0'; */
-    for(j=0; j<= lg; j++) {
+ /*    for(j=0; j<= lg; j++) { */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   }
+ /*   } */
- }
+ /* } */
  /********************** nrerror ********************/
- Line 327  void free_vector(double*v, int nl, int n
+ Line 831  void free_vector(double*v, int nl, int n
  }
  /************************ivector *******************************/
- char *cvector(long nl,long nh)
+ int *ivector(long nl,long nh)
  {
-   char *v;
+   int *v;
-   v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-   if (!v) nrerror("allocation failure in cvector");
+   if (!v) nrerror("allocation failure in ivector");
    return v-nl+NR_END;
  }
  /******************free ivector **************************/
- void free_cvector(char *v, long nl, long nh)
+ void free_ivector(int *v, long nl, long nh)
  {
    free((FREE_ARG)(v+nl-NR_END));
  }
- /************************ivector *******************************/
+ /************************lvector *******************************/
- int *ivector(long nl,long nh)
+ long *lvector(long nl,long nh)
  {
-   int *v;
+   long *v;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
    if (!v) nrerror("allocation failure in ivector");
    return v-nl+NR_END;
  }
- /******************free ivector **************************/
+ /******************free lvector **************************/
- void free_ivector(int *v, long nl, long nh)
+ void free_lvector(long *v, long nl, long nh)
  {
    free((FREE_ARG)(v+nl-NR_END));
  }
- Line 410  double **matrix(long nrl, long nrh, long
+ Line 914  double **matrix(long nrl, long nrh, long
    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    return m;
-   /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     */
  }
- Line 465  void free_ma3x(double ***m, long nrl, lo
+ Line 971  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 640  void linmin(double p[], double xi[], int
+ Line 1181  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,"%ld day(s) %ld hour(s) %ld minute(s) %ld 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 650  void powell(double p[], double **xi, int
+ Line 1204  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 660  void powell(double p[], double **xi, int
+ Line 1216  void powell(double p[], double **xi, int
      fp=(*fret);
      ibig=0;
      del=0.0;
-     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+     last_time=curr_time;
-     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+     (void) gettimeofday(&curr_time,&tzp);
-     fprintf(ficrespow,"%d %.12f",*iter,*fret);
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
-     for (i=1;i<=n;i++) {
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+    for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12lf",i, p[i]);
        fprintf(ficrespow," %.12lf", p[i]);
      }
      printf("\n");
      fprintf(ficlog,"\n");
-     fprintf(ficrespow,"\n");
+     fprintf(ficrespow,"\n");fflush(ficrespow);
+     if(*iter <=3){
+       tm = *localtime(&curr_time.tv_sec);
+       strcpy(strcurr,asctime(&tm));
+ /*       asctime_r(&tm,strcurr); */
+       forecast_time=curr_time;
+       itmp = strlen(strcurr);
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+         strcurr[itmp-1]='\0';
+       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       for(niterf=10;niterf<=30;niterf+=10){
+         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+         tmf = *localtime(&forecast_time.tv_sec);
+ /*      asctime_r(&tmf,strfor); */
+         strcpy(strfor,asctime(&tmf));
+         itmp = strlen(strfor);
+         if(strfor[itmp-1]=='\n')
+         strfor[itmp-1]='\0';
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+       }
+     }
      for (i=1;i<=n;i++) {
        for (j=1;j<=n;j++) xit[j]=xi[j][i];
        fptt=(*fret);
- Line 762  void powell(double p[], double **xi, int
+ Line 1342  void powell(double p[], double **xi, int
    }
  }
- /**** Prevalence limit (stable prevalence)  ****************/
+ /**** Prevalence limit (stable or period prevalence)  ****************/
  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
  {
- Line 771  double **prevalim(double **prlim, int nl
+ Line 1351  double **prevalim(double **prlim, int nl
    int i, ii,j,k;
    double min, max, maxmin, maxmax,sumnew=0.;
-   double **matprod2();
+   /* double **matprod2(); */ /* test */
-   double **out, cov[NCOVMAX], **pmij();
+   double **out, cov[NCOVMAX+1], **pmij();
    double **newm;
    double agefin, delaymax=50 ; /* Max number of years to converge */
- Line 787  double **prevalim(double **prlim, int nl
+ Line 1367  double **prevalim(double **prlim, int nl
    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
      newm=savm;
      /* Covariates have to be included here again */
-      cov[2]=agefin;
+     cov[2]=agefin;
-       for (k=1; k<=cptcovn;k++) {
+     for (k=1; k<=cptcovn;k++) {
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
-       }
+     }
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-       for (k=1; k<=cptcovprod;k++)
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      savm=oldm;
      oldm=newm;
      maxmax=0.;
- Line 812  double **prevalim(double **prlim, int nl
+ Line 1394  double **prevalim(double **prlim, int nl
          sumnew=0;
          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
          prlim[i][j]= newm[i][j]/(1-sumnew);
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
          max=FMAX(max,prlim[i][j]);
          min=FMIN(min,prlim[i][j]);
        }
- Line 828  double **prevalim(double **prlim, int nl
+ Line 1411  double **prevalim(double **prlim, int nl
  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
  {
-   double s1, s2;
+   /* According to parameters values stored in x and the covariate's values stored in cov,
+      computes the probability to be observed in state j being in state i by appying the
+      model to the ncovmodel covariates (including constant and age).
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+      ncth covariate in the global vector x is given by the formula:
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+      Outputs ps[i][j] the probability to be observed in j being in j according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
+   double s1, lnpijopii;
    /*double t34;*/
    int i,j,j1, nc, ii, jj;
      for(i=1; i<= nlstate; i++){
-     for(j=1; j<i;j++){
+       for(j=1; j<i;j++){
-       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         /*s2 += param[i][j][nc]*cov[nc];*/
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-       }
+         }
-       ps[i][j]=s2;
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-     }
+       }
-     for(j=i+1; j<=nlstate+ndeath;j++){
+       for(j=i+1; j<=nlstate+ndeath;j++){
-       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-       }
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-       ps[i][j]=s2;
+         }
-     }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-   }
+       }
-     /*ps[3][2]=1;*/
-   for(i=1; i<= nlstate; i++){
-      s1=0;
-     for(j=1; j<i; j++)
-       s1+=exp(ps[i][j]);
-     for(j=i+1; j<=nlstate+ndeath; j++)
-       s1+=exp(ps[i][j]);
-     ps[i][i]=1./(s1+1.);
-     for(j=1; j<i; j++)
-       ps[i][j]= exp(ps[i][j])*ps[i][i];
-     for(j=i+1; j<=nlstate+ndeath; j++)
-       ps[i][j]= exp(ps[i][j])*ps[i][i];
-     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-   } /* end i */
-   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-     for(jj=1; jj<= nlstate+ndeath; jj++){
-       ps[ii][jj]=0;
-       ps[ii][ii]=1;
      }
-   }
+     for(i=1; i<= nlstate; i++){
+       s1=0;
-   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
+       for(j=1; j<i; j++){
-     for(jj=1; jj<= nlstate+ndeath; jj++){
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-      printf("%lf ",ps[ii][jj]);
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-    }
+       }
-     printf("\n ");
+       for(j=i+1; j<=nlstate+ndeath; j++){
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       }
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
+       ps[i][i]=1./(s1+1.);
+       /* Computing other pijs */
+       for(j=1; j<i; j++)
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       for(j=i+1; j<=nlstate+ndeath; j++)
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+     } /* end i */
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       for(jj=1; jj<= nlstate+ndeath; jj++){
+         ps[ii][jj]=0;
+         ps[ii][ii]=1;
+       }
      }
-     printf("\n ");printf("%lf ",cov[2]);*/
- /*
-   for(i=1; i<= npar; i++) printf("%f ",x[i]);
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-   goto end;*/
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
+     /*   } */
+     /*   printf("\n "); */
+     /* } */
+     /* printf("\n ");printf("%lf ",cov[2]);*/
+     /*
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       goto end;*/
      return ps;
  }
  /**************** Product of 2 matrices ******************/
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
  {
    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
    /* in, b, out are matrice of pointers which should have been initialized
       before: only the contents of out is modified. The function returns
       a pointer to pointers identical to out */
-   long i, j, k;
+   int i, j, k;
    for(i=nrl; i<= nrh; i++)
-     for(k=ncolol; k<=ncoloh; k++)
+     for(k=ncolol; k<=ncoloh; k++){
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+       out[i][k]=0.;
-         out[i][k] +=in[i][j]*b[j][k];
+       for(j=ncl; j<=nch; j++)
+         out[i][k] +=in[i][j]*b[j][k];
+     }
    return out;
  }
- Line 923  double ***hpxij(double ***po, int nhstep
+ Line 1526  double ***hpxij(double ***po, int nhstep
       */
    int i, j, d, h, k;
-   double **out, cov[NCOVMAX];
+   double **out, cov[NCOVMAX+1];
    double **newm;
    /* Hstepm could be zero and should return the unit matrix */
- Line 939  double ***hpxij(double ***po, int nhstep
+ Line 1542  double ***hpxij(double ***po, int nhstep
        /* Covariates have to be included here again */
        cov[1]=1.;
        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       for (k=1; k<=cptcovn;k++)
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        for (k=1; k<=cptcovage;k++)
          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       for (k=1; k<=cptcovprod;k++)
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
- Line 956  double ***hpxij(double ***po, int nhstep
+ Line 1560  double ***hpxij(double ***po, int nhstep
      for(i=1; i<=nlstate+ndeath; i++)
        for(j=1;j<=nlstate+ndeath;j++) {
          po[i][j][h]=newm[i][j];
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-          */
        }
+     /*printf("h=%d ",h);*/
    } /* end h */
+ /*     printf("\n H=%d \n",h); */
    return po;
  }
- Line 968  double ***hpxij(double ***po, int nhstep
+ Line 1573  double ***hpxij(double ***po, int nhstep
  double func( double *x)
  {
    int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double sw; /* Sum of weights */
    double lli; /* Individual log likelihood */
- Line 987  double func( double *x)
+ Line 1592  double func( double *x)
    if(mle==1){
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       /* Computes the values of the ncovmodel covariates of the model
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
+          to be observed in j being in i according to the model.
+        */
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
+         cov[2+k]=covar[Tvar[k]][i];
+       }
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
+          has been calculated etc */
        for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 998  double func( double *x)
+ Line 1613  double func( double *x)
            newm=savm;
            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 1007  double func( double *x)
+ Line 1622  double func( double *x)
          } /* end mult */
          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         /* But now since version 0.9 we anticipate for bias and large stepm.
+         /* But now since version 0.9 we anticipate for bias at large stepm.
           * If stepm is larger than one month (smallest stepm) and if the exact delay
           * (in months) between two waves is not a multiple of stepm, we rounded to
           * the nearest (and in case of equal distance, to the lowest) interval but now
           * we keep into memory the bias bh[mi][i] and also the previous matrix product
-          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           * -stepm/2 to stepm/2 .
           * For stepm=1 the results are the same as for previous versions of Imach.
           * For stepm > 1 the results are less biased than in previous versions.
- Line 1022  double func( double *x)
+ Line 1637  double func( double *x)
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
-         /* bias is positive if real duration
+         /* bias bh is positive if real duration
           * is higher than the multiple of stepm and negative otherwise.
           */
          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
          if( s2 > nlstate){
-           /* i.e. if s2 is a death state and if the date of death is known then the contribution
+           /* i.e. if s2 is a death state and if the date of death is known
-              to the likelihood is the probability to die between last step unit time and current
+              then the contribution to the likelihood is the probability to
-              step unit time, which is also the differences between probability to die before dh
+              die between last step unit time and current  step unit time,
-              and probability to die before dh-stepm .
+              which is also equal to probability to die before dh
+              minus probability to die before dh-stepm .
               In version up to 0.92 likelihood was computed
          as if date of death was unknown. Death was treated as any other
          health state: the date of the interview describes the actual state
- Line 1050  double func( double *x)
+ Line 1666  double func( double *x)
          lower mortality.
            */
            lli=log(out[s1][s2] - savm[s1][s2]);
-         }else{
+         } else if  (s2==-2) {
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           /*survp += out[s1][j]; */
+           lli= log(survp);
+         }
+         else if  (s2==-4) {
+           for (j=3,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           lli= log(survp);
+         }
+         else if  (s2==-5) {
+           for (j=1,survp=0. ; j<=2; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           lli= log(survp);
+         }
+         else{
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
          }
- Line 1083  double func( double *x)
+ Line 1720  double func( double *x)
            oldm=newm;
          } /* end mult */
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         /* But now since version 0.9 we anticipate for bias and large stepm.
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
-          * (in months) between two waves is not a multiple of stepm, we rounded to
-          * the nearest (and in case of equal distance, to the lowest) interval but now
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
-          * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
-          * For stepm=1 the results are the same as for previous versions of Imach.
-          * For stepm > 1 the results are less biased than in previous versions.
-          */
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
-         /* bias is positive if real duration
-          * is higher than the multiple of stepm and negative otherwise.
-          */
          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-         /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-         /*if(lli ==000.0)*/
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          ipmx +=1;
          sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- Line 1134  double func( double *x)
+ Line 1750  double func( double *x)
            oldm=newm;
          } /* end mult */
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         /* But now since version 0.9 we anticipate for bias and large stepm.
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
-          * (in months) between two waves is not a multiple of stepm, we rounded to
-          * the nearest (and in case of equal distance, to the lowest) interval but now
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
-          * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
-          * For stepm=1 the results are the same as for previous versions of Imach.
-          * For stepm > 1 the results are less biased than in previous versions.
-          */
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
-         /* bias is positive if real duration
-          * is higher than the multiple of stepm and negative otherwise.
-          */
-         /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-         /*if(lli ==000.0)*/
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          ipmx +=1;
          sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        } /* end of wave */
      } /* end of individual */
-   }else{  /* ml=4 no inter-extrapolation */
+   }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++){
- Line 1185  double func( double *x)
+ Line 1816  double func( double *x)
            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 */
- Line 1198  double func( double *x)
+ Line 1832  double func( double *x)
    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+1], cov[NCOVMAX+1];
+   double **out;
+   double lli; /* Individual log likelihood */
+   double llt;
+   int s1, s2;
+   double bbh, survp;
+   /*extern weight */
+   /* We are differentiating ll according to initial status */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   /*for(i=1;i<imx;i++)
+     printf(" %d\n",s[4][i]);
+   */
+   cov[1]=1.;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     for(mi=1; mi<= wav[i]-1; mi++){
+       for (ii=1;ii<=nlstate+ndeath;ii++)
+         for (j=1;j<=nlstate+ndeath;j++){
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         }
+       for(d=0; d<dh[mi][i]; d++){
+         newm=savm;
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         for (kk=1; kk<=cptcovage;kk++) {
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         }
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
+         savm=oldm;
+         oldm=newm;
+       } /* end mult */
+       s1=s[mw[mi][i]][i];
+       s2=s[mw[mi+1][i]][i];
+       bbh=(double)bh[mi][i]/(double)stepm;
+       /* bias is positive if real duration
+        * is higher than the multiple of stepm and negative otherwise.
+        */
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         lli=log(out[s1][s2] - savm[s1][s2]);
+       } else if  (s2==-2) {
+         for (j=1,survp=0. ; j<=nlstate; j++)
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         lli= log(survp);
+       }else if (mle==1){
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+       } else if(mle==2){
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+       } else if(mle==3){  /* exponential inter-extrapolation */
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+         lli=log(out[s1][s2]); /* Original formula */
+       } else{  /* mle=0 back to 1 */
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         /*lli=log(out[s1][s2]); */ /* Original formula */
+       } /* End of if */
+       ipmx +=1;
+       sw += weight[i];
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       if(globpr){
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+  %11.6f %11.6f %11.6f ", \
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+           llt +=ll[k]*gipmx/gsw;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         }
+         fprintf(ficresilk," %10.6f\n", -llt);
+       }
+     } /* end of wave */
+   } /* end of individual */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   if(globpr==0){ /* First time we count the contributions and weights */
+     gipmx=ipmx;
+     gsw=sw;
+   }
+   return -l;
+ }
+ /*************** function likelione ***********/
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+ {
+   /* This routine should help understanding what is done with
+      the selection of individuals/waves and
+      to check the exact contribution to the likelihood.
+      Plotting could be done.
+    */
+   int k;
+   if(*globpri !=0){ /* Just counts and sums, no printings */
+     strcpy(fileresilk,"ilk");
+     strcat(fileresilk,fileres);
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", fileresilk);
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+     }
+     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+     for(k=1; k<=nlstate; k++)
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+   }
+   *fretone=(*funcone)(p);
+   if(*globpri !=0){
+     fclose(ficresilk);
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     fflush(fichtm);
+   }
+   return;
+ }
  /*********** Maximum Likelihood Estimation ***************/
- Line 1206  void mlikeli(FILE *ficres,double p[], in
+ Line 1970  void mlikeli(FILE *ficres,double p[], in
    int i,j, iter;
    double **xi;
    double fret;
-   char filerespow[FILENAMELENGTH];
+   double fretone; /* Only one call to likelihood */
+   /*  char filerespow[FILENAMELENGTH];*/
    xi=matrix(1,npar,1,npar);
    for (i=1;i<=npar;i++)
      for (j=1;j<=npar;j++)
- Line 1223  void mlikeli(FILE *ficres,double p[], in
+ Line 1988  void mlikeli(FILE *ficres,double p[], in
      for(j=1;j<=nlstate+ndeath;j++)
        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
    fprintf(ficrespow,"\n");
    powell(p,xi,npar,ftol,&iter,&fret,func);
+   free_matrix(xi,1,npar,1,npar);
    fclose(ficrespow);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
- Line 1240  void hesscov(double **matcov, double p[]
+ Line 2007  void hesscov(double **matcov, double p[]
    int i, j,jk;
    int *indx;
-   double hessii(double p[], double delta, int theta, double delti[]);
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-   double hessij(double p[], double delti[], int i, int j);
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
    void lubksb(double **a, int npar, int *indx, double b[]) ;
    void ludcmp(double **a, int npar, int *indx, double *d) ;
+   double gompertz(double p[]);
    hess=matrix(1,npar,1,npar);
    printf("\nCalculation of the hessian matrix. Wait...\n");
- Line 1252  void hesscov(double **matcov, double p[]
+ Line 2019  void hesscov(double **matcov, double p[]
    for (i=1;i<=npar;i++){
      printf("%d",i);fflush(stdout);
      fprintf(ficlog,"%d",i);fflush(ficlog);
-     hess[i][i]=hessii(p,ftolhess,i,delti);
-     /*printf(" %f ",p[i]);*/
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-     /*printf(" %lf ",hess[i][i]);*/
+     /*  printf(" %f ",p[i]);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
    }
    for (i=1;i<=npar;i++) {
- Line 1262  void hesscov(double **matcov, double p[]
+ Line 2031  void hesscov(double **matcov, double p[]
        if (j>i) {
          printf(".%d%d",i,j);fflush(stdout);
          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-         hess[i][j]=hessij(p,delti,i,j);
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
          hess[j][i]=hess[i][j];
          /*printf(" %lf ",hess[i][j]);*/
        }
- Line 1333  void hesscov(double **matcov, double p[]
+ Line 2103  void hesscov(double **matcov, double p[]
  }
  /*************** hessian matrix ****************/
- double hessii( double x[], double delta, int theta, double delti[])
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
  {
    int i;
    int l=1, lmax=20;
    double k1,k2;
-   double p2[NPARMAX+1];
+   double p2[MAXPARM+1]; /* identical to x */
    double res;
-   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
    double fx;
    int k=0,kmax=10;
    double l1;
    fx=func(x);
    for (i=1;i<=npar;i++) p2[i]=x[i];
-   for(l=0 ; l <=lmax; l++){
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
      l1=pow(10,l);
      delts=delt;
      for(k=1 ; k <kmax; k=k+1){
        delt = delta*(l1*k);
        p2[theta]=x[theta] +delt;
-       k1=func(p2)-fx;
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
        p2[theta]=x[theta]-delt;
        k2=func(p2)-fx;
        /*res= (k1-2.0*fx+k2)/delt/delt; */
        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
- #ifdef DEBUG
+ #ifdef DEBUGHESS
        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
  #endif
- Line 1380  double hessii( double x[], double delta,
+ Line 2150  double hessii( double x[], double delta,
  }
- double hessij( double x[], double delti[], int thetai,int thetaj)
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
  {
    int i;
    int l=1, l1, lmax=20;
    double k1,k2,k3,k4,res,fx;
-   double p2[NPARMAX+1];
+   double p2[MAXPARM+1];
    int k;
    fx=func(x);
- Line 1489  void lubksb(double **a, int n, int *indx
+ Line 2259  void lubksb(double **a, int n, int *indx
    }
  }
+ void pstamp(FILE *fichier)
+ {
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+ }
  /************ Frequencies ********************/
- void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, 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 i, m, jk, k1,i1, j1, bool, z1,j;
    int first;
    double ***freq; /* Frequencies */
    double *pp, **prop;
    double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   FILE *ficresp;
    char fileresp[FILENAMELENGTH];
    pp=vector(1,nlstate);
- Line 1510  void  freqsummary(char fileres[], int ia
+ Line 2284  void  freqsummary(char fileres[], int ia
      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      exit(0);
    }
-   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
    j1=0;
    j=cptcoveff;
- Line 1518  void  freqsummary(char fileres[], int ia
+ Line 2292  void  freqsummary(char fileres[], int ia
    first=1;
-   for(k1=1; k1<=j;k1++){
+   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
-       j1++;
+   /*    j1++;
+ */
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
          scanf("%d", i);*/
-       for (i=-1; i<=nlstate+ndeath; i++)
+       for (i=-5; i<=nlstate+ndeath; i++)
-         for (jk=-1; jk<=nlstate+ndeath; jk++)
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
            for(m=iagemin; m <= iagemax+3; m++)
              freq[i][jk][m]=0;
-     for (i=1; i<=nlstate; i++)
+       for (i=1; i<=nlstate; i++)
-       for(m=iagemin; m <= iagemax+3; m++)
+         for(m=iagemin; m <= iagemax+3; m++)
-         prop[i][m]=0;
+           prop[i][m]=0;
        dateintsum=0;
        k2cpt=0;
        for (i=1; i<=imx; i++) {
          bool=1;
-         if  (cptcovn>0) {
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
            for (z1=1; z1<=cptcoveff; z1++)
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-               bool=0;
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
+               bool=0;
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
+             }
          }
          if (bool==1){
            for(m=firstpass; m<=lastpass; m++){
              k2=anint[m][i]+(mint[m][i]/12.);
-             if ((k2>=dateprev1) && (k2<=dateprev2)) {
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                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];
- Line 1557  void  freqsummary(char fileres[], int ia
+ Line 2340  void  freqsummary(char fileres[], int ia
                  dateintsum=dateintsum+k2;
                  k2cpt++;
                }
-             }
+               /*}*/
            }
          }
-       }
+       } /* end i */
-       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]]);
          fprintf(ficresp, "**********\n#");
+         fprintf(ficlog, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficlog, "**********\n#");
        }
        for(i=1; i<=nlstate;i++)
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
- Line 1592  void  freqsummary(char fileres[], int ia
+ Line 2378  void  freqsummary(char fileres[], int ia
              pos += freq[jk][m][i];
            if(pp[jk]>=1.e-10){
              if(first==1){
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              }
              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
            }else{
- Line 1623  void  freqsummary(char fileres[], int ia
+ Line 2409  void  freqsummary(char fileres[], int ia
            if( i <= iagemax){
              if(pos>=1.e-5){
                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
- Line 1644  void  freqsummary(char fileres[], int ia
+ Line 2430  void  freqsummary(char fileres[], int ia
            printf("Others in log...\n");
          fprintf(ficlog,"\n");
        }
-     }
+       /*}*/
    }
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
-   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
    free_vector(pp,1,nlstate);
    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
    /* End of Freq */
  }
  /************ Prevalence ********************/
- void prevalence(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)
+ 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)
  {
    /* 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;
+   int i, m, jk, k1, i1, j1, bool, z1,j;
    double ***freq; /* Frequencies */
    double *pp, **prop;
    double pos,posprop;
    double  y2; /* in fractional years */
    int iagemin, iagemax;
+   int first; /** to stop verbosity which is redirected to log file */
    iagemin= (int) agemin;
    iagemax= (int) agemax;
- Line 1677  void prevalence(double agemin, double ag
+ Line 2464  void prevalence(double agemin, double ag
    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    j1=0;
-   j=cptcoveff;
+   /*j=cptcoveff;*/
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   for(k1=1; k1<=j;k1++){
+   first=1;
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-       j1++;
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
+       j1++;*/
        for (i=1; i<=nlstate; i++)
          for(m=iagemin; m <= iagemax+3; m++)
- Line 1712  void prevalence(double agemin, double ag
+ Line 2500  void prevalence(double agemin, double ag
          }
        }
        for(i=iagemin; i <= iagemax+3; i++){
          for(jk=1,posprop=0; jk <=nlstate ; jk++) {
            posprop += prop[jk][i];
          }
          for(jk=1; jk <=nlstate ; jk++){
            if( i <=  iagemax){
              if(posprop>=1.e-5){
                probs[i][jk][j1]= prop[jk][i]/posprop;
-             }
+             } else{
-           }
+               if(first==1){
+                 first=0;
+                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
+               }
+             }
+           }
          }/* end jk */
        }/* end i */
-     } /* end i1 */
+     /*} *//* end i1 */
-   } /* end k1 */
+   } /* end j1 */
    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    /*free_vector(pp,1,nlstate);*/
- Line 1758  void  concatwav(int wav[], int **dh, int
+ Line 2550  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 1774  void  concatwav(int wav[], int **dh, int
+ Line 2566  void  concatwav(int wav[], int **dh, int
      wav[i]=mi;
      if(mi==0){
+       nbwarn++;
        if(first==0){
-         printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
          first=1;
        }
        if(first==1){
-         fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
        }
      } /* end mi==0 */
    } /* End individuals */
- Line 1791  void  concatwav(int wav[], int **dh, int
+ Line 2584  void  concatwav(int wav[], int **dh, int
        else{
          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
            if (agedc[i] < 2*AGESUP) {
-           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-           if(j==0) j=1;  /* Survives at least one month after exam */
+             if(j==0) j=1;  /* Survives at least one month after exam */
-           k=k+1;
+             else if(j<0){
-           if (j >= jmax) jmax=j;
+               nberr++;
-           if (j <= jmin) jmin=j;
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-           sum=sum+j;
+               j=1; /* Temporary Dangerous patch */
-           /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-           /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-           if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+             }
+             k=k+1;
+             if (j >= jmax){
+               jmax=j;
+               ijmax=i;
+             }
+             if (j <= jmin){
+               jmin=j;
+               ijmin=i;
+             }
+             sum=sum+j;
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
            }
          }
          else{
            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-           /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+ /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
            k=k+1;
-           if (j >= jmax) jmax=j;
+           if (j >= jmax) {
-           else if (j <= jmin)jmin=j;
+             jmax=j;
+             ijmax=i;
+           }
+           else if (j <= jmin){
+             jmin=j;
+             ijmin=i;
+           }
            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-           if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+           if(j<0){
+             nberr++;
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+           }
            sum=sum+j;
          }
          jk= j/stepm;
          jl= j -jk*stepm;
          ju= j -(jk+1)*stepm;
-         if(mle <=1){
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
            if(jl==0){
              dh[mi][i]=jk;
              bh[mi][i]=0;
            }else{ /* We want a negative bias in order to only have interpolation ie
-                   * at the price of an extra matrix product in likelihood */
+                   * to avoid the price of an extra matrix product in likelihood */
              dh[mi][i]=jk+1;
              bh[mi][i]=ju;
            }
- Line 1841  void  concatwav(int wav[], int **dh, int
+ Line 2658  void  concatwav(int wav[], int **dh, int
              bh[mi][i]=ju; /* At least one step */
              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
            }
-         }
+         } /* end if mle */
-       } /* end if mle */
+       }
      } /* end wave */
    }
    jmean=sum/k;
-   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   }
  /*********** Tricode ****************************/
- void tricode(int *Tvar, int **nbcode, int imx)
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
  {
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-   int cptcode=0;
+   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
+   /* nbcode[Tvar[j]][1]=
+   */
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+   int modmaxcovj=0; /* Modality max of covariates j */
+   int cptcode=0; /* Modality max of covariates j */
+   int modmincovj=0; /* Modality min of covariates j */
    cptcoveff=0;
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+   /* Loop on covariates without age and products */
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
-                                modality*/
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+                                modality of this covariate Vj*/
-       Ndum[ij]++; /*store the modality */
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+                                     * If product of Vn*Vm, still boolean *:
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
+                                       modality of the nth covariate of individual i. */
+       if (ij > modmaxcovj)
+         modmaxcovj=ij;
+       else if (ij < modmincovj)
+         modmincovj=ij;
+       if ((ij < -1) && (ij > NCOVMAX)){
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
+         exit(1);
+       }else
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+       /* getting the maximum value of the modality of the covariate
-                                        Tvar[j]. If V=sex and male is 0 and
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-                                        female is 1, then  cptcode=1.*/
+          female is 1, then modmaxcovj=1.*/
      }
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-     for (i=0; i<=cptcode; i++) {
+     cptcode=modmaxcovj;
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-     }
+    /*for (i=0; i<=cptcode; i++) {*/
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
-     ij=1;
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
-     for (i=1; i<=ncodemax[j]; i++) {
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-       for (k=0; k<= maxncov; k++) {
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
-         if (Ndum[k] != 0) {
+       }
-           nbcode[Tvar[j]][ij]=k;
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+     } /* Ndum[-1] number of undefined modalities */
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
+        modmincovj=3; modmaxcovj = 7;
+        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
+        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
+        variables V1_1 and V1_2.
+        nbcode[Tvar[j]][ij]=k;
+        nbcode[Tvar[j]][1]=0;
+        nbcode[Tvar[j]][2]=1;
+        nbcode[Tvar[j]][3]=2;
+     */
+     ij=1; /* ij is similar to i but can jumps over null modalities */
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
+         /*recode from 0 */
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
+                                      k is a modality. If we have model=V1+V1*sex
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
            ij++;
          }
          if (ij > ncodemax[j]) break;
-       }
+       }  /* end of loop on */
-     }
+     } /* end of loop on modality */
-   }
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-  for (i=1; i<=ncovmodel-2; i++) {
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-    /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-    ij=Tvar[i];
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
     Ndum[ij]++;
   }
   ij=1;
-  for (i=1; i<= maxncov; i++) {
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
     if((Ndum[i]!=0) && (i<=ncovcol)){
-      Tvaraff[ij]=i; /*For printing */
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+      Tvaraff[ij]=i; /*For printing (unclear) */
       ij++;
-    }
+    }else
+        Tvaraff[ij]=0;
   }
+  ij--;
-  cptcoveff=ij-1; /*Number of simple covariates*/
+  cptcoveff=ij; /*Number of total covariates*/
  }
  /*********** Health Expectancies ****************/
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+ {
+   /* Health expectancies, no variances */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+   int nhstepma, nstepma; /* Decreasing with age */
+   double age, agelim, hf;
+   double ***p3mat;
+   double eip;
+   pstamp(ficreseij);
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+   fprintf(ficreseij,"# Age");
+   for(i=1; i<=nlstate;i++){
+     for(j=1; j<=nlstate;j++){
+       fprintf(ficreseij," e%1d%1d ",i,j);
+     }
+     fprintf(ficreseij," e%1d. ",i);
+   }
+   fprintf(ficreseij,"\n");
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else  hstepm=estepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
+    * if stepm=24 months pijx are given only every 2 years and by summing them
+    * we are calculating an estimate of the Life Expectancy assuming a linear
+    * progression in between and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+    * to compare the new estimate of Life expectancy with the same linear
+    * hypothesis. A more precise result, taking into account a more precise
+    * curvature will be obtained if estepm is as small as stepm. */
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like estepm months */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed only each two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+      results. So we changed our mind and took the option of the best precision.
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   agelim=AGESUP;
+   /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+ /* nhstepm age range expressed in number of stepm */
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   /* if (stepm >= YEARM) hstepm=1;*/
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   for (age=bage; age<=fage; age ++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     /* if (stepm >= YEARM) hstepm=1;*/
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
+     /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     printf("%d|",(int)age);fflush(stdout);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+     /* Computing expectancies */
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++)
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+         }
+     fprintf(ficreseij,"%3.0f",age );
+     for(i=1; i<=nlstate;i++){
+       eip=0;
+       for(j=1; j<=nlstate;j++){
+         eip +=eij[i][j][(int)age];
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       }
+       fprintf(ficreseij,"%9.4f", eip );
+     }
+     fprintf(ficreseij,"\n");
+   }
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   printf("\n");
+   fprintf(ficlog,"\n");
+ }
+ void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
  {
-   /* Health expectancies */
+   /* Covariances of health expectancies eij and of total life expectancies according
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
+    to initial status i, ei. .
+   */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+   int nhstepma, nstepma; /* Decreasing with age */
    double age, agelim, hf;
-   double ***p3mat,***varhe;
+   double ***p3matp, ***p3matm, ***varhe;
    double **dnewm,**doldm;
-   double *xp;
+   double *xp, *xm;
    double **gp, **gm;
    double ***gradg, ***trgradg;
    int theta;
+   double eip, vip;
    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
    xp=vector(1,npar);
+   xm=vector(1,npar);
    dnewm=matrix(1,nlstate*nlstate,1,npar);
    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-   fprintf(ficreseij,"# Health expectancies\n");
+   pstamp(ficresstdeij);
-   fprintf(ficreseij,"# Age");
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-   for(i=1; i<=nlstate;i++)
+   fprintf(ficresstdeij,"# Age");
+   for(i=1; i<=nlstate;i++){
      for(j=1; j<=nlstate;j++)
-       fprintf(ficreseij," %1d-%1d (SE)",i,j);
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-   fprintf(ficreseij,"\n");
+     fprintf(ficresstdeij," e%1d. ",i);
+   }
+   fprintf(ficresstdeij,"\n");
+   pstamp(ficrescveij);
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   fprintf(ficrescveij,"# Age");
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++){
+       cptj= (j-1)*nlstate+i;
+       for(i2=1; i2<=nlstate;i2++)
+         for(j2=1; j2<=nlstate;j2++){
+           cptj2= (j2-1)*nlstate+i2;
+           if(cptj2 <= cptj)
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+         }
+     }
+   fprintf(ficrescveij,"\n");
    if(estepm < stepm){
      printf ("Problem %d lower than %d\n",estepm, stepm);
    }
- Line 1965  void evsij(char fileres[], double ***eij
+ Line 2965  void evsij(char fileres[], double ***eij
    */
    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   /* If stepm=6 months */
+   /* nhstepm age range expressed in number of stepm */
    agelim=AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-     /* nhstepm age range expressed in number of stepm */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm);
+   /* if (stepm >= YEARM) hstepm=1;*/
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+   for (age=bage; age<=fage; age ++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      /* Typically if 20 years nstepm = 20*12/6=40 stepm */
      /* if (stepm >= YEARM) hstepm=1;*/
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-     gp=matrix(0,nhstepm,1,nlstate*nlstate);
-     gm=matrix(0,nhstepm,1,nlstate*nlstate);
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
+     /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     /* Computing Variances of health expectancies */
+     /* Computing  Variances of health expectancies */
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-      for(theta=1; theta <=npar; theta++){
+        decrease memory allocation */
+     for(theta=1; theta <=npar; theta++){
        for(i=1; i<=npar; i++){
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-       cptj=0;
        for(j=1; j<= nlstate; j++){
          for(i=1; i<=nlstate; i++){
-           cptj=cptj+1;
+           for(h=0; h<=nhstepm-1; h++){
-           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
            }
          }
        }
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-       for(i=1; i<=npar; i++)
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       cptj=0;
-       for(j=1; j<= nlstate; j++){
-         for(i=1;i<=nlstate;i++){
-           cptj=cptj+1;
-           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
-             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
-           }
-         }
-       }
-       for(j=1; j<= nlstate*nlstate; j++)
          for(h=0; h<=nhstepm-1; h++){
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
          }
-      }
+     }/* End theta */
- /* End theta */
+     for(h=0; h<=nhstepm-1; h++)
-      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-      for(h=0; h<=nhstepm-1; h++)
        for(j=1; j<=nlstate*nlstate;j++)
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
-      for(i=1;i<=nlstate*nlstate;i++)
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-       for(j=1;j<=nlstate*nlstate;j++)
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-         varhe[i][j][(int)age] =0.;
+         varhe[ij][ji][(int)age] =0.;
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
- Line 2043  void evsij(char fileres[], double ***eij
+ Line 3035  void evsij(char fileres[], double ***eij
        for(k=0;k<=nhstepm-1;k++){
          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-         for(i=1;i<=nlstate*nlstate;i++)
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-           for(j=1;j<=nlstate*nlstate;j++)
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
        }
      }
      /* Computing expectancies */
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
- /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
          }
-     fprintf(ficreseij,"%3.0f",age );
+     fprintf(ficresstdeij,"%3.0f",age );
-     cptj=0;
+     for(i=1; i<=nlstate;i++){
+       eip=0.;
+       vip=0.;
+       for(j=1; j<=nlstate;j++){
+         eip += eij[i][j][(int)age];
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+       }
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+     }
+     fprintf(ficresstdeij,"\n");
+     fprintf(ficrescveij,"%3.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
-         cptj++;
+         cptj= (j-1)*nlstate+i;
-         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
+         for(i2=1; i2<=nlstate;i2++)
+           for(j2=1; j2<=nlstate;j2++){
+             cptj2= (j2-1)*nlstate+i2;
+             if(cptj2 <= cptj)
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+           }
        }
-     fprintf(ficreseij,"\n");
+     fprintf(ficrescveij,"\n");
-     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    printf("\n");
    fprintf(ficlog,"\n");
+   free_vector(xm,1,npar);
    free_vector(xp,1,npar);
    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
- Line 2083  void evsij(char fileres[], double ***eij
+ Line 3097  void evsij(char fileres[], double ***eij
  }
  /************ Variance ******************/
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
+ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
  {
    /* Variance of health expectancies */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
- Line 2134  void varevsij(char optionfilefiname[], d
+ Line 3148  void varevsij(char optionfilefiname[], d
      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
    }
    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   pstamp(ficresprobmorprev);
    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
- Line 2143  void varevsij(char optionfilefiname[], d
+ Line 3159  void varevsij(char optionfilefiname[], d
        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
    }
    fprintf(ficresprobmorprev,"\n");
-   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+   fprintf(ficgp,"\n# Routine varevsij");
-     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-     exit(0);
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-   }
+ /*   } */
-   else{
-     fprintf(ficgp,"\n# Routine varevsij");
-   }
-   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
-     printf("Problem with html file: %s\n", optionfilehtm);
-     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
-     exit(0);
-   }
-   else{
-     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-   }
    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   pstamp(ficresvij);
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+   if(popbased==1)
+     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
+   else
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
    fprintf(ficresvij,"# Age");
    for(i=1; i<=nlstate;i++)
      for(j=1; j<=nlstate;j++)
-       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
    fprintf(ficresvij,"\n");
    xp=vector(1,npar);
- Line 2188  void varevsij(char optionfilefiname[], d
+ Line 3196  void varevsij(char optionfilefiname[], d
    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
       nhstepm is the number of hstepm from age to agelim
       nstepm is the number of stepm from age to agelin.
-      Look at hpijx to understand the reason of that which relies in memory size
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-      and note for a fixed period like k years */
    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       survival function given by stepm (the optimization length). Unfortunately it
       means that if the survival funtion is printed every two years of age and if
- Line 2255  void varevsij(char optionfilefiname[], d
+ Line 3262  void varevsij(char optionfilefiname[], d
          }
        }
-       for(j=1; j<= nlstate; j++){
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
          for(h=0; h<=nhstepm; h++){
            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
- Line 2365  void varevsij(char optionfilefiname[], d
+ Line 3372  void varevsij(char optionfilefiname[], d
    free_vector(gmp,nlstate+1,nlstate+ndeath);
    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
  */
-   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    free_vector(xp,1,npar);
    free_matrix(doldm,1,nlstate,1,nlstate);
- Line 2388  void varevsij(char optionfilefiname[], d
+ Line 3396  void varevsij(char optionfilefiname[], d
    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    fclose(ficresprobmorprev);
-   fclose(ficgp);
+   fflush(ficgp);
-   fclose(fichtm);
+   fflush(fichtm);
- }
+ }  /* end varevsij */
  /************ Variance of prevlim ******************/
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
+ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
  {
    /* Variance of prevalence limit */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
- Line 2406  void varprevlim(char fileres[], double *
+ Line 3414  void varprevlim(char fileres[], double *
    double **gradg, **trgradg;
    double age,agelim;
    int theta;
-   fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
+   pstamp(ficresvpl);
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
    fprintf(ficresvpl,"# Age");
    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %1d-%1d",i,i);
- Line 2476  void varprevlim(char fileres[], double *
+ Line 3485  void varprevlim(char fileres[], double *
  }
  /************ Variance of one-step probabilities  ******************/
- void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
  {
    int i, j=0,  i1, k1, l1, t, tj;
    int k2, l2, j1,  z1;
    int k=0,l, cptcode;
-   int first=1, first1;
+   int first=1, first1, first2;
    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
    double **dnewm,**doldm;
    double *xp;
    double *gp, *gm;
    double **gradg, **trgradg;
    double **mu;
-   double age,agelim, cov[NCOVMAX];
+   double age,agelim, cov[NCOVMAX+1];
    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
    int theta;
    char fileresprob[FILENAMELENGTH];
    char fileresprobcov[FILENAMELENGTH];
    char fileresprobcor[FILENAMELENGTH];
    double ***varpij;
    strcpy(fileresprob,"prob");
- Line 2521  void varprob(char optionfilefiname[], do
+ Line 3529  void varprob(char optionfilefiname[], do
    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   pstamp(ficresprob);
    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
    fprintf(ficresprob,"# Age");
+   pstamp(ficresprobcov);
    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
    fprintf(ficresprobcov,"# Age");
+   pstamp(ficresprobcor);
    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-   fprintf(ficresprobcov,"# Age");
+   fprintf(ficresprobcor,"# Age");
    for(i=1; i<=nlstate;i++)
- Line 2540  void varprob(char optionfilefiname[], do
+ Line 3550  void varprob(char optionfilefiname[], do
    fprintf(ficresprobcov,"\n");
    fprintf(ficresprobcor,"\n");
   */
-  xp=vector(1,npar);
+   xp=vector(1,npar);
    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
    first=1;
-   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+   fprintf(ficgp,"\n# Routine varprob");
-     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+   fprintf(fichtm,"\n");
-     exit(0);
-   }
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   else{
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-     fprintf(ficgp,"\n# Routine varprob");
+   file %s<br>\n",optionfilehtmcov);
-   }
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+ and drawn. It helps understanding how is the covariance between two incidences.\
-     printf("Problem with html file: %s\n", optionfilehtm);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
-     exit(0);
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-   }
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-   else{
+ standard deviations wide on each axis. <br>\
-     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-     fprintf(fichtm,"\n");
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
-     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
-   }
    cov[1]=1;
-   tj=cptcoveff;
+   /* tj=cptcoveff; */
+   tj = (int) pow(2,cptcoveff);
    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
    j1=0;
-   for(t=1; t<=tj;t++){
+   for(j1=1; j1<=tj;j1++){
-     for(i1=1; i1<=ncodemax[t];i1++){
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
-       j1++;
+     /*j1++;*/
        if  (cptcovn>0) {
          fprintf(ficresprob, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- Line 2589  void varprob(char optionfilefiname[], do
+ Line 3595  void varprob(char optionfilefiname[], do
          fprintf(ficgp, "**********\n#\n");
-         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
          fprintf(ficresprobcor, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          fprintf(ficresprobcor, "**********\n#");
        }
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
        for (age=bage; age<=fage; age ++){
          cov[2]=age;
          for (k=1; k<=cptcovn;k++) {
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
+                                                          * 1  1 1 1 1
+                                                          * 2  2 1 1 1
+                                                          * 3  1 2 1 1
+                                                          */
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
          }
          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          for (k=1; k<=cptcovprod;k++)
            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
          for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++)
- Line 2648  void varprob(char optionfilefiname[], do
+ Line 3659  void varprob(char optionfilefiname[], do
          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
          pmij(pmmij,cov,ncovmodel,x,nlstate);
- Line 2685  void varprob(char optionfilefiname[], do
+ Line 3692  void varprob(char optionfilefiname[], do
          i=0;
          for (k=1; k<=(nlstate);k++){
            for (l=1; l<=(nlstate+ndeath);l++){
-             i=i++;
+             i++;
              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
              for (j=1; j<=i;j++){
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
              }
            }
          }/* end of loop for state */
        } /* end of loop for age */
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
        /* Confidence intervalle of pij  */
        /*
-         fprintf(ficgp,"\nset noparametric;unset label");
+         fprintf(ficgp,"\nunset parametric;unset label");
          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
- Line 2708  void varprob(char optionfilefiname[], do
+ Line 3720  void varprob(char optionfilefiname[], do
        */
        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-       first1=1;
+       first1=1;first2=2;
        for (k2=1; k2<=(nlstate);k2++){
          for (l2=1; l2<=(nlstate+ndeath);l2++){
            if(l2==k2) continue;
- Line 2729  void varprob(char optionfilefiname[], do
+ Line 3741  void varprob(char optionfilefiname[], do
                    /* Computing eigen value of matrix of covariance */
                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                   if ((lc2 <0) || (lc1 <0) ){
+                     if(first2==1){
+                       first1=0;
+                     printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+                     }
+                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
+                     /* lc2=fabs(lc2); */
+                   }
                    /* Eigen vectors */
                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                    /*v21=sqrt(1.-v11*v11); *//* error */
- Line 2748  void varprob(char optionfilefiname[], do
+ Line 3770  void varprob(char optionfilefiname[], do
                      first=0;
                      fprintf(ficgp,"\nset parametric;unset label");
                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
-                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
- Line 2760  void varprob(char optionfilefiname[], do
+ Line 3786  void varprob(char optionfilefiname[], do
                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                    }else{
                      first=0;
-                     fprintf(fichtm," %d (%.3f),",(int) age, c12);
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
- Line 2769  void varprob(char optionfilefiname[], do
+ Line 3795  void varprob(char optionfilefiname[], do
                    }/* if first */
                  } /* age mod 5 */
                } /* end loop age */
-               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                first=1;
              } /*l12 */
            } /* k12 */
          } /*l1 */
        }/* k1 */
-     } /* loop covariates */
+       /* } /* loop covariates */
    }
    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
    free_vector(xp,1,npar);
    fclose(ficresprob);
    fclose(ficresprobcov);
    fclose(ficresprobcor);
-   fclose(ficgp);
+   fflush(ficgp);
-   fclose(fichtm);
+   fflush(fichtmcov);
  }
- Line 2796  void printinghtml(char fileres[], char t
+ Line 3824  void printinghtml(char fileres[], char t
                    double jprev1, double mprev1,double anprev1, \
                    double jprev2, double mprev2,double anprev2){
    int jj1, k1, i1, cpt;
-   /*char optionfilehtm[FILENAMELENGTH];*/
-   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
-     printf("Problem with %s \n",optionfilehtm), exit(0);
-     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
-   }
-    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
+ </ul>");
-  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-  - Life expectancies by age and initial health status (estepm=%2d months):
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-    <a href=\"e%s\">e%s</a> <br>\n</li>", \
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
+    fprintf(fichtm,"\
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+    fprintf(fichtm,"\
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+    fprintf(fichtm,"\
+  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n",
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+    fprintf(fichtm,"\
+  - Population projections by age and states: \
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-  m=cptcoveff;
+  m=pow(2,cptcoveff);
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   jj1=0;
- Line 2826  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3861  fprintf(fichtm," \n<ul><li><b>Graphs</b>
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
       /* Pij */
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
- <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
       /* Quasi-incidences */
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
-        /* Stable prevalence in each health state */
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+        /* Period (stable) prevalence in each health state */
         for(cpt=1; cpt<nlstate;cpt++){
-          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
+          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
- <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         }
       for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
+         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
- <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and
- health expectancies in states (1) and (2): e%s%d.png<br>
- <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     } /* end i1 */
   }/* End k1 */
   fprintf(fichtm,"</ul>");
-  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
+  fprintf(fichtm,"\
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
-  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
+  fprintf(fichtm,"\
-  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+  fprintf(fichtm,"\
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+  fprintf(fichtm,"\
+  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+  fprintf(fichtm,"\
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+  fprintf(fichtm,"\
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
- Line 2863  health expectancies in states (1) and (2
+ Line 3918  health expectancies in states (1) and (2
  /*      <br>",fileres,fileres,fileres,fileres); */
  /*  else  */
  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
- fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+  fflush(fichtm);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-  m=cptcoveff;
+  m=pow(2,cptcoveff);
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   jj1=0;
- Line 2879  fprintf(fichtm," <ul><li><b>Graphs</b></
+ Line 3935  fprintf(fichtm," <ul><li><b>Graphs</b></
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed and period prevalence (with confident
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- interval) in state (%d): v%s%d%d.png <br>
+ prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
- <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
       }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+ true period expectancies (those weighted with period prevalences are also\
+  drawn in addition to the population based expectancies computed using\
+  observed and cahotic prevalences: %s%d.png<br>\
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     } /* end i1 */
   }/* End k1 */
   fprintf(fichtm,"</ul>");
- fclose(fichtm);
+  fflush(fichtm);
  }
  /******************* Gnuplot file **************/
- void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   char dirfileres[132],optfileres[132];
-   int ng;
+   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+   int ng=0;
-     printf("Problem with file %s",optionfilegnuplot);
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-   }
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+ /*   } */
    /*#ifdef windows */
-     fprintf(ficgp,"cd \"%s\" \n",pathc);
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
      /*#endif */
- m=pow(2,cptcoveff);
+   m=pow(2,cptcoveff);
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
   /* 1eme*/
    for (cpt=1; cpt<= nlstate ; cpt ++) {
-    for (k1=1; k1<= m ; k1 ++) {
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
+      fprintf(ficgp,"set xlabel \"Age\" \n\
+ set ylabel \"Probability\" \n\
+ set ter png small size 320, 240\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+        else        fprintf(ficgp," \%%*lf (\%%*lf)");
       }
-      fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
+      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
+      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }
-      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     }
    }
    /*2 eme*/
    for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\nset out \"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);
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
      for (i=1; i<= nlstate+1 ; i ++) {
        k=2*i;
-       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
-       fprintf(ficgp,"\" t\"\" w l 0,");
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
      }
    }
- Line 2962  m=pow(2,cptcoveff);
+ Line 4031  m=pow(2,cptcoveff);
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<= nlstate ; cpt ++) {
-       k=2+nlstate*(2*cpt-2);
+       /*       k=2+nlstate*(2*cpt-2); */
-       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       k=2+(nlstate+1)*(cpt-1);
-       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+       fprintf(ficgp,"set ter png small size 320, 240\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
- Line 2974  m=pow(2,cptcoveff);
+ Line 4045  m=pow(2,cptcoveff);
        */
        for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
        }
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
      }
    }
- Line 2984  m=pow(2,cptcoveff);
+ Line 4057  m=pow(2,cptcoveff);
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<=nlstate ; cpt ++) {
        k=3;
-       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter png small size 320, 240\n\
+ unset log y\n\
+ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
-       for (i=1; i<= nlstate ; i ++)
+       for (i=1; i< nlstate ; i ++)
          fprintf(ficgp,"+$%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 3013  m=pow(2,cptcoveff);
+ Line 4089  m=pow(2,cptcoveff);
        }
      }
     }
+   /*goto avoid;*/
     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       for(jk=1; jk <=m; jk++) {
-        fprintf(ficgp,"\nset out \"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
           fprintf(ficgp,"\nset title \"Probability\"\n");
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
         i=1;
         for(k2=1; k2<=nlstate; k2++) {
           k3=i;
- Line 3031  m=pow(2,cptcoveff);
+ Line 4107  m=pow(2,cptcoveff);
                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
               else
                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-              ij=1;
+              ij=1;/* To be checked else nbcode[0][0] wrong */
               for(j=3; j <=ncovmodel; j++) {
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
-                  ij++;
+                /*        ij++; */
-                }
+                /* } */
-                else
+                /* else */
                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
               }
               fprintf(ficgp,")/(1");
- Line 3046  m=pow(2,cptcoveff);
+ Line 4122  m=pow(2,cptcoveff);
                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                 ij=1;
                 for(j=3; j <=ncovmodel; j++){
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
-                    ij++;
+                  /*   ij++; */
-                  }
+                  /* } */
-                  else
+                  /* else */
                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                 }
                 fprintf(ficgp,")");
- Line 3063  m=pow(2,cptcoveff);
+ Line 4139  m=pow(2,cptcoveff);
         } /* end k2 */
       } /* end jk */
     } /* end ng */
-    fclose(ficgp);
+  avoid:
+    fflush(ficgp);
  }  /* end gnuplot */
- Line 3126  prevforecast(char fileres[], double anpr
+ Line 4203  prevforecast(char fileres[], double anpr
    char fileresf[FILENAMELENGTH];
    agelim=AGESUP;
-   prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    strcpy(fileresf,"f");
    strcat(fileresf,fileres);
- Line 3249  populforecast(char fileres[], double anp
+ Line 4326  populforecast(char fileres[], double anp
    agelim=AGESUP;
    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    strcpy(filerespop,"pop");
- Line 3391  populforecast(char fileres[], double anp
+ Line 4468  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)
- /**************** Main Program *****************/
- /***********************************************/
- int main(int argc, char *argv[])
  {
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+     printf("Problem with file: %s\n", optionfich);
-   double agedeb, agefin,hf;
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+     return (0);
+   }
-   double fret;
+   fflush(fichier);
-   double **xi,tmp,delta;
+   return (1);
+ }
-   double dum; /* Dummy variable */
-   double ***p3mat;
-   double ***mobaverage;
-   int *indx;
-   char line[MAXLINE], linepar[MAXLINE];
-   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
-   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,*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=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;
+ /**************** function prwizard **********************/
-   double ftolpl=FTOL;
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-   double **prlim;
+ {
-   double *severity;
-   double ***param; /* Matrix of parameters */
-   double  *p;
-   double **matcov; /* Matrix of covariance */
-   double ***delti3; /* Scale */
-   double *delti; /* Scale */
-   double ***eij, ***vareij;
-   double **varpl; /* Variances of prevalence limits by age */
-   double *epj, vepp;
-   double kk1, kk2;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+   /* 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;
-   char z[1]="c", occ;
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- #include <sys/time.h>
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- #include <time.h>
+   for(i=1; i <=nlstate; i++){
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
-   /* long total_usecs;
+       if(j==i) continue;
-      struct timeval start_time, end_time;
+       jj++;
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-      gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+       printf("%1d%1d",i,j);
-   getcwd(pathcd, size);
+       fprintf(ficparo,"%1d%1d",i,j);
-   printf("\n%s",version);
-   if(argc <=1){
-     printf("\nEnter the parameter file name: ");
-     scanf("%s",pathtot);
-   }
-   else{
-     strcpy(pathtot,argv[1]);
-   }
-   /*if(getcwd(pathcd, 80)!= 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(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-   chdir(path);
-   replace(pathc,path);
-   /*-------- 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",version);
-   fprintf(ficlog,"\nEnter the parameter file name: ");
-   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-   fflush(ficlog);
-   /* */
-   strcpy(fileres,"r");
-   strcat(fileres, optionfilefiname);
-   strcat(fileres,".txt");    /* Other files have txt extension */
-   /*---------arguments file --------*/
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-     printf("Problem with optionfile %s\n",optionfile);
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
-     goto end;
-   }
-   strcpy(filereso,"o");
-   strcat(filereso,fileres);
-   if((ficparo=fopen(filereso,"w"))==NULL) {
-     printf("Problem with Output resultfile: %s\n", filereso);
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-     goto end;
-   }
-   /* Reads comments: lines beginning with '#' */
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
-   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){
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   covar=matrix(0,NCOVMAX,1,n);
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-   /* Read guess parameters */
-   /* Reads comments: lines beginning with '#' */
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-   for(i=1; i <=nlstate; i++)
-     for(j=1; j <=nlstate+ndeath-1; j++){
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
-       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]);
+         /*        printf(" %lf",param[i][j][k]); */
-         if(mle==1){
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-           printf(" %lf",param[i][j][k]);
+         printf(" 0.");
-           fprintf(ficlog," %lf",param[i][j][k]);
+         fprintf(ficparo," 0.");
-         }
-         else
-           fprintf(ficlog," %lf",param[i][j][k]);
-         fprintf(ficparo," %lf",param[i][j][k]);
        }
-       fscanf(ficpar,"\n");
+       printf("\n");
-       if(mle==1)
-         printf("\n");
-       fprintf(ficlog,"\n");
        fprintf(ficparo,"\n");
      }
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-   p=param[1][1];
-   /* Reads comments: lines beginning with '#' */
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
    }
-   ungetc(c,ficpar);
+   printf("# Scales (for hessian or gradient estimation)\n");
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-   /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
    for(i=1; i <=nlstate; i++){
-     for(j=1; j <=nlstate+ndeath-1; j++){
+     jj=0;
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
+       jj++;
+       fprintf(ficparo,"%1d%1d",i,j);
        printf("%1d%1d",i,j);
-       fprintf(ficparo,"%1d%1d",i1,j1);
+       fflush(stdout);
        for(k=1; k<=ncovmodel;k++){
-         fscanf(ficpar,"%le",&delti3[i][j][k]);
+         /*      printf(" %le",delti3[i][j][k]); */
-         printf(" %le",delti3[i][j][k]);
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-         fprintf(ficparo," %le",delti3[i][j][k]);
+         printf(" 0.");
+         fprintf(ficparo," 0.");
        }
-       fscanf(ficpar,"\n");
+       numlinepar++;
        printf("\n");
        fprintf(ficparo,"\n");
      }
    }
-   delti=delti3[1][1];
+   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 */
-   /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+   for (i=0;i<=imx-1 ; i++) {
+     sump=sump+weight[i];
-   /* Reads comments: lines beginning with '#' */
+     /*    sump=sump+1;*/
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     num=num+1;
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
    }
-   ungetc(c,ficpar);
-   matcov=matrix(1,npar,1,npar);
+   /* for (i=0; i<=imx; i++)
-   for(i=1; i <=npar; 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]);*/
-     fscanf(ficpar,"%s",&str);
-     if(mle==1)
+   for (i=1;i<=imx ; i++)
-       printf("%s",str);
+     {
-     fprintf(ficlog,"%s",str);
+       if (cens[i] == 1 && wav[i]>1)
-     fprintf(ficparo,"%s",str);
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-     for(j=1; j <=i; j++){
-       fscanf(ficpar," %le",&matcov[i][j]);
+       if (cens[i] == 0 && wav[i]>1)
-       if(mle==1){
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-         printf(" %.5le",matcov[i][j]);
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-         fprintf(ficlog," %.5le",matcov[i][j]);
+       /*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]);*/
        }
-       else
-         fprintf(ficlog," %.5le",matcov[i][j]);
-       fprintf(ficparo," %.5le",matcov[i][j]);
      }
-     fscanf(ficpar,"\n");
-     if(mle==1)
-       printf("\n");
-     fprintf(ficlog,"\n");
-     fprintf(ficparo,"\n");
-   }
-   for(i=1; i <=npar; i++)
-     for(j=i+1;j<=npar;j++)
-       matcov[i][j]=matcov[j][i];
-   if(mle==1)
-     printf("\n");
-   fprintf(ficlog,"\n");
+  /*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;
+ }
-   /*-------- Rewriting paramater file ----------*/
+ #ifdef GSL
-   strcpy(rfileres,"r");    /* "Rparameterfile */
+ /******************* Gompertz_f Likelihood ******************************/
-   strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+ double gompertz_f(const gsl_vector *v, void *params)
-   strcat(rfileres,".");    /* */
+ {
-   strcat(rfileres,optionfilext);    /* Other files have txt extension */
+   double A,B,LL=0.0,sump=0.,num=0.;
-   if((ficres =fopen(rfileres,"w"))==NULL) {
+   double *x= (double *) v->data;
-     printf("Problem writing new parameter file: %s\n", fileres);goto end;
+   int i,n=0; /* n is the size of the sample */
-     fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+   for (i=0;i<=imx-1 ; i++) {
+     sump=sump+weight[i];
+     /*    sump=sump+1;*/
+     num=num+1;
    }
-   fprintf(ficres,"#%s\n",version);
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
+   for (i=1;i<=imx ; i++)
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
+       if (cens[i] == 0 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
+         LL=LL+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+       }
+     }
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
+   return -2*LL*num/sump;
+ }
+ #endif
+ /******************* Printing html file ***********/
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   int imx,  double p[],double **matcov,double agemortsup){
+   int i,k;
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   for (i=1;i<=2;i++)
+     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+   fprintf(fichtm,"</ul>");
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+  for (k=agegomp;k<(agemortsup-2);k++)
+    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+   fflush(fichtm);
+ }
+ /******************* Gnuplot file **************/
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   char dirfileres[132],optfileres[132];
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   int ng;
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     /*#endif */
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+ }
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
+ {
    /*-------- data file ----------*/
+   FILE *fic;
+   char dummy[]="                         ";
+   int i, j, n;
+   int linei, month, year,iout;
+   char line[MAXLINE], linetmp[MAXLINE];
+   char stra[80], strb[80];
+   char *stratrunc;
+   int lstra;
    if((fic=fopen(datafile,"r"))==NULL)    {
-     printf("Problem with datafile: %s\n", datafile);goto end;
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
    }
-   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);
-   tab=ivector(1,NCOVMAX);
-   ncodemax=ivector(1,8);
    i=1;
-   while (fgets(line, MAXLINE, fic) != NULL)    {
+   linei=0;
-     if ((i >= firstobs) && (i <=lastobs)) {
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+     linei=linei+1;
-       for (j=maxwav;j>=1;j--){
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-         cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
+       if(line[j] == '\t')
-         strcpy(line,stra);
+         line[j] = ' ';
-         cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+     }
-         cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+       ;
+     };
+     line[j+1]=0;  /* Trims blanks at end of line */
+     if(line[0]=='#'){
+       fprintf(ficlog,"Comment line\n%s\n",line);
+       printf("Comment line\n%s\n",line);
+       continue;
+     }
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
+     for (j=0; line[j]!='\0';j++){
+       line[j]=linetmp[j];
+     }
+     for (j=maxwav;j>=1;j--){
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
+       }else{
+         errno=0;
+         lval=strtol(strb,&endptr,10);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
+           return 1;
+         }
        }
+       s[j][i]=lval;
-       cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
-       cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
+       strcpy(line,stra);
+       cutv(stra, strb,line,' ');
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       }
+       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+         month=99;
+         year=9999;
+       }else{
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
+         return 1;
+       }
+       anint[j][i]= (double) year;
+       mint[j][i]= (double)month;
+       strcpy(line,stra);
+     } /* ENd Waves */
+     cutv(stra, strb,line,' ');
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     andc[i]=(double) year;
+     moisdc[i]=(double) month;
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
+     else  if(iout=sscanf(strb,"%s.", dummy) != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     if (year==9999) {
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     annais[i]=(double)(year);
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     errno=0;
+     dval=strtod(strb,&endptr);
+     if( strb[0]=='\0' || (*endptr != '\0')){
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fflush(ficlog);
+       return 1;
+     }
+     weight[i]=dval;
+     strcpy(line,stra);
+     for (j=ncovcol;j>=1;j--){
+       cutv(stra, strb,line,' ');
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
+       }else{
+         errno=0;
+         lval=strtol(strb,&endptr,10);
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
+           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
+           return 1;
+         }
+       }
+       if(lval <-1 || lval >1){
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n \
+  Exiting.\n",lval,linei, i,line,j);
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n \
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
+         return 1;
+       }
+       covar[j][i]=(double)(lval);
+       strcpy(line,stra);
+     }
+     lstra=strlen(stra);
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       stratrunc = &(stra[lstra-9]);
+       num[i]=atol(stratrunc);
+     }
+     else
+       num[i]=atol(stra);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+     i=i+1;
+   } /* End loop reading  data */
-       cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
+   *imax=i-1; /* Number of individuals */
-       cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
+   fclose(fic);
+   return (0);
+   endread:
+     printf("Exiting readdata: ");
+     fclose(fic);
+     return (1);
-       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;
-     }
-   }
-   /* printf("ii=%d", ij);
-      scanf("%d",i);*/
-   imx=i-1; /* Number of individuals */
-   /* for (i=1; i<=imx; i++){
+ }
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+ void removespace(char *str) {
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+   char *p1 = str, *p2 = str;
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+   do
-     }*/
+     while (*p2 == ' ')
-    /*  for (i=1; i<=imx; i++){
+       p2++;
-      if (s[4][i]==9)  s[4][i]=-1;
+   while (*p1++ = *p2++);
-      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]));}*/
+ }
-  for (i=1; i<=imx; i++)
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
-      else weight[i]=1;*/
-   /* Calculation of the number of parameter from char model*/
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
-   Tprod=ivector(1,15);
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
-   Tvaraff=ivector(1,15);
+    * - cptcovn or number of covariates k of the models excluding age*products =6
-   Tvard=imatrix(1,15,1,2);
+    * - cptcovage number of covariates with age*products =2
-   Tage=ivector(1,15);
+    * - cptcovs number of simple covariates
+    * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
+    *     which is a new column after the 9 (ncovcol) variables.
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
+  */
+ {
+   int i, j, k, ks;
+   int i1, j1, k1, k2;
+   char modelsav[80];
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
+   /*removespace(model);*/
    if (strlen(model) >1){ /* If there is at least 1 covariate */
-     j=0, j1=0, k1=1, k2=1;
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-     j=nbocc(model,'+'); /* j=Number of '+' */
+     j=nbocc(model,'+'); /**< j=Number of '+' */
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
-     cptcovn=j+1;
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-     cptcovprod=j1; /*Number of products */
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
+                   /* including age products which are counted in cptcovage.
+                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
      strcpy(modelsav,model);
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+     if (strstr(model,"AGE") !=0){
-       printf("Error. Non available option model=%s ",model);
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
-       goto end;
+       return 1;
+     }
+     if (strstr(model,"v") !=0){
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
+       return 1;
      }
-     /* This loop fills the array Tvar from the string 'model'.*/
+     /*   Design
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
+      *  <          ncovcol=8                >
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
+      *   k=  1    2      3       4     5       6      7        8
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
+      *  covar[k,i], value of kth covariate if not including age for individual i:
+      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
+      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
+      *  Tage[++cptcovage]=k
+      *       if products, new covar are created after ncovcol with k1
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
+      *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
+      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
+      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
+      *  <          ncovcol=8                >
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
+      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
+      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
+      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+      * p Tprod[1]@2={                         6, 5}
+      *p Tvard[1][1]@4= {7, 8, 5, 6}
+      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
+      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+      *How to reorganize?
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
+      * Struct []
+      */
-     for(i=(j+1); i>=1;i--){
+     /* This loop fills the array Tvar from the string 'model'.*/
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
+     /*  k=1 Tvar[1]=2 (from V2) */
+     /*  k=5 Tvar[5] */
+     /* for (k=1; k<=cptcovn;k++) { */
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+     /*  } */
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+     /*
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
+         Tvar[k]=0;
+     cptcovage=0;
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
        /*scanf("%d",i);*/
-       if (strchr(strb,'*')) {  /* Model includes a product */
+       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+           /* covar is not filled and then is empty */
            cptcovprod--;
-           cutv(strb,stre,strd,'V');
+           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
-           cptcovage++;
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-             Tage[cptcovage]=i;
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-             /*printf("stre=%s ", stre);*/
+           /*printf("stre=%s ", stre);*/
-         }
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
            cptcovprod--;
-           cutv(strb,stre,strc,'V');
+           cutl(stre,strb,strc,'V');
-           Tvar[i]=atoi(stre);
+           Tvar[k]=atoi(stre);
            cptcovage++;
-           Tage[cptcovage]=i;
+           Tage[cptcovage]=k;
-         }
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-         else {  /* Age is not in the model */
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+           cptcovn++;
-           Tvar[i]=ncovcol+k1;
+           cptcovprodnoage++;k1++;
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-           Tprod[k1]=i;
+           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
-           Tvard[k1][1]=atoi(strc); /* m*/
+                                   because this model-covariate is a construction we invent a new column
-           Tvard[k1][2]=atoi(stre); /* n */
+                                   ncovcol + k1
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-           for (k=1; k<=lastobs;k++)
+           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-           k1++;
+           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
            k2=k2+2;
-         }
+           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
-       }
+           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
+           for (i=1; i<=lastobs;i++){
+             /* Computes the new covariate which is a product of
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+           }
+         } /* End age is not in the model */
+       } /* End if model includes a product */
        else { /* no more sum */
          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
         /*  scanf("%d",i);*/
-       cutv(strd,strc,strb,'V');
+         cutl(strd,strc,strb,'V');
-       Tvar[i]=atoi(strc);
+         ks++; /**< Number of simple covariates */
+         cptcovn++;
+         Tvar[k]=atoi(strd);
        }
-       strcpy(modelsav,stra);
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
          scanf("%d",i);*/
      } /* end of loop + */
- Line 3808  int main(int argc, char *argv[])
+ Line 5083  int main(int argc, char *argv[])
    printf("cptcovprod=%d ", cptcovprod);
    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-   scanf("%d ",i);
+   scanf("%d ",i);*/
-   fclose(fic);*/
-     /*  if(mle==1){*/
-   if (weightopt != 1) { /* Maximisation without weights*/
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-     for(i=1;i<=n;i++) weight[i]=1.0;
+   endread:
-   }
+     printf("Exiting decodemodel: ");
-     /*-calculation of age at interview from date of interview and age at death -*/
+     return (1);
-   agev=matrix(1,maxwav,1,imx);
+ }
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+ {
+   int i, m;
    for (i=1; i<=imx; i++) {
      for(m=2; (m<= maxwav); m++) {
- Line 3825  int main(int argc, char *argv[])
+ Line 5103  int main(int argc, char *argv[])
          s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+         *nberr++;
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
          s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-         printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+         *nberr++;
-         fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
-         s[m][i]=-1;
+         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
        }
      }
    }
- Line 3840  int main(int argc, char *argv[])
+ Line 5120  int main(int argc, char *argv[])
    for (i=1; i<=imx; i++)  {
      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
      for(m=firstpass; (m<= lastpass); m++){
-       if(s[m][i] >0){
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
          if (s[m][i] >= nlstate+1) {
            if(agedc[i]>0)
              if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
- Line 3848  int main(int argc, char *argv[])
+ Line 5128  int main(int argc, char *argv[])
            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
              else {
                if ((int)andc[i]!=9999){
-                 printf("Warning negative age at death: %d line:%d\n",num[i],i);
+                 nbwarn++;
-                 fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                  agev[m][i]=-1;
                }
              }
          }
          else if(s[m][i] !=9){ /* Standard case, age in fractional
-                                  years but with the precision of a
+                                  years but with the precision of a month */
-                                  month */
            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
            if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
              agev[m][i]=1;
-           else if(agev[m][i] <agemin){
+           else if(agev[m][i] < *agemin){
-             agemin=agev[m][i];
+             *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);*/
+             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){
+           else if(agev[m][i] >*agemax){
-             agemax=agev[m][i];
+             *agemax=agev[m][i];
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+             printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
            }
            /*agev[m][i]=anint[m][i]-annais[i];*/
            /*     agev[m][i] = age[i]+2*m;*/
- Line 3884  int main(int argc, char *argv[])
+ Line 5164  int main(int argc, char *argv[])
    for (i=1; i<=imx; i++)  {
      for(m=firstpass; (m<=lastpass); m++){
        if (s[m][i] > (nlstate+ndeath)) {
+         *nberr++;
          printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
          fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-         goto end;
+         return 1;
        }
      }
    }
    /*for (i=1; i<=imx; i++){
    for (m=firstpass; (m<lastpass); m++){
-      printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
  }
  }*/
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-   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);
-   /* free_matrix(mint,1,maxwav,1,n);
-      free_matrix(anint,1,maxwav,1,n);*/
-   free_vector(moisdc,1,n);
-   free_vector(andc,1,n);
+   return (0);
-   wav=ivector(1,imx);
+   endread:
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+     printf("Exiting calandcheckages: ");
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+     return (1);
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+ }
+ /***********************************************/
+ /**************** Main Program *****************/
+ /***********************************************/
+ int main(int argc, char *argv[])
+ {
+ #ifdef GSL
+   const gsl_multimin_fminimizer_type *T;
+   size_t iteri = 0, it;
+   int rval = GSL_CONTINUE;
+   int status = GSL_SUCCESS;
+   double ssval;
+ #endif
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+   int linei, month, year,iout;
+   int jj, ll, li, lj, lk, imk;
+   int numlinepar=0; /* Current linenumber of parameter file */
+   int itimes;
+   int NDIM=2;
+   int vpopbased=0;
+   char ca[32], cb[32], cc[32];
+   /*  FILE *fichtm; *//* Html File */
+   /* FILE *ficgp;*/ /*Gnuplot File */
+   struct stat info;
+   double agedeb, agefin,hf;
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   double fret;
+   double **xi,tmp,delta;
+   double dum; /* Dummy variable */
+   double ***p3mat;
+   double ***mobaverage;
+   int *indx;
+   char line[MAXLINE], linepar[MAXLINE];
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   char pathr[MAXLINE], pathimach[MAXLINE];
+   char **bp, *tok, *val; /* pathtot */
+   int firstobs=1, lastobs=10;
+   int sdeb, sfin; /* Status at beginning and end */
+   int c,  h , cpt,l;
+   int ju,jl, mi;
+   int i1,j1, jk,aa,bb, stepsize, ij;
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   int mobilav=0,popforecast=0;
+   int hstepm, nhstepm;
+   int agemortsup;
+   float  sumlpop=0.;
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+   double bage, fage, age, agelim, agebase;
+   double ftolpl=FTOL;
+   double **prlim;
+   double ***param; /* Matrix of parameters */
+   double  *p;
+   double **matcov; /* Matrix of covariance */
+   double ***delti3; /* Scale */
+   double *delti; /* Scale */
+   double ***eij, ***vareij;
+   double **varpl; /* Variances of prevalence limits by age */
+   double *epj, vepp;
+   double kk1, kk2;
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double **ximort;
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
+   int *dcwave;
+   char z[1]="c", occ;
+   /*char  *strt;*/
+   char strtend[80];
+   long total_usecs;
+ /*   setlocale (LC_ALL, ""); */
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   (void) gettimeofday(&start_time,&tzp);
+   curr_time=start_time;
+   tm = *localtime(&start_time.tv_sec);
+   tmg = *gmtime(&start_time.tv_sec);
+   strcpy(strstart,asctime(&tm));
+ /*  printf("Localtime (at start)=%s",strstart); */
+ /*  tp.tv_sec = tp.tv_sec +86400; */
+ /*  tm = *localtime(&start_time.tv_sec); */
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ /*   tp.tv_sec = mktime(&tmg); */
+ /*   strt=asctime(&tmg); */
+ /*   printf("Time(after) =%s",strstart);  */
+ /*  (void) time (&time_value);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+ *  tm = *localtime(&time_value);
+ *  strstart=asctime(&tm);
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+ */
+   nberr=0; /* Number of errors and warnings */
+   nbwarn=0;
+   getcwd(pathcd, size);
+   printf("\n%s\n%s",version,fullversion);
+   if(argc <=1){
+     printf("\nEnter the parameter file name: ");
+     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, 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("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   chdir(path); /* Can be a relative path */
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+     printf("Current directory %s!\n",pathcd);
+   strcpy(command,"mkdir ");
+   strcat(command,optionfilefiname);
+   if((outcmd=system(command)) != 0){
+     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 */
+   /*---------arguments file --------*/
+   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) { /* opened on subdirectory */
+     printf("Problem with Output resultfile: %s\n", filereso);
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     fflush(ficlog);
+     goto end;
+   }
+   /* Reads comments: lines beginning with '#' */
+   numlinepar=0;
+   while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     numlinepar++;
+     fputs(line,stdout);
+     fputs(line,ficparo);
+     fputs(line,ficlog);
+   }
+   ungetc(c,ficpar);
+   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   numlinepar++;
+   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fflush(ficlog);
+   while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     numlinepar++;
+     fputs(line, stdout);
+     //puts(line);
+     fputs(line,ficparo);
+     fputs(line,ficlog);
+   }
+   ungetc(c,ficpar);
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
+      v1+v2*age+v2*v3 makes cptcovn = 3
+   */
+   if (strlen(model)>1)
+     ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
+   else
+     ncovmodel=2;
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
+     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fflush(stdout);
+     fclose (ficlog);
+     goto end;
+   }
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   delti=delti3[1][1];
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     fclose (ficparo);
+     fclose (ficlog);
+     goto end;
+     exit(0);
+   }
+   else if(mle==-3) {
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     matcov=matrix(1,npar,1,npar);
+   }
+   else{
+     /* Read guessed parameters */
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     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);
+     /* Reads scales values */
+     p=param[1][1];
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath-1; j++){
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ((i1-i)*(j1-j)!=0){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           exit(1);
+         }
+         printf("%1d%1d",i,j);
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficlog,"%1d%1d",i1,j1);
+         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");
+       }
+     }
+     fflush(ficlog);
+     /* Reads covariance matrix */
+     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 '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     matcov=matrix(1,npar,1,npar);
+     for(i=1; i <=npar; i++)
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
+     for(i=1; i <=npar; i++){
+       fscanf(ficpar,"%s",str);
+       if(mle==1)
+         printf("%s",str);
+       fprintf(ficlog,"%s",str);
+       fprintf(ficparo,"%s",str);
+       for(j=1; j <=i; j++){
+         fscanf(ficpar," %le",&matcov[i][j]);
+         if(mle==1){
+           printf(" %.5le",matcov[i][j]);
+         }
+         fprintf(ficlog," %.5le",matcov[i][j]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
+       }
+       fscanf(ficpar,"\n");
+       numlinepar++;
+       if(mle==1)
+         printf("\n");
+       fprintf(ficlog,"\n");
+       fprintf(ficparo,"\n");
+     }
+     for(i=1; i <=npar; i++)
+       for(j=i+1;j<=npar;j++)
+         matcov[i][j]=matcov[j][i];
+     if(mle==1)
+       printf("\n");
+     fprintf(ficlog,"\n");
+     fflush(ficlog);
+     /*-------- Rewriting parameter file ----------*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     strcat(rfileres,".");    /* */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     if((ficres =fopen(rfileres,"w"))==NULL) {
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+     }
+     fprintf(ficres,"#%s\n",version);
+   }    /* End of mle != -3 */
+   n= lastobs;
+   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); /* s[i][j] health state for wave i and individual j */
+   tab=ivector(1,NCOVMAX);
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
+   /* Reads data from file datafile */
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
+     goto end;
+   /* Calculation of the number of parameters from char model */
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
+         k=3 V4 Tvar[k=3]= 4 (from V4)
+         k=2 V1 Tvar[k=2]= 1 (from V1)
+         k=1 Tvar[1]=2 (from V2)
+     */
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+   */
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
+     Tvar[3=V1*V4]=4+1 etc */
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+   */
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
+   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+covariates (3 plus signs)
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+                       */
+   if(decodemodel(model, lastobs) == 1)
+     goto end;
+   if((double)(lastobs-imx)/(double)imx > 1.10){
+     nbwarn++;
+     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+   }
+     /*  if(mle==1){*/
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
+   }
+     /*-calculation of age at interview from date of interview and age at death -*/
+   agev=matrix(1,maxwav,1,imx);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+     goto end;
+   agegomp=(int)agemin;
+   free_vector(moisnais,1,n);
+   free_vector(annais,1,n);
+   /* free_matrix(mint,1,maxwav,1,n);
+      free_matrix(anint,1,maxwav,1,n);*/
+   free_vector(moisdc,1,n);
+   free_vector(andc,1,n);
+   /* */
+   wav=ivector(1,imx);
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
    /* Concatenates waves */
    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   /* */
    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-   Tcode=ivector(1,100);
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
    ncodemax[1]=1;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   Ndum =ivector(-1,NCOVMAX);
+   if (ncovmodel > 2)
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-                                  the estimations*/
+   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
    h=0;
+   /*if (cptcovn > 0) */
    m=pow(2,cptcoveff);
-   for(k=1;k<=cptcoveff; k++){
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-     for(i=1; i <=(m/pow(2,k));i++){
+     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
-       for(j=1; j <= ncodemax[k]; j++){
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
            h++;
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+           if (h>m)
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+             h=1;
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
+            *     h     1     2     3     4
+            *______________________________
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
+            *     2     2     1     1     1
+            *     3 i=2 1     2     1     1
+            *     4     2     2     1     1
+            *     5 i=3 1 i=2 1     2     1
+            *     6     2     1     2     1
+            *     7 i=4 1     2     2     1
+            *     8     2     2     2     1
+            *     9 i=5 1 i=3 1 i=2 1     1
+            *    10     2     1     1     1
+            *    11 i=6 1     2     1     1
+            *    12     2     2     1     1
+            *    13 i=7 1 i=4 1     2     1
+            *    14     2     1     2     1
+            *    15 i=8 1     2     2     1
+            *    16     2     2     2     1
+            */
+           codtab[h][k]=j;
+           /*codtab[h][Tvar[k]]=j;*/
+           printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
          }
        }
      }
    }
    /* 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("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
       }
       printf("\n");
       }
       scanf("%d",i);*/
+  free_ivector(Ndum,-1,NCOVMAX);
+   /*------------ gnuplot -------------*/
+   strcpy(optionfilegnuplot,optionfilefiname);
+   if(mle==-3)
+     strcat(optionfilegnuplot,"-mort");
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+   else{
+     fprintf(ficgp,"\n# %s\n", version);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     //fprintf(ficgp,"set missing 'NaNq'\n");
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
+   }
+   /*  fclose(ficgp);*/
+   /*--------- index.htm --------*/
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   if(mle==-3)
+     strcat(optionfilehtm,"-mort");
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm);
+     exit(0);
+   }
+   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] */
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   if (mle==-3){
+     ximort=matrix(1,NDIM,1,NDIM);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
+     cens=ivector(1,n);
+     ageexmed=vector(1,n);
+     agecens=vector(1,n);
+     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]);*/
+ #ifdef GSL
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
+ #elsedef
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ #endif
+     strcpy(filerespow,"pow-mort");
+     strcat(filerespow,fileres);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", filerespow);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+     }
+ #ifdef GSL
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+ #elsedef
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
+     /*  for (i=1;i<=nlstate;i++)
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     */
+     fprintf(ficrespow,"\n");
+ #ifdef GSL
+     /* gsl starts here */
+     T = gsl_multimin_fminimizer_nmsimplex;
+     gsl_multimin_fminimizer *sfm = NULL;
+     gsl_vector *ss, *x;
+     gsl_multimin_function minex_func;
+     /* Initial vertex size vector */
+     ss = gsl_vector_alloc (NDIM);
+     if (ss == NULL){
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+     }
+     /* Set all step sizes to 1 */
+     gsl_vector_set_all (ss, 0.001);
+     /* Starting point */
+     x = gsl_vector_alloc (NDIM);
+     if (x == NULL){
+       gsl_vector_free(ss);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+     }
+     /* Initialize method and iterate */
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
+ /*     gsl_vector_set(x, 0, 0.0268); */
+ /*     gsl_vector_set(x, 1, 0.083); */
+     gsl_vector_set(x, 0, p[1]);
+     gsl_vector_set(x, 1, p[2]);
+     minex_func.f = &gompertz_f;
+     minex_func.n = NDIM;
+     minex_func.params = (void *)&p; /* ??? */
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+     printf("Iterations beginning .....\n\n");
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
+     iteri=0;
+     while (rval == GSL_CONTINUE){
+       iteri++;
+       status = gsl_multimin_fminimizer_iterate(sfm);
+       if (status) printf("error: %s\n", gsl_strerror (status));
+       fflush(0);
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
-      and prints on file fileres'p'. */
-     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 */
+     gsl_vector_free(x); /* initial values */
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+     gsl_vector_free(ss); /* inital step size */
-      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+     for (it=0; it<NDIM; it++){
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ #endif
+     fclose(ficrespow);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
-   if(mle>=1){ /* Could be 1 or 2 */
+     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;
-   /*--------- results files --------------*/
+     for (k=agegomp;k<=AGESUP;k++) {
-   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);
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
+     }
+     tpop[agegomp]=sumlpop;
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+                      stepm, weightopt,\
+                      model,imx,p,matcov,agemortsup);
+     free_vector(lsurv,1,AGESUP);
+     free_vector(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
+   } /* Endof if mle==-3 */
+   else{ /* For mle >=1 */
-   jk=1;
+     globpr=0;/* debug */
-   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for (k=1; k<=npar;k++)
-   for(i=1,jk=1; i <=nlstate; i++){
+       printf(" %d %8.5f",k,p[k]);
-     for(k=1; k <=(nlstate+ndeath); k++){
+     printf("\n");
-       if (k != i)
+     globpr=1; /* to print the contributions */
-         {
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     if(mle>=1){ /* Could be 1 or 2 */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     /*--------- results files --------------*/
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
            printf("%d%d ",i,k);
            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);
            for(j=1; j <=ncovmodel; j++){
-             printf("%f ",p[jk]);
+             printf("%lf ",p[jk]);
-             fprintf(ficlog,"%f ",p[jk]);
+             fprintf(ficlog,"%lf ",p[jk]);
-             fprintf(ficres,"%f ",p[jk]);
+             fprintf(ficres,"%lf ",p[jk]);
              jk++;
            }
            printf("\n");
            fprintf(ficlog,"\n");
            fprintf(ficres,"\n");
          }
+       }
      }
-   }
+     if(mle!=0){
-   if(mle==1){
+       /* Computing hessian and covariance matrix */
-     /* Computing hessian and covariance matrix */
+       ftolhess=ftol; /* Usually correct */
-     ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, p, npar, delti, ftolhess, func);
-     hesscov(matcov, p, npar, delti, ftolhess, func);
+     }
-   }
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
-   fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
-   printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
-   for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
-     for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
-       if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
-         fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
-         printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
-         fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
-         for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
-           printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
-           fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
-           fprintf(ficres," %.5e",delti[jk]);
+             jk++;
-           jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
          }
-         printf("\n");
-         fprintf(ficlog,"\n");
-         fprintf(ficres,"\n");
        }
      }
-   }
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-   fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     if(mle>=1)
-   if(mle==1)
+       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-   fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     /* # 121 Var(a12)\n\ */
-   for(i=1,k=1;i<=npar;i++){
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     /*  if (k>nlstate) k=1;
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-         i1=(i-1)/(ncovmodel*nlstate)+1;
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-         fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-         printf("%s%d%d",alph[k],i1,tab[i]);
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
      */
-     fprintf(ficres,"%3d",i);
+     for(itimes=1;itimes<=2;itimes++){
-     if(mle==1)
+       jj=0;
-       printf("%3d",i);
+       for(i=1; i <=nlstate; i++){
-     fprintf(ficlog,"%3d",i);
+         for(j=1; j <=nlstate+ndeath; j++){
-     for(j=1; j<=i;j++){
+           if(j==i) continue;
-       fprintf(ficres," %.5e",matcov[i][j]);
+           for(k=1; k<=ncovmodel;k++){
-       if(mle==1)
+             jj++;
-         printf(" %.5e",matcov[i][j]);
+             ca[0]= k+'a'-1;ca[1]='\0';
-       fprintf(ficlog," %.5e",matcov[i][j]);
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
      }
-     fprintf(ficres,"\n");
-     if(mle==1)
-       printf("\n");
-     fprintf(ficlog,"\n");
-     k++;
-   }
-   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
+     estepm=0;
-     fputs(line,ficparo);
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
-   }
+     if (estepm==0 || estepm < stepm) estepm=stepm;
-   ungetc(c,ficpar);
+     if (fage <= 2) {
+       bage = ageminpar;
-   estepm=0;
+       fage = agemaxpar;
-   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     }
-   if (estepm==0 || estepm < stepm) estepm=stepm;
-   if (fage <= 2) {
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     bage = ageminpar;
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-     fage = agemaxpar;
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-   }
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+       ungetc(c,ficpar);
-   fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+       fgets(line, MAXLINE, ficpar);
-   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+       fputs(line,stdout);
+       fputs(line,ficparo);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
+     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
-     fputs(line,ficparo);
+     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   }
+     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   ungetc(c,ficpar);
+     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
-   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+       ungetc(c,ficpar);
-   printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+       fgets(line, MAXLINE, ficpar);
-   fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+       fputs(line,stdout);
+       fputs(line,ficparo);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     }
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-   }
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-   ungetc(c,ficpar);
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
+     fprintf(ficparo,"pop_based=%d\n",popbased);
+     fprintf(ficres,"pop_based=%d\n",popbased);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     /* day and month of proj2 are not used but only year anproj2.*/
+      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
+     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+    /*------------ free_vector  -------------*/
+    /*  chdir(path); */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     free_lvector(num,1,n);
+     free_vector(agedc,1,n);
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     fclose(ficparo);
+     fclose(ficres);
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+ #include "prevlim.h"  /* Use ficrespl, ficlog */
+     fclose(ficrespl);
-   dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+ #ifdef FREEEXIT2
-   dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+ #include "freeexit2.h"
+ #endif
-   fscanf(ficpar,"pop_based=%d\n",&popbased);
+     /*------------- h Pij x at various ages ------------*/
-   fprintf(ficparo,"pop_based=%d\n",popbased);
+ #include "hpijx.h"
-   fprintf(ficres,"pop_based=%d\n",popbased);
+     fclose(ficrespij);
+   /*-------------- Variance of one-step probabilities---*/
+     k=1;
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(i=1;i<=AGESUP;i++)
+       for(j=1;j<=NCOVMAX;j++)
+         for(k=1;k<=NCOVMAX;k++)
+           probs[i][j][k]=0.;
+     /*---------- Forecasting ------------------*/
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
+       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+       /*      }  */
+       /*      else{ */
+       /*        erreur=108; */
+       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*      } */
+     }
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
-   fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-   /* day and month of proj2 are not used but only year anproj2.*/
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
-   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);
-   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
-   /*------------ gnuplot -------------*/
-   strcpy(optionfilegnuplot,optionfilefiname);
-   strcat(optionfilegnuplot,".gp");
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-     printf("Problem with file %s",optionfilegnuplot);
-   }
-   else{
-     fprintf(ficgp,"\n# %s\n", version);
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-     fprintf(ficgp,"set missing 'NaNq'\n");
-   }
-   fclose(ficgp);
-   printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
-   /*--------- index.htm --------*/
-   strcpy(optionfilehtm,optionfile);
-   strcat(optionfilehtm,".htm");
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-     printf("Problem with %s \n",optionfilehtm), exit(0);
-   }
-   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
- \n
- Total number of observations=%d <br>\n
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
- <hr  size=\"2\" color=\"#EC5E5E\">
-  <ul><li><h4>Parameter files</h4>\n
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n
-  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
-    fclose(fichtm);
-   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+     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",\
-   /*------------ free_vector  -------------*/
+         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
-   chdir(path);
+     */
-   free_ivector(wav,1,imx);
-   free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-   free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
-   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-   free_ivector(num,1,n);
-   free_vector(agedc,1,n);
-   /*free_matrix(covar,0,NCOVMAX,1,n);*/
-   /*free_matrix(covar,1,NCOVMAX,1,n);*/
-   fclose(ficparo);
-   fclose(ficres);
-   /*--------------- Prevalence limit  (stable prevalence) --------------*/
-   strcpy(filerespl,"pl");
-   strcat(filerespl,fileres);
-   if((ficrespl=fopen(filerespl,"w"))==NULL) {
-     printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
-     fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
-   }
-   printf("Computing stable prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficrespl,"#Stable prevalence \n");
-   fprintf(ficrespl,"#Age ");
-   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-   fprintf(ficrespl,"\n");
-   prlim=matrix(1,nlstate,1,nlstate);
-   agebase=ageminpar;
-   agelim=agemaxpar;
-   ftolpl=1.e-10;
-   i1=cptcoveff;
-   if (cptcovn < 1){i1=1;}
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     if (mobilav!=0) {
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       k=k+1;
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       fprintf(ficrespl,"\n#******");
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       printf("\n#******");
-       fprintf(ficlog,"\n#******");
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       }
-       fprintf(ficrespl,"******\n");
-       printf("******\n");
-       fprintf(ficlog,"******\n");
-       for (age=agebase; age<=agelim; age++){
-         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-         fprintf(ficrespl,"%.0f ",age );
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         for(i=1; i<=nlstate;i++)
-           fprintf(ficrespl," %.5f", prlim[i][i]);
-         fprintf(ficrespl,"\n");
        }
      }
-   }
-   fclose(ficrespl);
-   /*------------- h Pij x at various ages ------------*/
-   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-   if((ficrespij=fopen(filerespij,"w"))==NULL) {
-     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-   }
-   printf("Computing pij: result on file '%s' \n", filerespij);
-   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   /*if (stepm<=24) stepsize=2;*/
-   agelim=AGESUP;
+     /*---------- Health expectancies, no variances ------------*/
-   hstepm=stepsize*YEARM; /* Every year of age */
-   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-   /* hstepm=1;   aff par mois*/
-   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-       k=k+1;
-       fprintf(ficrespij,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficrespij,"******\n");
-       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-         /*        nhstepm=nhstepm*YEARM; aff par mois*/
+     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);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficreseij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficreseij,"******\n");
-         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
          oldm=oldms;savm=savms;
-         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
-         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-         for(i=1; i<=nlstate;i++)
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-           for(j=1; j<=nlstate+ndeath;j++)
+       /*}*/
-             fprintf(ficrespij," %1d-%1d",i,j);
-         fprintf(ficrespij,"\n");
-         for (h=0; h<=nhstepm; h++){
-           fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
-           for(i=1; i<=nlstate;i++)
-             for(j=1; j<=nlstate+ndeath;j++)
-               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-           fprintf(ficrespij,"\n");
-         }
-         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         fprintf(ficrespij,"\n");
-       }
      }
-   }
+     fclose(ficreseij);
-   varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
-   fclose(ficrespij);
+     /*---------- Health expectancies and variances ------------*/
-   /*---------- Forecasting ------------------*/
+     strcpy(filerest,"t");
-   /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     strcat(filerest,fileres);
-   if(prevfcast==1){
+     if((ficrest=fopen(filerest,"w"))==NULL) {
-     /*    if(stepm ==1){*/
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+     }
- /*      }  */
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
- /*      else{ */
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
- /*        erreur=108; */
- /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
- /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
- /*      } */
-   }
-   /*---------- Health expectancies and variances ------------*/
-   strcpy(filerest,"t");
+     strcpy(fileresstde,"stde");
-   strcat(filerest,fileres);
+     strcat(fileresstde,fileres);
-   if((ficrest=fopen(filerest,"w"))==NULL) {
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
-     printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
-     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
-   }
+     }
-   printf("Computing Total LEs with variances: file '%s' \n", filerest);
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
-   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"cve");
+     strcat(filerescve,fileres);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
-   strcpy(filerese,"e");
+     strcpy(fileresv,"v");
-   strcat(filerese,fileres);
+     strcat(fileresv,fileres);
-   if((ficreseij=fopen(filerese,"w"))==NULL) {
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
-     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
-     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
-   }
+     }
-   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-   strcpy(fileresv,"v");
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-   strcat(fileresv,fileres);
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-   if((ficresvij=fopen(fileresv,"w"))==NULL) {
-     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
-     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+         fprintf(ficrest,"\n#****** ");
-   }
+         for(j=1;j<=cptcoveff;j++)
-   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+         fprintf(ficrest,"******\n");
-   /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+         fprintf(ficresstdeij,"\n#****** ");
-   prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+         fprintf(ficrescveij,"\n#****** ");
-   /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+         for(j=1;j<=cptcoveff;j++) {
- ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   */
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficresstdeij,"******\n");
+         fprintf(ficrescveij,"******\n");
-   if (mobilav!=0) {
+         fprintf(ficresvij,"\n#****** ");
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         for(j=1;j<=cptcoveff;j++)
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         fprintf(ficresvij,"******\n");
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
-   }
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         oldm=oldms;savm=savms;
-       k=k+1;
+         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
-       fprintf(ficrest,"\n#****** ");
+         /*
-       for(j=1;j<=cptcoveff;j++)
+          */
-         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         /* goto endfree; */
-       fprintf(ficrest,"******\n");
-       fprintf(ficreseij,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficreseij,"******\n");
-       fprintf(ficresvij,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficresvij,"******\n");
-       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
-       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
-       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
+         pstamp(ficrest);
-       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
-       if(popbased==1){
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
-       }
-       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           oldm=oldms;savm=savms; /* Segmentation fault */
-       fprintf(ficrest,"\n");
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
+           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
-       epj=vector(1,nlstate+1);
+           if(vpopbased==1)
-       for(age=bage; age <=fage ;age++){
+             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
-         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           else
-         if (popbased==1) {
+             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
-           if(mobilav ==0){
+           fprintf(ficrest,"# Age e.. (std) ");
-             for(i=1; i<=nlstate;i++)
+           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-               prlim[i][i]=probs[(int)age][i][k];
+           fprintf(ficrest,"\n");
-           }else{ /* mobilav */
-             for(i=1; i<=nlstate;i++)
+           epj=vector(1,nlstate+1);
-               prlim[i][i]=mobaverage[(int)age][i][k];
+           for(age=bage; age <=fage ;age++){
-           }
+             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-         }
+             if (vpopbased==1) {
+               if(mobilav ==0){
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=probs[(int)age][i][k];
+               }else{ /* mobilav */
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=mobaverage[(int)age][i][k];
+               }
+             }
-         fprintf(ficrest," %4.0f",age);
+             fprintf(ficrest," %4.0f",age);
-         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-           for(i=1, epj[j]=0.;i <=nlstate;i++) {
+               for(i=1, epj[j]=0.;i <=nlstate;i++) {
-             epj[j] += prlim[i][i]*eij[i][j][(int)age];
+                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
-             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               }
+               epj[nlstate+1] +=epj[j];
+             }
+             for(i=1, vepp=0.;i <=nlstate;i++)
+               for(j=1;j <=nlstate;j++)
+                 vepp += vareij[i][j][(int)age];
+             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+             for(j=1;j <=nlstate;j++){
+               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             }
+             fprintf(ficrest,"\n");
            }
-           epj[nlstate+1] +=epj[j];
          }
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         for(i=1, vepp=0.;i <=nlstate;i++)
+         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-           for(j=1;j <=nlstate;j++)
+         free_vector(epj,1,nlstate+1);
-             vepp += vareij[i][j][(int)age];
+       /*}*/
-         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+     }
-         for(j=1;j <=nlstate;j++){
+     free_vector(weight,1,n);
-           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
-         }
+     free_imatrix(s,1,maxwav+1,1,n);
-         fprintf(ficrest,"\n");
+     free_matrix(anint,1,maxwav,1,n);
-       }
+     free_matrix(mint,1,maxwav,1,n);
-       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     free_ivector(cod,1,n);
-       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     free_ivector(tab,1,NCOVMAX);
-       free_vector(epj,1,nlstate+1);
+     fclose(ficresstdeij);
-     }
+     fclose(ficrescveij);
-   }
+     fclose(ficresvij);
-   free_vector(weight,1,n);
+     fclose(ficrest);
-   free_imatrix(Tvard,1,15,1,2);
+     fclose(ficpar);
-   free_imatrix(s,1,maxwav+1,1,n);
-   free_matrix(anint,1,maxwav,1,n);
+     /*------- Variance of period (stable) prevalence------*/
-   free_matrix(mint,1,maxwav,1,n);
-   free_ivector(cod,1,n);
+     strcpy(fileresvpl,"vpl");
-   free_ivector(tab,1,NCOVMAX);
+     strcat(fileresvpl,fileres);
-   fclose(ficreseij);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-   fclose(ficresvij);
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
-   fclose(ficrest);
+       exit(0);
-   fclose(ficpar);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
-   /*------- Variance of stable prevalence------*/
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-   strcpy(fileresvpl,"vpl");
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-   strcat(fileresvpl,fileres);
-   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
-     printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
+         fprintf(ficresvpl,"\n#****** ");
-     exit(0);
+         for(j=1;j<=cptcoveff;j++)
-   }
+           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
+         fprintf(ficresvpl,"******\n");
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-       k=k+1;
-       fprintf(ficresvpl,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficresvpl,"******\n");
-       varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         varpl=matrix(1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
+         oldm=oldms;savm=savms;
-       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
+         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
-       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
-     }
+       /*}*/
-   }
+     }
-   fclose(ficresvpl);
+     fclose(ficresvpl);
-   /*---------- End : free ----------------*/
+     /*---------- End : free ----------------*/
-   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   }  /* mle==-3 arrives here for freeing */
-   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+  endfree:
+     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
-   free_matrix(covar,0,NCOVMAX,1,n);
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(matcov,1,npar,1,npar);
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   /*free_vector(delti,1,npar);*/
+     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   free_matrix(agev,1,maxwav,1,imx);
+     free_matrix(covar,0,NCOVMAX,1,n);
-   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(matcov,1,npar,1,npar);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     /*free_vector(delti,1,npar);*/
-   free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
-   free_ivector(ncodemax,1,8);
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-   free_ivector(Tvar,1,15);
-   free_ivector(Tprod,1,15);
+     free_ivector(ncodemax,1,NCOVMAX);
-   free_ivector(Tvaraff,1,15);
+     free_ivector(Tvar,1,NCOVMAX);
-   free_ivector(Tage,1,15);
+     free_ivector(Tprod,1,NCOVMAX);
-   free_ivector(Tcode,1,100);
+     free_ivector(Tvaraff,1,NCOVMAX);
+     free_ivector(Tage,1,NCOVMAX);
-   /*  fclose(fichtm);*/
-   /*  fclose(ficgp);*/ /* ALready done */
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     free_imatrix(codtab,1,100,1,10);
+   fflush(fichtm);
-   if(erreur >0){
+   fflush(ficgp);
-     printf("End of Imach with error or warning %d\n",erreur);
-     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+   if((nberr >0) || (nbwarn>0)){
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
    }else{
-    printf("End of Imach\n");
+     printf("End of Imach\n");
-    fprintf(ficlog,"End of Imach\n");
+     fprintf(ficlog,"End of Imach\n");
    }
    printf("See log file on %s\n",filelog);
-   fclose(ficlog);
    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   (void) gettimeofday(&end_time,&tzp);
-   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
+   tm = *localtime(&end_time.tv_sec);
-   /*printf("Total time was %d uSec.\n", total_usecs);*/
+   tmg = *gmtime(&end_time.tv_sec);
+   strcpy(strtend,asctime(&tm));
+   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ /*   if(fileappend(fichtm,optionfilehtm)){ */
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtm);
+   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtmcov);
+   fclose(ficgp);
+   fclose(ficlog);
    /*------ End -----------*/
-   end:
- #ifdef windows
-   /* chdir(pathcd);*/
- #endif
-  /*system("wgnuplot graph.plt");*/
-  /*system("../gp37mgw/wgnuplot graph.plt");*/
-  /*system("cd ../gp37mgw");*/
-  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
-   strcpy(plotcmd,GNUPLOTPROGRAM);
-   strcat(plotcmd," ");
-   strcat(plotcmd,optionfilegnuplot);
-   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
-   system(plotcmd);
-   printf(" Wait...");
-  /*#ifdef windows*/
+    printf("Before Current directory %s!\n",pathcd);
+    if(chdir(pathcd) != 0)
+     printf("Can't move to directory %s!\n",path);
+   if(getcwd(pathcd,MAXLINE) > 0)
+     printf("Current directory %s!\n",pathcd);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
+   sprintf(plotcmd,"gnuplot");
+ #ifndef UNIX
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef UNIX
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+   if((outcmd=system(plotcmd)) != 0){
+     printf("\n Problem with gnuplot\n");
+   }
+   printf(" Wait...");
    while (z[0] != 'q') {
      /* chdir(path); */
-     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
+     printf("\nType e to edit output files, g to graph again and q for exiting: ");
      scanf("%s",z);
-     if (z[0] == 'c') system("./imach");
+ /*     if (z[0] == 'c') system("./imach"); */
-     else if (z[0] == 'e') system(optionfilehtm);
+     if (z[0] == 'e') {
+       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+       system(optionfilehtm);
+     }
      else if (z[0] == 'g') system(plotcmd);
      else if (z[0] == 'q') exit(0);
    }
-   /*#endif */
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: ");
+     scanf("%s",z);
+   }
  }

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