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Diff for /imach/src/imach.c between versions 1.168 and 1.337

-version 1.168, 2014/12/22 15:17:42
+version 1.337, 2022/09/02 14:26:02
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.337  2022/09/02 14:26:02  brouard
+   Summary: version 0.99r35
+   * src/imach.c: Version 0.99r35 because it outputs same results with
++age+V1+V1*age for females and 1+age for females only
+   (education=1 noweight)
+   Revision 1.336  2022/08/31 09:52:36  brouard
+   *** empty log message ***
+   Revision 1.335  2022/08/31 08:23:16  brouard
+   Summary: improvements...
+   Revision 1.334  2022/08/25 09:08:41  brouard
+   Summary: In progress for quantitative
+   Revision 1.333  2022/08/21 09:10:30  brouard
+   * src/imach.c (Module): Version 0.99r33 A lot of changes in
+   reassigning covariates: my first idea was that people will always
+   use the first covariate V1 into the model but in fact they are
+   producing data with many covariates and can use an equation model
+   with some of the covariate; it means that in a model V2+V3 instead
+   of codtabm(k,Tvaraff[j]) which calculates for combination k, for
+   three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
+   the equation model is restricted to two variables only (V2, V3)
+   and the combination for V2 should be codtabm(k,1) instead of
+   (codtabm(k,2), and the code should be
+   codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
+   made. All of these should be simplified once a day like we did in
+   hpxij() for example by using precov[nres] which is computed in
+   decoderesult for each nres of each resultline. Loop should be done
+   on the equation model globally by distinguishing only product with
+   age (which are changing with age) and no more on type of
+   covariates, single dummies, single covariates.
+   Revision 1.332  2022/08/21 09:06:25  brouard
+   Summary: Version 0.99r33
+   * src/imach.c (Module): Version 0.99r33 A lot of changes in
+   reassigning covariates: my first idea was that people will always
+   use the first covariate V1 into the model but in fact they are
+   producing data with many covariates and can use an equation model
+   with some of the covariate; it means that in a model V2+V3 instead
+   of codtabm(k,Tvaraff[j]) which calculates for combination k, for
+   three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
+   the equation model is restricted to two variables only (V2, V3)
+   and the combination for V2 should be codtabm(k,1) instead of
+   (codtabm(k,2), and the code should be
+   codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
+   made. All of these should be simplified once a day like we did in
+   hpxij() for example by using precov[nres] which is computed in
+   decoderesult for each nres of each resultline. Loop should be done
+   on the equation model globally by distinguishing only product with
+   age (which are changing with age) and no more on type of
+   covariates, single dummies, single covariates.
+   Revision 1.331  2022/08/07 05:40:09  brouard
+   *** empty log message ***
+   Revision 1.330  2022/08/06 07:18:25  brouard
+   Summary: last 0.99r31
+   *  imach.c (Module): Version of imach using partly decoderesult to rebuild xpxij function
+   Revision 1.329  2022/08/03 17:29:54  brouard
+   *  imach.c (Module): Many errors in graphs fixed with Vn*age covariates.
+   Revision 1.328  2022/07/27 17:40:48  brouard
+   Summary: valgrind bug fixed by initializing to zero DummyV as well as Tage
+   Revision 1.327  2022/07/27 14:47:35  brouard
+   Summary: Still a problem for one-step probabilities in case of quantitative variables
+   Revision 1.326  2022/07/26 17:33:55  brouard
+   Summary: some test with nres=1
+   Revision 1.325  2022/07/25 14:27:23  brouard
+   Summary: r30
+   * imach.c (Module): Error cptcovn instead of nsd in bmij (was
+   coredumped, revealed by Feiuno, thank you.
+   Revision 1.324  2022/07/23 17:44:26  brouard
+   *** empty log message ***
+   Revision 1.323  2022/07/22 12:30:08  brouard
+   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
+   Revision 1.322  2022/07/22 12:27:48  brouard
+   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
+   Revision 1.321  2022/07/22 12:04:24  brouard
+   Summary: r28
+   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
+   Revision 1.320  2022/06/02 05:10:11  brouard
+   *** empty log message ***
+   Revision 1.319  2022/06/02 04:45:11  brouard
+   * imach.c (Module): Adding the Wald tests from the log to the main
+   htm for better display of the maximum likelihood estimators.
+   Revision 1.318  2022/05/24 08:10:59  brouard
+   * imach.c (Module): Some attempts to find a bug of wrong estimates
+   of confidencce intervals with product in the equation modelC
+   Revision 1.317  2022/05/15 15:06:23  brouard
+   * imach.c (Module):  Some minor improvements
+   Revision 1.316  2022/05/11 15:11:31  brouard
+   Summary: r27
+   Revision 1.315  2022/05/11 15:06:32  brouard
+   *** empty log message ***
+   Revision 1.314  2022/04/13 17:43:09  brouard
+   * imach.c (Module): Adding link to text data files
+   Revision 1.313  2022/04/11 15:57:42  brouard
+   * imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed
+   Revision 1.312  2022/04/05 21:24:39  brouard
+   *** empty log message ***
+   Revision 1.311  2022/04/05 21:03:51  brouard
+   Summary: Fixed quantitative covariates
+           Fixed covariates (dummy or quantitative)
+         with missing values have never been allowed but are ERRORS and
+         program quits. Standard deviations of fixed covariates were
+         wrongly computed. Mean and standard deviations of time varying
+         covariates are still not computed.
+   Revision 1.310  2022/03/17 08:45:53  brouard
+   Summary: 99r25
+   Improving detection of errors: result lines should be compatible with
+   the model.
+   Revision 1.309  2021/05/20 12:39:14  brouard
+   Summary: Version 0.99r24
+   Revision 1.308  2021/03/31 13:11:57  brouard
+   Summary: Version 0.99r23
+   * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
+   Revision 1.307  2021/03/08 18:11:32  brouard
+   Summary: 0.99r22 fixed bug on result:
+   Revision 1.306  2021/02/20 15:44:02  brouard
+   Summary: Version 0.99r21
+   * imach.c (Module): Fix bug on quitting after result lines!
+   (Module): Version 0.99r21
+   Revision 1.305  2021/02/20 15:28:30  brouard
+   * imach.c (Module): Fix bug on quitting after result lines!
+   Revision 1.304  2021/02/12 11:34:20  brouard
+   * imach.c (Module): The use of a Windows BOM (huge) file is now an error
+   Revision 1.303  2021/02/11 19:50:15  brouard
+   *  (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
+   Revision 1.302  2020/02/22 21:00:05  brouard
+   *  (Module): imach.c Update mle=-3 (for computing Life expectancy
+   and life table from the data without any state)
+   Revision 1.301  2019/06/04 13:51:20  brouard
+   Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
+   Revision 1.300  2019/05/22 19:09:45  brouard
+   Summary: version 0.99r19 of May 2019
+   Revision 1.299  2019/05/22 18:37:08  brouard
+   Summary: Cleaned 0.99r19
+   Revision 1.298  2019/05/22 18:19:56  brouard
+   *** empty log message ***
+   Revision 1.297  2019/05/22 17:56:10  brouard
+   Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
+   Revision 1.296  2019/05/20 13:03:18  brouard
+   Summary: Projection syntax simplified
+   We can now start projections, forward or backward, from the mean date
+   of inteviews up to or down to a number of years of projection:
+   prevforecast=1 yearsfproj=15.3 mobil_average=0
+   or
+   prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
+   or
+   prevbackcast=1 yearsbproj=12.3 mobil_average=1
+   or
+   prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
+   Revision 1.295  2019/05/18 09:52:50  brouard
+   Summary: doxygen tex bug
+   Revision 1.294  2019/05/16 14:54:33  brouard
+   Summary: There was some wrong lines added
+   Revision 1.293  2019/05/09 15:17:34  brouard
+   *** empty log message ***
+   Revision 1.292  2019/05/09 14:17:20  brouard
+   Summary: Some updates
+   Revision 1.291  2019/05/09 13:44:18  brouard
+   Summary: Before ncovmax
+   Revision 1.290  2019/05/09 13:39:37  brouard
+   Summary: 0.99r18 unlimited number of individuals
+   The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.
+   Revision 1.289  2018/12/13 09:16:26  brouard
+   Summary: Bug for young ages (<-30) will be in r17
+   Revision 1.288  2018/05/02 20:58:27  brouard
+   Summary: Some bugs fixed
+   Revision 1.287  2018/05/01 17:57:25  brouard
+   Summary: Bug fixed by providing frequencies only for non missing covariates
+   Revision 1.286  2018/04/27 14:27:04  brouard
+   Summary: some minor bugs
+   Revision 1.285  2018/04/21 21:02:16  brouard
+   Summary: Some bugs fixed, valgrind tested
+   Revision 1.284  2018/04/20 05:22:13  brouard
+   Summary: Computing mean and stdeviation of fixed quantitative variables
+   Revision 1.283  2018/04/19 14:49:16  brouard
+   Summary: Some minor bugs fixed
+   Revision 1.282  2018/02/27 22:50:02  brouard
+   *** empty log message ***
+   Revision 1.281  2018/02/27 19:25:23  brouard
+   Summary: Adding second argument for quitting
+   Revision 1.280  2018/02/21 07:58:13  brouard
+   Summary: 0.99r15
+   New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
+   Revision 1.279  2017/07/20 13:35:01  brouard
+   Summary: temporary working
+   Revision 1.278  2017/07/19 14:09:02  brouard
+   Summary: Bug for mobil_average=0 and prevforecast fixed(?)
+   Revision 1.277  2017/07/17 08:53:49  brouard
+   Summary: BOM files can be read now
+   Revision 1.276  2017/06/30 15:48:31  brouard
+   Summary: Graphs improvements
+   Revision 1.275  2017/06/30 13:39:33  brouard
+   Summary: Saito's color
+   Revision 1.274  2017/06/29 09:47:08  brouard
+   Summary: Version 0.99r14
+   Revision 1.273  2017/06/27 11:06:02  brouard
+   Summary: More documentation on projections
+   Revision 1.272  2017/06/27 10:22:40  brouard
+   Summary: Color of backprojection changed from 6 to 5(yellow)
+   Revision 1.271  2017/06/27 10:17:50  brouard
+   Summary: Some bug with rint
+   Revision 1.270  2017/05/24 05:45:29  brouard
+   *** empty log message ***
+   Revision 1.269  2017/05/23 08:39:25  brouard
+   Summary: Code into subroutine, cleanings
+   Revision 1.268  2017/05/18 20:09:32  brouard
+   Summary: backprojection and confidence intervals of backprevalence
+   Revision 1.267  2017/05/13 10:25:05  brouard
+   Summary: temporary save for backprojection
+   Revision 1.266  2017/05/13 07:26:12  brouard
+   Summary: Version 0.99r13 (improvements and bugs fixed)
+   Revision 1.265  2017/04/26 16:22:11  brouard
+   Summary: imach 0.99r13 Some bugs fixed
+   Revision 1.264  2017/04/26 06:01:29  brouard
+   Summary: Labels in graphs
+   Revision 1.263  2017/04/24 15:23:15  brouard
+   Summary: to save
+   Revision 1.262  2017/04/18 16:48:12  brouard
+   *** empty log message ***
+   Revision 1.261  2017/04/05 10:14:09  brouard
+   Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
+   Revision 1.260  2017/04/04 17:46:59  brouard
+   Summary: Gnuplot indexations fixed (humm)
+   Revision 1.259  2017/04/04 13:01:16  brouard
+   Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
+   Revision 1.258  2017/04/03 10:17:47  brouard
+   Summary: Version 0.99r12
+   Some cleanings, conformed with updated documentation.
+   Revision 1.257  2017/03/29 16:53:30  brouard
+   Summary: Temp
+   Revision 1.256  2017/03/27 05:50:23  brouard
+   Summary: Temporary
+   Revision 1.255  2017/03/08 16:02:28  brouard
+   Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
+   Revision 1.254  2017/03/08 07:13:00  brouard
+   Summary: Fixing data parameter line
+   Revision 1.253  2016/12/15 11:59:41  brouard
+   Summary: 0.99 in progress
+   Revision 1.252  2016/09/15 21:15:37  brouard
+   *** empty log message ***
+   Revision 1.251  2016/09/15 15:01:13  brouard
+   Summary: not working
+   Revision 1.250  2016/09/08 16:07:27  brouard
+   Summary: continue
+   Revision 1.249  2016/09/07 17:14:18  brouard
+   Summary: Starting values from frequencies
+   Revision 1.248  2016/09/07 14:10:18  brouard
+   *** empty log message ***
+   Revision 1.247  2016/09/02 11:11:21  brouard
+   *** empty log message ***
+   Revision 1.246  2016/09/02 08:49:22  brouard
+   *** empty log message ***
+   Revision 1.245  2016/09/02 07:25:01  brouard
+   *** empty log message ***
+   Revision 1.244  2016/09/02 07:17:34  brouard
+   *** empty log message ***
+   Revision 1.243  2016/09/02 06:45:35  brouard
+   *** empty log message ***
+   Revision 1.242  2016/08/30 15:01:20  brouard
+   Summary: Fixing a lots
+   Revision 1.241  2016/08/29 17:17:25  brouard
+   Summary: gnuplot problem in Back projection to fix
+   Revision 1.240  2016/08/29 07:53:18  brouard
+   Summary: Better
+   Revision 1.239  2016/08/26 15:51:03  brouard
+   Summary: Improvement in Powell output in order to copy and paste
+   Author:
+   Revision 1.238  2016/08/26 14:23:35  brouard
+   Summary: Starting tests of 0.99
+   Revision 1.237  2016/08/26 09:20:19  brouard
+   Summary: to valgrind
+   Revision 1.236  2016/08/25 10:50:18  brouard
+   *** empty log message ***
+   Revision 1.235  2016/08/25 06:59:23  brouard
+   *** empty log message ***
+   Revision 1.234  2016/08/23 16:51:20  brouard
+   *** empty log message ***
+   Revision 1.233  2016/08/23 07:40:50  brouard
+   Summary: not working
+   Revision 1.232  2016/08/22 14:20:21  brouard
+   Summary: not working
+   Revision 1.231  2016/08/22 07:17:15  brouard
+   Summary: not working
+   Revision 1.230  2016/08/22 06:55:53  brouard
+   Summary: Not working
+   Revision 1.229  2016/07/23 09:45:53  brouard
+   Summary: Completing for func too
+   Revision 1.228  2016/07/22 17:45:30  brouard
+   Summary: Fixing some arrays, still debugging
+   Revision 1.226  2016/07/12 18:42:34  brouard
+   Summary: temp
+   Revision 1.225  2016/07/12 08:40:03  brouard
+   Summary: saving but not running
+   Revision 1.224  2016/07/01 13:16:01  brouard
+   Summary: Fixes
+   Revision 1.223  2016/02/19 09:23:35  brouard
+   Summary: temporary
+   Revision 1.222  2016/02/17 08:14:50  brouard
+   Summary: Probably last 0.98 stable version 0.98r6
+   Revision 1.221  2016/02/15 23:35:36  brouard
+   Summary: minor bug
+   Revision 1.219  2016/02/15 00:48:12  brouard
+   *** empty log message ***
+   Revision 1.218  2016/02/12 11:29:23  brouard
+   Summary: 0.99 Back projections
+   Revision 1.217  2015/12/23 17:18:31  brouard
+   Summary: Experimental backcast
+   Revision 1.216  2015/12/18 17:32:11  brouard
+   Summary: 0.98r4 Warning and status=-2
+   Version 0.98r4 is now:
+    - displaying an error when status is -1, date of interview unknown and date of death known;
+    - permitting a status -2 when the vital status is unknown at a known date of right truncation.
+   Older changes concerning s=-2, dating from 2005 have been supersed.
+   Revision 1.215  2015/12/16 08:52:24  brouard
+   Summary: 0.98r4 working
+   Revision 1.214  2015/12/16 06:57:54  brouard
+   Summary: temporary not working
+   Revision 1.213  2015/12/11 18:22:17  brouard
+   Summary: 0.98r4
+   Revision 1.212  2015/11/21 12:47:24  brouard
+   Summary: minor typo
+   Revision 1.211  2015/11/21 12:41:11  brouard
+   Summary: 0.98r3 with some graph of projected cross-sectional
+   Author: Nicolas Brouard
+   Revision 1.210  2015/11/18 17:41:20  brouard
+   Summary: Start working on projected prevalences  Revision 1.209  2015/11/17 22:12:03  brouard
+   Summary: Adding ftolpl parameter
+   Author: N Brouard
+   We had difficulties to get smoothed confidence intervals. It was due
+   to the period prevalence which wasn't computed accurately. The inner
+   parameter ftolpl is now an outer parameter of the .imach parameter
+   file after estepm. If ftolpl is small 1.e-4 and estepm too,
+   computation are long.
+   Revision 1.208  2015/11/17 14:31:57  brouard
+   Summary: temporary
+   Revision 1.207  2015/10/27 17:36:57  brouard
+   *** empty log message ***
+   Revision 1.206  2015/10/24 07:14:11  brouard
+   *** empty log message ***
+   Revision 1.205  2015/10/23 15:50:53  brouard
+   Summary: 0.98r3 some clarification for graphs on likelihood contributions
+   Revision 1.204  2015/10/01 16:20:26  brouard
+   Summary: Some new graphs of contribution to likelihood
+   Revision 1.203  2015/09/30 17:45:14  brouard
+   Summary: looking at better estimation of the hessian
+   Also a better criteria for convergence to the period prevalence And
+   therefore adding the number of years needed to converge. (The
+   prevalence in any alive state shold sum to one
+   Revision 1.202  2015/09/22 19:45:16  brouard
+   Summary: Adding some overall graph on contribution to likelihood. Might change
+   Revision 1.201  2015/09/15 17:34:58  brouard
+   Summary: 0.98r0
+   - Some new graphs like suvival functions
+   - Some bugs fixed like model=1+age+V2.
+   Revision 1.200  2015/09/09 16:53:55  brouard
+   Summary: Big bug thanks to Flavia
+   Even model=1+age+V2. did not work anymore
+   Revision 1.199  2015/09/07 14:09:23  brouard
+   Summary: 0.98q6 changing default small png format for graph to vectorized svg.
+   Revision 1.198  2015/09/03 07:14:39  brouard
+   Summary: 0.98q5 Flavia
+   Revision 1.197  2015/09/01 18:24:39  brouard
+   *** empty log message ***
+   Revision 1.196  2015/08/18 23:17:52  brouard
+   Summary: 0.98q5
+   Revision 1.195  2015/08/18 16:28:39  brouard
+   Summary: Adding a hack for testing purpose
+   After reading the title, ftol and model lines, if the comment line has
+   a q, starting with #q, the answer at the end of the run is quit. It
+   permits to run test files in batch with ctest. The former workaround was
+   $ echo q | imach foo.imach
+   Revision 1.194  2015/08/18 13:32:00  brouard
+   Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
+   Revision 1.193  2015/08/04 07:17:42  brouard
+   Summary: 0.98q4
+   Revision 1.192  2015/07/16 16:49:02  brouard
+   Summary: Fixing some outputs
+   Revision 1.191  2015/07/14 10:00:33  brouard
+   Summary: Some fixes
+   Revision 1.190  2015/05/05 08:51:13  brouard
+   Summary: Adding digits in output parameters (7 digits instead of 6)
+   Fix 1+age+.
+   Revision 1.189  2015/04/30 14:45:16  brouard
+   Summary: 0.98q2
+   Revision 1.188  2015/04/30 08:27:53  brouard
+   *** empty log message ***
+   Revision 1.187  2015/04/29 09:11:15  brouard
+   *** empty log message ***
+   Revision 1.186  2015/04/23 12:01:52  brouard
+   Summary: V1*age is working now, version 0.98q1
+   Some codes had been disabled in order to simplify and Vn*age was
+   working in the optimization phase, ie, giving correct MLE parameters,
+   but, as usual, outputs were not correct and program core dumped.
+   Revision 1.185  2015/03/11 13:26:42  brouard
+   Summary: Inclusion of compile and links command line for Intel Compiler
+   Revision 1.184  2015/03/11 11:52:39  brouard
+   Summary: Back from Windows 8. Intel Compiler
+   Revision 1.183  2015/03/10 20:34:32  brouard
+   Summary: 0.98q0, trying with directest, mnbrak fixed
+   We use directest instead of original Powell test; probably no
+   incidence on the results, but better justifications;
+   We fixed Numerical Recipes mnbrak routine which was wrong and gave
+   wrong results.
+   Revision 1.182  2015/02/12 08:19:57  brouard
+   Summary: Trying to keep directest which seems simpler and more general
+   Author: Nicolas Brouard
+   Revision 1.181  2015/02/11 23:22:24  brouard
+   Summary: Comments on Powell added
+   Author:
+   Revision 1.180  2015/02/11 17:33:45  brouard
+   Summary: Finishing move from main to function (hpijx and prevalence_limit)
+   Revision 1.179  2015/01/04 09:57:06  brouard
+   Summary: back to OS/X
+   Revision 1.178  2015/01/04 09:35:48  brouard
+   *** empty log message ***
+   Revision 1.177  2015/01/03 18:40:56  brouard
+   Summary: Still testing ilc32 on OSX
+   Revision 1.176  2015/01/03 16:45:04  brouard
+   *** empty log message ***
+   Revision 1.175  2015/01/03 16:33:42  brouard
+   *** empty log message ***
+   Revision 1.174  2015/01/03 16:15:49  brouard
+   Summary: Still in cross-compilation
+   Revision 1.173  2015/01/03 12:06:26  brouard
+   Summary: trying to detect cross-compilation
+   Revision 1.172  2014/12/27 12:07:47  brouard
+   Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
+   Revision 1.171  2014/12/23 13:26:59  brouard
+   Summary: Back from Visual C
+   Still problem with utsname.h on Windows
+   Revision 1.170  2014/12/23 11:17:12  brouard
+   Summary: Cleaning some \%% back to %%
+   The escape was mandatory for a specific compiler (which one?), but too many warnings.
+   Revision 1.169  2014/12/22 23:08:31  brouard
+   Summary: 0.98p
+   Outputs some informations on compiler used, OS etc. Testing on different platforms.
    Revision 1.168  2014/12/22 15:17:42  brouard
-   Summary: udate
+   Summary: update
    Revision 1.167  2014/12/22 13:50:56  brouard
    Summary: Testing uname and compiler version and if compiled 32 or 64
- Line 325
+ Line 954
    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
+   Agnès, who wrote this part of the code, tried to keep most of the
    former routines in order to include the new code within the former code.
    The output is very simple: only an estimate of the intercept and of
- Line 420
+ Line 1049
    Short summary of the programme:
-   This program computes Healthy Life Expectancies from
+   This program computes Healthy Life Expectancies or State-specific
-   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
+   (if states aren't health statuses) Expectancies from
-   first survey ("cross") where individuals from different ages are
+   cross-longitudinal data. Cross-longitudinal data consist in:
-   interviewed on their health status or degree of disability (in the
-   case of a health survey which is our main interest) -2- at least a
+   -1- a first survey ("cross") where individuals from different ages
-   second wave of interviews ("longitudinal") which measure each change
+   are interviewed on their health status or degree of disability (in
-   (if any) in individual health status.  Health expectancies are
+   the case of a health survey which is our main interest)
-   computed from the time spent in each health state according to a
-   model. More health states you consider, more time is necessary to reach the
+   -2- at least a second wave of interviews ("longitudinal") which
-   Maximum Likelihood of the parameters involved in the model.  The
+   measure each change (if any) in individual health status.  Health
-   simplest model is the multinomial logistic model where pij is the
+   expectancies are computed from the time spent in each health state
-   probability to be observed in state j at the second wave
+   according to a model. More health states you consider, more time is
-   conditional to be observed in state i at the first wave. Therefore
+   necessary to reach the Maximum Likelihood of the parameters involved
-   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
+   in the model.  The simplest model is the multinomial logistic model
-   'age' is age and 'sex' is a covariate. If you want to have a more
+   where pij is the probability to be observed in state j at the second
-   complex model than "constant and age", you should modify the program
+   wave conditional to be observed in state i at the first
-   where the markup *Covariates have to be included here again* invites
+   wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
-   you to do it.  More covariates you add, slower the
+   etc , where 'age' is age and 'sex' is a covariate. If you want to
+   have a more complex model than "constant and age", you should modify
+   the program where the markup *Covariates have to be included here
+   again* invites you to do it.  More covariates you add, slower the
    convergence.
    The advantage of this computer programme, compared to a simple
- Line 456
+ Line 1088
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
    of the life expectancies. It also computes the period (stable) prevalence.
+ Back prevalence and projections:
+  - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
+    double agemaxpar, double ftolpl, int *ncvyearp, double
+    dateprev1,double dateprev2, int firstpass, int lastpass, int
+    mobilavproj)
+     Computes the back prevalence limit for any combination of
+     covariate values k at any age between ageminpar and agemaxpar and
+     returns it in **bprlim. In the loops,
+    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
+        **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
+    - hBijx Back Probability to be in state i at age x-h being in j at x
+    Computes for any combination of covariates k and any age between bage and fage
+    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                         oldm=oldms;savm=savms;
+    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
+      Computes the transition matrix starting at age 'age' over
+      'nhstepm*hstepm*stepm' months (i.e. until
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+      nhstepm*hstepm matrices.
+      Returns p3mat[i][j][h] after calling
+      p3mat[i][j][h]=matprod2(newm,
+      bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
+      dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+      oldm);
+ Important routines
+ - func (or funcone), computes logit (pij) distinguishing
+   o fixed variables (single or product dummies or quantitative);
+   o varying variables by:
+    (1) wave (single, product dummies, quantitative),
+    (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
+        % fixed dummy (treated) or quantitative (not done because time-consuming);
+        % varying dummy (not done) or quantitative (not done);
+ - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
+   and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
+ - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
+   o There are 2**cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
+     race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
-   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
-            Institut national d'études démographiques, 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 513
+ Line 1193
   end
  */
+ /* #define DEBUG */
+ /* #define DEBUGBRENT */
+ /* #define DEBUGLINMIN */
+ /* #define DEBUGHESS */
+ #define DEBUGHESSIJ
+ /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
  #define POWELL /* Instead of NLOPT */
+ #define POWELLNOF3INFF1TEST /* Skip test */
+ /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
+ /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
+ /* #define FLATSUP  *//* Suppresses directions where likelihood is flat */
  #include <math.h>
  #include <stdio.h>
  #include <stdlib.h>
  #include <string.h>
+ #include <ctype.h>
  #ifdef _WIN32
  #include <io.h>
+ #include <windows.h>
+ #include <tchar.h>
  #else
  #include <unistd.h>
  #endif
  #include <limits.h>
  #include <sys/types.h>
- #include <sys/utsname.h>
+ #if defined(__GNUC__)
+ #include <sys/utsname.h> /* Doesn't work on Windows */
+ #endif
  #include <sys/stat.h>
  #include <errno.h>
  /* extern int errno; */
- Line 558  typedef struct {
+ Line 1255  typedef struct {
  /* #include <libintl.h> */
  /* #define _(String) gettext (String) */
- #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
+ #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
  #define GNUPLOTPROGRAM "gnuplot"
  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- #define FILENAMELENGTH 132
+ #define FILENAMELENGTH 256
  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- Line 573  typedef struct {
+ Line 1270  typedef struct {
  #define NINTERVMAX 8
  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
+ #define NCOVMAX 30  /**< Maximum number of covariates used in the model, including generated covariates V1*V2 or V1*age */
- #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
+ #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
- #define MAXN 20000
+ /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
+ #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
+ /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
  #define YEARM 12. /**< Number of months per year */
- #define AGESUP 130
+ /* #define AGESUP 130 */
+ /* #define AGESUP 150 */
+ #define AGESUP 200
+ #define AGEINF 0
+ #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
  #define AGEBASE 40
+ #define AGEOVERFLOW 1.e20
  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
  #ifdef _WIN32
  #define DIRSEPARATOR '\\'
- Line 592  typedef struct {
+ Line 1296  typedef struct {
  /* $Id$ */
  /* $State$ */
+ #include "version.h"
- char version[]="Imach version 0.98nY, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
+ char version[]=__IMACH_VERSION__;
+ char copyright[]="September 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022";
  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 */
+ int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
- /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
+ /* Number of covariates model (1)=V2+V1+ V3*age+V2*V4 */
- int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
+ /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
- int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
+ int cptcovn=0; /**< cptcovn decodemodel: number of covariates k of the models excluding age*products =6 and age*age but including products */
- int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
+ int cptcovt=0; /**< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
+ int cptcovs=0; /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
+ int cptcovsnq=0; /**< cptcovsnq number of SIMPLE covariates in the model but non quantitative 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 cptcoveff=0; /* Total number of single dummy covariates (fixed or time varying) to vary for printing results (2**cptcoveff combinations of dummies)(computed in tricode as cptcov) */
+ int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
+ int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
+ int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
+ int nsd=0; /**< Total number of single dummy variables (output) */
+ int nsq=0; /**< Total number of single quantitative variables (output) */
+ int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
+ int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
+ int ntveff=0; /**< ntveff number of effective time varying variables */
+ int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
  int cptcov=0; /* Working variable */
- int npar=NPARMAX;
+ int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs+1 declared globally ;*/
+ int nobs=10;  /* Number of observations in the data lastobs-firstobs */
+ int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
+ int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
  int nlstate=2; /* Number of live states */
  int ndeath=1; /* Number of dead states */
  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
- Line 625  int **dh; /* dh[mi][i] is number of step
+ Line 1345  int **dh; /* dh[mi][i] is number of step
  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. */
  int countcallfunc=0;  /* Count the number of calls to func */
+ int selected(int kvar); /* Is covariate kvar selected for printing results */
  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 */
+ double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
  /*FILE *fic ; */ /* Used in readdata only */
- FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
  FILE *ficlog, *ficrespow;
  int globpr=0; /* Global variable for printing or not */
  double fretone; /* Only one call to likelihood */
- Line 650  FILE *ficrescveij;
+ Line 1374  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 model[MAXLINE]; /**< The model line */
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[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 fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char fileresu[FILENAMELENGTH]; /* fileres without r in front */
  char filelog[FILENAMELENGTH]; /* Log file */
  char filerest[FILENAMELENGTH];
  char fileregp[FILENAMELENGTH];
- Line 690  double dval;
+ Line 1414  double dval;
  #define FTOL 1.0e-10
  #define NRANSI
  #define ITMAX 200
+ #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
  #define TOL 2.0e-4
- Line 709  static double maxarg1,maxarg2;
+ Line 1434  static double maxarg1,maxarg2;
  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
  #define rint(a) floor(a+0.5)
  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
- /* #define mytinydouble 1.0e-16 */
+ #define mytinydouble 1.0e-16
  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
  /* static double dsqrarg; */
- Line 728  int estepm;
+ Line 1453  int estepm;
  int m,nb;
  long *num;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ int firstpass=0, lastpass=4,*cod, *cens;
+ int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
+                    covariate for which somebody answered excluding
+                    undefined. Usually 2: 0 and 1. */
+ int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
+                              covariate for which somebody answered including
+                              undefined. Usually 3: -1, 0 and 1. */
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- double **pmmij, ***probs;
+ double **pmmij, ***probs; /* Global pointer */
+ double ***mobaverage, ***mobaverages; /* New global variable */
+ double **precov; /* New global variable to store for each resultline, values of model covariates given by the resultlines (in order to speed up)  */
  double *ageexmed,*agecens;
  double dateintmean=0;
+   double anprojd, mprojd, jprojd; /* For eventual projections */
+   double anprojf, mprojf, jprojf;
+   double anbackd, mbackd, jbackd; /* For eventual backprojections */
+   double anbackf, mbackf, jbackf;
+   double jintmean,mintmean,aintmean;
  double *weight;
  int **s; /* Status */
  double *agedc;
  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]; */
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
+ double **coqvar; /* Fixed quantitative covariate nqv */
+ double ***cotvar; /* Time varying covariate ntv */
+ double ***cotqvar; /* Time varying quantitative covariate itqv */
  double  idx;
  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+ /* Some documentation */
+       /*   Design original data
+        *  V1   V2   V3   V4  V5  V6  V7  V8  Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12
+        *  <          ncovcol=6   >   nqv=2 (V7 V8)                   dv dv  dv  qtv    dv dv  dvv qtv
+        *                                                             ntv=3     nqtv=1
+        *  cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11
+        * For time varying covariate, quanti or dummies
+        *       cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
+        *       cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti
+        *       cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
+        *       cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
+        *       covar[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:
+        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
+        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + V9 + V9*age + V10
+        *   k=  1    2      3       4     5       6      7        8   9     10       11
+        */
+ /* According to the model, more columns can be added to covar by the product of covariates */
+ /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
+   # States 1=Coresidence, 2 Living alone, 3 Institution
+   # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
+ */
+ /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ /*    k        1  2   3   4     5    6    7     8    9 */
+ /*Typevar[k]=  0  0   0   2     1    0    2     1    0 *//*0 for simple covariate (dummy, quantitative,*/
+                                                          /* fixed or varying), 1 for age product, 2 for*/
+                                                          /* product */
+ /*Dummy[k]=    1  0   0   1     3    1    1     2    0 *//*Dummy[k] 0=dummy (0 1), 1 quantitative */
+                                                          /*(single or product without age), 2 dummy*/
+                                                          /* with age product, 3 quant with age product*/
+ /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */
+ /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */
+ /*TnsdVar[Tvar]   1   2                              3 */
+ /*Tvaraff[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
+ /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
+ /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */
+ /*    nsq      1                     2                 */ /* Counting single quantit tv */
+ /* TvarsQ[k]   5                     2                 */ /* Number of single quantitative cova */
+ /* TvarsQind   1                     6                 */ /* position K of single quantitative cova */
+ /* Tprod[i]=k             1               2            */ /* Position in model of the ith prod without age */
+ /* cptcovage                    1               2      */ /* Counting cov*age in the model equation */
+ /* Tage[cptcovage]=k            5               8      */ /* Position in the model of ith cov*age */
+ /* Tvard[1][1]@4={4,3,1,2}    V4*V3 V1*V2              */ /* Position in model of the ith prod without age */
+ /* Tvardk[4][1]=4;Tvardk[4][2]=3;Tvardk[7][1]=1;Tvardk[7][2]=2 */ /* Variables of a prod at position in the model equation*/
+ /* TvarF TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
+ /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
+ /* Type                    */
+ /* V         1  2  3  4  5 */
+ /*           F  F  V  V  V */
+ /*           D  Q  D  D  Q */
+ /*                         */
+ int *TvarsD;
+ int *TnsdVar;
+ int *TvarsDind;
+ int *TvarsQ;
+ int *TvarsQind;
+ #define MAXRESULTLINESPONE 10+1
+ int nresult=0;
+ int parameterline=0; /* # of the parameter (type) line */
+ int TKresult[MAXRESULTLINESPONE]; /* TKresult[nres]=k for each resultline nres give the corresponding combination of dummies */
+ int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model corresponds to the k3 position in the resultline */
+ int modelresult[MAXRESULTLINESPONE][NCOVMAX];/* modelresult[k3]=k1: k1th position in the model corresponds to the k3 position in the resultline */
+ int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline */
+ int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line  */
+ double TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */
+ int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvresult[nres][result_position]= name of the dummy variable at the result_position in the nres resultline */
+ double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
+ double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
+ int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline */
+ /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
+   # States 1=Coresidence, 2 Living alone, 3 Institution
+   # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
+ */
+ /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
+ int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+ int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+ int *Tvarsel; /**< Selected covariates for output */
+ double *Tvalsel; /**< Selected modality value of covariate for output */
+ int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
+ int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
+ int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
+ int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
+ int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
+ int *Tage;
+ int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
+ int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1  */
  int *Ndum; /** Freq of modality (tricode */
- int **codtab; /**< codtab=imatrix(1,100,1,10); */
+ /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
- int **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ int **Tvard;
+ int **Tvardk;
+ int *Tprod;/**< Gives the k position of the k1 product */
+ /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
+ int *Tposprod; /**< Gives the k1 product from the k position */
+    /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
+    /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
+ int cptcovprod, *Tvaraff, *invalidvarcomb;
  double *lsurv, *lpop, *tpop;
+ #define FD 1; /* Fixed dummy covariate */
+ #define FQ 2; /* Fixed quantitative covariate */
+ #define FP 3; /* Fixed product covariate */
+ #define FPDD 7; /* Fixed product dummy*dummy covariate */
+ #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
+ #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
+ #define VD 10; /* Varying dummy covariate */
+ #define VQ 11; /* Varying quantitative covariate */
+ #define VP 12; /* Varying product covariate */
+ #define VPDD 13; /* Varying product dummy*dummy covariate */
+ #define VPDQ 14; /* Varying product dummy*quantitative covariate */
+ #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
+ #define APFD 16; /* Age product * fixed dummy covariate */
+ #define APFQ 17; /* Age product * fixed quantitative covariate */
+ #define APVD 18; /* Age product * varying dummy covariate */
+ #define APVQ 19; /* Age product * varying quantitative covariate */
+ #define FTYPE 1; /* Fixed covariate */
+ #define VTYPE 2; /* Varying covariate (loop in wave) */
+ #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
+ struct kmodel{
+         int maintype; /* main type */
+         int subtype; /* subtype */
+ };
+ struct kmodel modell[NCOVMAX];
  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
  double ftolhess; /**< Tolerance for computing hessian */
- Line 757  static int split( char *path, char *dirc
+ Line 1634  static int split( char *path, char *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 */
+   int   l1=0, l2=0;                             /* length counters */
    l1 = strlen(path );                   /* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
- Line 768  static int split( char *path, char *dirc
+ Line 1645  static int split( char *path, char *dirc
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      /* get current working directory */
      /*    extern  char* getcwd ( char *buf , int len);*/
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #ifdef WIN32
+     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #else
+         if (getcwd(dirc, FILENAME_MAX) == NULL) {
+ #endif
        return( GLOCK_ERROR_GETCWD );
      }
      /* got dirc from getcwd*/
      printf(" DIRC = %s \n",dirc);
-   } else {                              /* strip direcotry from path */
+   } else {                              /* strip directory from path */
      ss++;                               /* after this, the filename */
      l2 = strlen( ss );                  /* length of filename */
      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
      strcpy( name, ss );         /* save file name */
      strncpy( dirc, path, l1 - l2 );     /* now the directory */
-     dirc[l1-l2] = 0;                    /* add zero */
+     dirc[l1-l2] = '\0';                 /* add zero */
      printf(" DIRC2 = %s \n",dirc);
    }
    /* We add a separator at the end of dirc if not exists */
- Line 831  char *trimbb(char *out, char *in)
+ Line 1712  char *trimbb(char *out, char *in)
    return s;
  }
- char *cutl(char *blocc, char *alocc, char *in, char occ)
+ /* char *substrchaine(char *out, char *in, char *chain) */
- {
+ /* { */
-   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
+ /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
-      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+ /*   char *s, *t; */
-      gives blocc="abcdef2ghi" and alocc="j".
+ /*   t=in;s=out; */
+ /*   while ((*in != *chain) && (*in != '\0')){ */
+ /*     *out++ = *in++; */
+ /*   } */
+ /*   /\* *in matches *chain *\/ */
+ /*   while ((*in++ == *chain++) && (*in != '\0')){ */
+ /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+ /*   } */
+ /*   in--; chain--; */
+ /*   while ( (*in != '\0')){ */
+ /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+ /*     *out++ = *in++; */
+ /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+ /*   } */
+ /*   *out='\0'; */
+ /*   out=s; */
+ /*   return out; */
+ /* } */
+ char *substrchaine(char *out, char *in, char *chain)
+ {
+   /* Substract chain 'chain' from 'in', return and output 'out' */
+   /* in="V1+V1*age+age*age+V2", chain="age*age" */
+   char *strloc;
+   strcpy (out, in);
+   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
+   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
+   if(strloc != NULL){
+     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
+     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
+     /* strcpy (strloc, strloc +strlen(chain));*/
+   }
+   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
+   return out;
+ }
+ 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 alocc="abcdef" and blocc="ghi2j".
       If occ is not found blocc is null and alocc is equal to in. Returns blocc
    */
    char *s, *t;
- Line 861  char *cutl(char *blocc, char *alocc, cha
+ Line 1785  char *cutl(char *blocc, char *alocc, cha
  }
  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'
+   /* 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
- Line 895  int nbocc(char *s, char occ)
+ Line 1819  int nbocc(char *s, char occ)
    i=0;
    lg=strlen(s);
    for(i=0; i<= lg; i++) {
-   if  (s[i] == occ ) j++;
+     if  (s[i] == occ ) j++;
    }
    return j;
  }
- Line 1117  char *subdirf(char fileres[])
+ Line 2041  char *subdirf(char fileres[])
  /*************** function subdirf2 ***********/
  char *subdirf2(char fileres[], char *preop)
  {
+   /* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte"
+  Errors in subdirf, 2, 3 while printing tmpout is
+  rewritten within the same printf. Workaround: many printfs */
    /* Caution optionfilefiname is hidden */
    strcpy(tmpout,optionfilefiname);
    strcat(tmpout,"/");
- Line 1138  char *subdirf3(char fileres[], char *pre
+ Line 2064  char *subdirf3(char fileres[], char *pre
    strcat(tmpout,fileres);
    return tmpout;
  }
+ /*************** function subdirfext ***********/
+ char *subdirfext(char fileres[], char *preop, char *postop)
+ {
+   strcpy(tmpout,preop);
+   strcat(tmpout,fileres);
+   strcat(tmpout,postop);
+   return tmpout;
+ }
+ /*************** function subdirfext3 ***********/
+ char *subdirfext3(char fileres[], char *preop, char *postop)
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
+   strcat(tmpout,fileres);
+   strcat(tmpout,postop);
+   return tmpout;
+ }
  char *asc_diff_time(long time_sec, char ascdiff[])
  {
    long sec_left, days, hours, minutes;
- Line 1172  double f1dim(double x)
+ Line 2121  double f1dim(double x)
  /*****************brent *************************/
  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
  {
+   /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
+    * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
+    * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
+    * the minimum is returned as xmin, and the minimum function value is returned as brent , the
+    * returned function value.
+   */
    int iter;
    double a,b,d,etemp;
    double fu=0,fv,fw,fx;
- Line 1210  double brent(double ax, double bx, doubl
+ Line 2165  double brent(double ax, double bx, doubl
        etemp=e;
        e=d;
        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+                                 d=CGOLD*(e=(x >= xm ? a-x : b-x));
        else {
-         d=p/q;
+                                 d=p/q;
-         u=x+d;
+                                 u=x+d;
-         if (u-a < tol2 || b-u < tol2)
+                                 if (u-a < tol2 || b-u < tol2)
-           d=SIGN(tol1,xm-x);
+                                         d=SIGN(tol1,xm-x);
        }
      } else {
        d=CGOLD*(e=(x >= xm ? a-x : b-x));
- Line 1225  double brent(double ax, double bx, doubl
+ Line 2180  double brent(double ax, double bx, doubl
      if (fu <= fx) {
        if (u >= x) a=x; else b=x;
        SHFT(v,w,x,u)
-         SHFT(fv,fw,fx,fu)
+       SHFT(fv,fw,fx,fu)
-         } else {
+     } else {
-           if (u < x) a=u; else b=u;
+       if (u < x) a=u; else b=u;
-           if (fu <= fw || w == x) {
+       if (fu <= fw || w == x) {
-             v=w;
+                                 v=w;
-             w=u;
+                                 w=u;
-             fv=fw;
+                                 fv=fw;
-             fw=fu;
+                                 fw=fu;
-           } else if (fu <= fv || v == x || v == w) {
+       } else if (fu <= fv || v == x || v == w) {
-             v=u;
+                                 v=u;
-             fv=fu;
+                                 fv=fu;
-           }
+       }
-         }
+     }
    }
    nrerror("Too many iterations in brent");
    *xmin=x;
- Line 1248  double brent(double ax, double bx, doubl
+ Line 2203  double brent(double ax, double bx, doubl
  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
              double (*func)(double))
- {
+ { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
+ the downhill direction (defined by the function as evaluated at the initial points) and returns
+ new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
+ values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
+    */
    double ulim,u,r,q, dum;
    double fu;
-   *fa=(*func)(*ax);
+   double scale=10.;
-   *fb=(*func)(*bx);
+   int iterscale=0;
+   *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
+   *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
+   /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
+   /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
+   /*   *bx = *ax - (*ax - *bx)/scale; */
+   /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
+   /* } */
    if (*fb > *fa) {
      SHFT(dum,*ax,*bx,dum)
-       SHFT(dum,*fb,*fa,dum)
+     SHFT(dum,*fb,*fa,dum)
-       }
+   }
    *cx=(*bx)+GOLD*(*bx-*ax);
    *fc=(*func)(*cx);
-   while (*fb > *fc) { /* Declining fa, fb, fc */
+ #ifdef DEBUG
+   printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
+   fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
+ #endif
+   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
      r=(*bx-*ax)*(*fb-*fc);
-     q=(*bx-*cx)*(*fb-*fa);
+     q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
-     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
-     if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
        fu=(*func)(u);
  #ifdef DEBUG
        /* f(x)=A(x-u)**2+f(u) */
        double A, fparabu;
        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
        fparabu= *fa - A*(*ax-u)*(*ax-u);
-       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+       printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
-       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+       fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
+       /* And thus,it can be that fu > *fc even if fparabu < *fc */
+       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
+         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
+       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
  #endif
+ #ifdef MNBRAKORIGINAL
+ #else
+ /*       if (fu > *fc) { */
+ /* #ifdef DEBUG */
+ /*       printf("mnbrak4  fu > fc \n"); */
+ /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
+ /* #endif */
+ /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
+ /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
+ /*      dum=u; /\* Shifting c and u *\/ */
+ /*      u = *cx; */
+ /*      *cx = dum; */
+ /*      dum = fu; */
+ /*      fu = *fc; */
+ /*      *fc =dum; */
+ /*       } else { /\* end *\/ */
+ /* #ifdef DEBUG */
+ /*       printf("mnbrak3  fu < fc \n"); */
+ /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
+ /* #endif */
+ /*      dum=u; /\* Shifting c and u *\/ */
+ /*      u = *cx; */
+ /*      *cx = dum; */
+ /*      dum = fu; */
+ /*      fu = *fc; */
+ /*      *fc =dum; */
+ /*       } */
+ #ifdef DEBUGMNBRAK
+                  double A, fparabu;
+      A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
+      fparabu= *fa - A*(*ax-u)*(*ax-u);
+      printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
+      fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
+ #endif
+       dum=u; /* Shifting c and u */
+       u = *cx;
+       *cx = dum;
+       dum = fu;
+       fu = *fc;
+       *fc =dum;
+ #endif
      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
+ #ifdef DEBUG
+       printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
+       fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
+ #endif
        fu=(*func)(u);
        if (fu < *fc) {
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+ #ifdef DEBUG
-           SHFT(*fb,*fc,fu,(*func)(u))
+                                 printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
-           }
+                           fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
+ #endif
+                           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+                                 SHFT(*fb,*fc,fu,(*func)(u))
+ #ifdef DEBUG
+                                         printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
+ #endif
+       }
      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
+ #ifdef DEBUG
+       printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
+       fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
+ #endif
        u=ulim;
        fu=(*func)(u);
-     } else {
+     } else { /* u could be left to b (if r > q parabola has a maximum) */
+ #ifdef DEBUG
+       printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
+       fprintf(ficlog,"\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
+ #endif
        u=(*cx)+GOLD*(*cx-*bx);
        fu=(*func)(u);
-     }
+ #ifdef DEBUG
+       printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
+       fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
+ #endif
+     } /* end tests */
      SHFT(*ax,*bx,*cx,u)
-       SHFT(*fa,*fb,*fc,fu)
+     SHFT(*fa,*fb,*fc,fu)
-       }
+ #ifdef DEBUG
+       printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
+       fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
+ #endif
+   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
  }
  /*************** linmin ************************/
- Line 1304  int ncom;
+ Line 2350  int ncom;
  double *pcom,*xicom;
  double (*nrfunc)(double []);
+ #ifdef LINMINORIGINAL
  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+ #else
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
+ #endif
  {
    double brent(double ax, double bx, double cx,
                 double (*f)(double), double tol, double *xmin);
- Line 1314  void linmin(double p[], double xi[], int
+ Line 2364  void linmin(double p[], double xi[], int
    int j;
    double xx,xmin,bx,ax;
    double fx,fb,fa;
+ #ifdef LINMINORIGINAL
+ #else
+   double scale=10., axs, xxs; /* Scale added for infinity */
+ #endif
    ncom=n;
    pcom=vector(1,n);
    xicom=vector(1,n);
    nrfunc=func;
    for (j=1;j<=n;j++) {
      pcom[j]=p[j];
-     xicom[j]=xi[j];
+     xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
    }
-   ax=0.0;
-   xx=1.0;
+ #ifdef LINMINORIGINAL
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
+   xx=1.;
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
+ #else
+   axs=0.0;
+   xxs=1.;
+   do{
+     xx= xxs;
+ #endif
+     ax=0.;
+     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
+     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
+     /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
+     /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
+     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
+     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
+     /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
+ #ifdef LINMINORIGINAL
+ #else
+     if (fx != fx){
+                         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
+                         printf("|");
+                         fprintf(ficlog,"|");
+ #ifdef DEBUGLINMIN
+                         printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
+ #endif
+     }
+   }while(fx != fx && xxs > 1.e-5);
+ #endif
+ #ifdef DEBUGLINMIN
+   printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
+   fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
+ #endif
+ #ifdef LINMINORIGINAL
+ #else
+   if(fb == fx){ /* Flat function in the direction */
+     xmin=xx;
+     *flat=1;
+   }else{
+     *flat=0;
+ #endif
+                 /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
+   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
+   /* fmin = f(p[j] + xmin * xi[j]) */
+   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
+   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
  #ifdef DEBUG
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
+ #endif
+ #ifdef LINMINORIGINAL
+ #else
+                         }
+ #endif
+ #ifdef DEBUGLINMIN
+   printf("linmin end ");
+   fprintf(ficlog,"linmin end ");
  #endif
    for (j=1;j<=n;j++) {
+ #ifdef LINMINORIGINAL
      xi[j] *= xmin;
-     p[j] += xi[j];
+ #else
+ #ifdef DEBUGLINMIN
+     if(xxs <1.0)
+       printf(" before xi[%d]=%12.8f", j,xi[j]);
+ #endif
+     xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
+ #ifdef DEBUGLINMIN
+     if(xxs <1.0)
+       printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
+ #endif
+ #endif
+     p[j] += xi[j]; /* Parameters values are updated accordingly */
    }
+ #ifdef DEBUGLINMIN
+   printf("\n");
+   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
+   fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
+   for (j=1;j<=n;j++) {
+     printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
+     fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
+     if(j % ncovmodel == 0){
+       printf("\n");
+       fprintf(ficlog,"\n");
+     }
+   }
+ #else
+ #endif
    free_vector(xicom,1,n);
    free_vector(pcom,1,n);
  }
- Line 1342  void linmin(double p[], double xi[], int
+ Line 2475  void linmin(double p[], double xi[], int
  /*************** powell ************************/
  /*
- Minimization of a function func of n variables. Input consists of an initial starting point
+ Minimization of a function func of n variables. Input consists in an initial starting point
- p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
+ p[1..n] ; an initial matrix xi[1..n][1..n]  whose columns contain the initial set of di-
- rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
+ rections (usually the n unit vectors); and ftol, the fractional tolerance in the function value
- such that failure to decrease by more than this amount on one iteration signals doneness. On
+ such that failure to decrease by more than this amount in one iteration signals doneness. On
  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
  function value at p , and iter is the number of iterations taken. The routine linmin is used.
   */
+ #ifdef LINMINORIGINAL
+ #else
+         int *flatdir; /* Function is vanishing in that direction */
+         int flat=0, flatd=0; /* Function is vanishing in that direction */
+ #endif
  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
              double (*func)(double []))
  {
-   void linmin(double p[], double xi[], int n, double *fret,
+ #ifdef LINMINORIGINAL
+  void linmin(double p[], double xi[], int n, double *fret,
                double (*func)(double []));
-   int i,ibig,j;
+ #else
+  void linmin(double p[], double xi[], int n, double *fret,
+              double (*func)(double []),int *flat);
+ #endif
+  int i,ibig,j,jk,k;
    double del,t,*pt,*ptt,*xit;
+   double directest;
    double fp,fptt;
    double *xits;
    int niterf, itmp;
- Line 1366  void powell(double p[], double **xi, int
+ Line 2510  void powell(double p[], double **xi, int
    xits=vector(1,n);
    *fret=(*func)(p);
    for (j=1;j<=n;j++) pt[j]=p[j];
-     rcurr_time = time(NULL);
+   rcurr_time = time(NULL);
    for (*iter=1;;++(*iter)) {
-     fp=(*fret);
      ibig=0;
      del=0.0;
      rlast_time=rcurr_time;
      /* (void) gettimeofday(&curr_time,&tzp); */
      rcurr_time = time(NULL);
      curr_time = *localtime(&rcurr_time);
-     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
+     /* printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); */
-     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
+     /* fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); */
+     printf("\nPowell iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-    for (i=1;i<=n;i++) {
+     fp=(*fret); /* From former iteration or initial value */
-       printf(" %d %.12f",i, p[i]);
+     for (i=1;i<=n;i++) {
-       fprintf(ficlog," %d %.12lf",i, p[i]);
        fprintf(ficrespow," %.12lf", p[i]);
      }
+     fprintf(ficrespow,"\n");fflush(ficrespow);
+     printf("\n#model=  1      +     age ");
+     fprintf(ficlog,"\n#model=  1      +     age ");
+     if(nagesqr==1){
+         printf("  + age*age  ");
+         fprintf(ficlog,"  + age*age  ");
+     }
+     for(j=1;j <=ncovmodel-2;j++){
+       if(Typevar[j]==0) {
+         printf("  +      V%d  ",Tvar[j]);
+         fprintf(ficlog,"  +      V%d  ",Tvar[j]);
+       }else if(Typevar[j]==1) {
+         printf("  +    V%d*age ",Tvar[j]);
+         fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
+       }else if(Typevar[j]==2) {
+         printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+       }
+     }
      printf("\n");
+ /*     printf("12   47.0114589    0.0154322   33.2424412    0.3279905    2.3731903  */
+ /* 13  -21.5392400    0.1118147    1.2680506    1.2973408   -1.0663662  */
      fprintf(ficlog,"\n");
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+     for(i=1,jk=1; i <=nlstate; i++){
-     if(*iter <=3){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
+           printf("%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
+           for(j=1; j <=ncovmodel; j++){
+             printf("%12.7f ",p[jk]);
+             fprintf(ficlog,"%12.7f ",p[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+         }
+       }
+     }
+     if(*iter <=3 && *iter >1){
        tml = *localtime(&rcurr_time);
        strcpy(strcurr,asctime(&tml));
        rforecast_time=rcurr_time;
- Line 1401  void powell(double p[], double **xi, int
+ Line 2580  void powell(double p[], double **xi, int
          strcpy(strfor,asctime(&forecast_time));
          itmp = strlen(strfor);
          if(strfor[itmp-1]=='\n')
-         strfor[itmp-1]='\0';
+           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(rforecast_time-rcurr_time,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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
        }
      }
-     for (i=1;i<=n;i++) {
+     for (i=1;i<=n;i++) { /* For each direction i */
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
        fptt=(*fret);
  #ifdef DEBUG
-           printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
+       printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-           fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
+       fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
  #endif
-       printf("%d",i);fflush(stdout);
+       printf("%d",i);fflush(stdout); /* print direction (parameter) i */
        fprintf(ficlog,"%d",i);fflush(ficlog);
-       linmin(p,xit,n,fret,func);
+ #ifdef LINMINORIGINAL
-       if (fabs(fptt-(*fret)) > del) {
+       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-         del=fabs(fptt-(*fret));
+ #else
-         ibig=i;
+       linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
+                         flatdir[i]=flat; /* Function is vanishing in that direction i */
+ #endif
+                         /* Outputs are fret(new point p) p is updated and xit rescaled */
+       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
+                                 /* because that direction will be replaced unless the gain del is small */
+                                 /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
+                                 /* Unless the n directions are conjugate some gain in the determinant may be obtained */
+                                 /* with the new direction. */
+                                 del=fabs(fptt-(*fret));
+                                 ibig=i;
        }
  #ifdef DEBUG
        printf("%d %.12e",i,(*fret));
        fprintf(ficlog,"%d %.12e",i,(*fret));
        for (j=1;j<=n;j++) {
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+                                 xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-         printf(" x(%d)=%.12e",j,xit[j]);
+                                 printf(" x(%d)=%.12e",j,xit[j]);
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+                                 fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
        }
        for(j=1;j<=n;j++) {
-         printf(" p(%d)=%.12e",j,p[j]);
+                                 printf(" p(%d)=%.12e",j,p[j]);
-         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
+                                 fprintf(ficlog," p(%d)=%.12e",j,p[j]);
        }
        printf("\n");
        fprintf(ficlog,"\n");
  #endif
-     } /* end i */
+     } /* end loop on each direction i */
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
+     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
+     /* New value of last point Pn is not computed, P(n-1) */
+     for(j=1;j<=n;j++) {
+       if(flatdir[j] >0){
+         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
+         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
+       }
+       /* printf("\n"); */
+       /* fprintf(ficlog,"\n"); */
+     }
+     /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
+     if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
+       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
+       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
+       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
+       /* decreased of more than 3.84  */
+       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
+       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
+       /* By adding 10 parameters more the gain should be 18.31 */
+       /* Starting the program with initial values given by a former maximization will simply change */
+       /* the scales of the directions and the directions, because the are reset to canonical directions */
+       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
+       /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
  #ifdef DEBUG
        int k[2],l;
        k[0]=1;
- Line 1460  void powell(double p[], double **xi, int
+ Line 2673  void powell(double p[], double **xi, int
        }
  #endif
        free_vector(xit,1,n);
        free_vector(xits,1,n);
        free_vector(ptt,1,n);
        free_vector(pt,1,n);
        return;
-     }
+     } /* enough precision */
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+     if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
-     for (j=1;j<=n;j++) { /* Computes an extrapolated point */
+     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
        ptt[j]=2.0*p[j]-pt[j];
        xit[j]=p[j]-pt[j];
        pt[j]=p[j];
      }
-     fptt=(*func)(ptt);
+     fptt=(*func)(ptt); /* f_3 */
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
+                 if (*iter <=4) {
+ #else
+ #endif
+ #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
+ #else
      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
+ #endif
        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-       /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
-       /* Thus we compare delta(2h) with observed f1-f3 */
+       /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
-       /* or best gain on one ancient line 'del' with total  */
+       /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
-       /* gain f1-f2 = f1 - f2 - 'del' with del  */
        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
+       /*  Even if f3 <f1, directest can be negative and t >0 */
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
+       /* mu² and del² are equal when f3=f1 */
+                         /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
+                         /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
+                         /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
+                         /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
+ #ifdef NRCORIGINAL
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
+ #else
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
        t= t- del*SQR(fp-fptt);
-       printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
+ #endif
-       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
+       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
  #ifdef DEBUG
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
+       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
- Line 1498  void powell(double p[], double **xi, int
+ Line 2726  void powell(double p[], double **xi, int
        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
  #endif
-       if (t < 0.0) { /* Then we use it for last direction */
+ #ifdef POWELLORIGINAL
-         linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
+       if (t < 0.0) { /* Then we use it for new direction */
+ #else
+       if (directest*t < 0.0) { /* Contradiction between both tests */
+                                 printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
+         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
+         fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
+         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
+       }
+       if (directest < 0.0) { /* Then we use it for new direction */
+ #endif
+ #ifdef DEBUGLINMIN
+         printf("Before linmin in direction P%d-P0\n",n);
+         for (j=1;j<=n;j++) {
+           printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           if(j % ncovmodel == 0){
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+ #endif
+ #ifdef LINMINORIGINAL
+         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+ #else
+         linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+         flatdir[i]=flat; /* Function is vanishing in that direction i */
+ #endif
+ #ifdef DEBUGLINMIN
          for (j=1;j<=n;j++) {
-           xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
+           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
+           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           if(j % ncovmodel == 0){
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
          }
-         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+ #endif
-         fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
+         for (j=1;j<=n;j++) {
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
+         }
+ #ifdef LINMINORIGINAL
+ #else
+         for (j=1, flatd=0;j<=n;j++) {
+           if(flatdir[j]>0)
+             flatd++;
+         }
+         if(flatd >0){
+           printf("%d flat directions: ",flatd);
+           fprintf(ficlog,"%d flat directions :",flatd);
+           for (j=1;j<=n;j++) {
+             if(flatdir[j]>0){
+               printf("%d ",j);
+               fprintf(ficlog,"%d ",j);
+             }
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+ #ifdef FLATSUP
+           free_vector(xit,1,n);
+           free_vector(xits,1,n);
+           free_vector(ptt,1,n);
+           free_vector(pt,1,n);
+           return;
+ #endif
+         }
+ #endif
+         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
  #ifdef DEBUG
          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
          for(j=1;j<=n;j++){
-           printf(" %.12e",xit[j]);
+           printf(" %lf",xit[j]);
-           fprintf(ficlog," %.12e",xit[j]);
+           fprintf(ficlog," %lf",xit[j]);
          }
          printf("\n");
          fprintf(ficlog,"\n");
  #endif
-       } /* end of t negative */
+       } /* end of t or directest negative */
-     } /* end if (fptt < fp)  */
+ #ifdef POWELLNOF3INFF1TEST
-   }
+ #else
+       } /* end if (fptt < fp)  */
+ #endif
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
+     } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
+ #else
+ #endif
+                 } /* loop iteration */
  }
  /**** Prevalence limit (stable or period prevalence)  ****************/
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
- {
+   {
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+     /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
-      matrix by transitions matrix until convergence is reached */
+      *   (and selected quantitative values in nres)
+      *  by left multiplying the unit
-   int i, ii,j,k;
+      *  matrix by transitions matrix until convergence is reached with precision ftolpl
-   double min, max, maxmin, maxmax,sumnew=0.;
+      * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I
+      * Wx is row vector: population in state 1, population in state 2, population dead
+      * or prevalence in state 1, prevalence in state 2, 0
+      * newm is the matrix after multiplications, its rows are identical at a factor.
+      * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
+      * Output is prlim.
+      * Initial matrix pimij
+      */
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
+   /*  0,                   0                  , 1} */
+   /*
+    * and after some iteration: */
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
+   /*  0,                   0                  , 1} */
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
+   /* {0.51571254859325999, 0.4842874514067399, */
+   /*  0.51326036147820708, 0.48673963852179264} */
+   /* If we start from prlim again, prlim tends to a constant matrix */
+     int i, ii,j,k, k1;
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
    /* double **matprod2(); */ /* test */
-   double **out, cov[NCOVMAX+1], **pmij();
+   double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
    double **newm;
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
+   int ncvloop=0;
+   int first=0;
+   min=vector(1,nlstate);
+   max=vector(1,nlstate);
+   meandiff=vector(1,nlstate);
+         /* Starting with matrix unity */
    for (ii=1;ii<=nlstate+ndeath;ii++)
      for (j=1;j<=nlstate+ndeath;j++){
        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      }
-    cov[1]=1.;
+   cov[1]=1.;
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+     ncvloop++;
      newm=savm;
      /* Covariates have to be included here again */
      cov[2]=agefin;
+      if(nagesqr==1){
-     for (k=1; k<=cptcovn;k++) {
+       cov[3]= agefin*agefin;
-       cov[2+k]=nbcode[Tvar[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]]);*/
+      /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
-     }
+      /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
-     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+      for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
-     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
+        if(Typevar[k1]==1){ /* A product with age */
-     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
+          cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
+        }else{
+          cov[2+nagesqr+k1]=precov[nres][k1];
+        }
+      }/* End of loop on model equation */
+ /* Start of old code (replaced by a loop on position in the model equation */
+     /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only of the model *\/ */
+     /*                  /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */
+     /*   /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; *\/ */
+     /*   cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])]; */
+     /*   /\* model = 1 +age + V1*V3 + age*V1 + V2 + V1 + age*V2 + V3 + V3*age + V1*V2  */
+     /*    * k                  1        2      3    4      5      6     7        8 */
+     /*    *cov[]   1    2      3        4      5    6      7      8     9       10 */
+     /*    *TypeVar[k]          2        1      0    0      1      0     1        2 */
+     /*    *Dummy[k]            0        2      0    0      2      0     2        0 */
+     /*    *Tvar[k]             4        1      2    1      2      3     3        5 */
+     /*    *nsd=3                              (1)  (2)           (3) */
+     /*    *TvarsD[nsd]                      [1]=2    1             3 */
+     /*    *TnsdVar                          [2]=2 [1]=1         [3]=3 */
+     /*    *TvarsDind[nsd](=k)               [1]=3 [2]=4         [3]=6 */
+     /*    *Tage[]                  [1]=1                  [2]=2      [3]=3 */
+     /*    *Tvard[]       [1][1]=1                                           [2][1]=1 */
+     /*    *                   [1][2]=3                                           [2][2]=2 */
+     /*    *Tprod[](=k)     [1]=1                                              [2]=8 */
+     /*    *TvarsDp(=Tvar)   [1]=1            [2]=2             [3]=3          [4]=5 */
+     /*    *TvarD (=k)       [1]=1            [2]=3 [3]=4       [3]=6          [4]=6 */
+     /*    *TvarsDpType */
+     /*    *si model= 1 + age + V3 + V2*age + V2 + V3*age */
+     /*    * nsd=1              (1)           (2) */
+     /*    *TvarsD[nsd]          3             2 */
+     /*    *TnsdVar           (3)=1          (2)=2 */
+     /*    *TvarsDind[nsd](=k)  [1]=1        [2]=3 */
+     /*    *Tage[]                  [1]=2           [2]= 3    */
+     /*    *\/ */
+     /*   /\* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; *\/ */
+     /*   /\* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
+     /* } */
+     /* for (k=1; k<=nsq;k++) { /\* For single quantitative varying covariates only of the model *\/ */
+     /*                  /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
+     /*   /\* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 *\/ */
+     /*   /\* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; *\/ */
+     /*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][resultmodel[nres][k1]] */
+     /*   /\* cov[++k1]=Tqresult[nres][k];  *\/ */
+     /*   /\* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
+     /* } */
+     /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
+     /*   if(Dummy[Tage[k]]==2){ /\* dummy with age *\/ */
+     /*  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+     /*  /\* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
+     /*   } else if(Dummy[Tage[k]]==3){ /\* quantitative with age *\/ */
+     /*  cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
+     /*  /\* cov[++k1]=Tqresult[nres][k];  *\/ */
+     /*   } */
+     /*   /\* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
+     /* } */
+     /* for (k=1; k<=cptcovprod;k++){ /\* For product without age *\/ */
+     /*   /\* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); *\/ */
+     /*   if(Dummy[Tvard[k][1]]==0){ */
+     /*  if(Dummy[Tvard[k][2]]==0){ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+     /*    /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
+     /*  }else{ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
+     /*    /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; *\/ */
+     /*  } */
+     /*   }else{ */
+     /*  if(Dummy[Tvard[k][2]]==0){ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
+     /*    /\* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; *\/ */
+     /*  }else{ */
+     /*    cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
+     /*    /\* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\/ */
+     /*  } */
+     /*   } */
+     /* } /\* End product without age *\/ */
+ /* ENd of old code */
      /*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 \n",ij, cov[3]);*/
      /* 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 *\/ */
+     /* age and covariate values of ij are in 'cov' */
      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.;
-     for(j=1;j<=nlstate;j++){
+     for(j=1; j<=nlstate; j++){
-       min=1.;
+       max[j]=0.;
-       max=0.;
+       min[j]=1.;
-       for(i=1; i<=nlstate; i++) {
+     }
-         sumnew=0;
+     for(i=1;i<=nlstate;i++){
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+       sumnew=0;
+       for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+       for(j=1; j<=nlstate; j++){
          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[j]=FMAX(max[j],prlim[i][j]);
-         max=FMAX(max,prlim[i][j]);
+         min[j]=FMIN(min[j],prlim[i][j]);
-         min=FMIN(min,prlim[i][j]);
        }
-       maxmin=max-min;
-       maxmax=FMAX(maxmax,maxmin);
      }
+     maxmax=0.;
+     for(j=1; j<=nlstate; j++){
+       meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
+       maxmax=FMAX(maxmax,meandiff[j]);
+       /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
+     } /* j loop */
+     *ncvyear= (int)age- (int)agefin;
+     /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
      if(maxmax < ftolpl){
+       /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
+       free_vector(min,1,nlstate);
+       free_vector(max,1,nlstate);
+       free_vector(meandiff,1,nlstate);
        return prlim;
      }
-   }
+   } /* agefin loop */
+     /* After some age loop it doesn't converge */
+   if(!first){
+     first=1;
+     printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
+     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
+   }else if (first >=1 && first <10){
+     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
+     first++;
+   }else if (first ==10){
+     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
+     printf("Warning: the stable prevalence dit not converge. This warning came too often, IMaCh will stop notifying, even in its log file. Look at the graphs to appreciate the non convergence.\n");
+     fprintf(ficlog,"Warning: the stable prevalence no convergence; too many cases, giving up noticing, even in log file\n");
+     first++;
+   }
+   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
+   free_vector(min,1,nlstate);
+   free_vector(max,1,nlstate);
+   free_vector(meandiff,1,nlstate);
+   return prlim; /* should not reach here */
  }
- /*************** transition probabilities ***************/
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+  /**** Back Prevalence limit (stable or period prevalence)  ****************/
- {
-   /* According to parameters values stored in x and the covariate's values stored in cov,
+  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
-      computes the probability to be observed in state j being in state i by appying the
+  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
-      model to the ncovmodel covariates (including constant and age).
+   double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
-      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
+   /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
-      ncth covariate in the global vector x is given by the formula:
+      matrix by transitions matrix until convergence is reached with precision ftolpl */
-      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
-      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
-      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+   /* or prevalence in state 1, prevalence in state 2, 0 */
-      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
-      Outputs ps[i][j] the probability to be observed in j being in j according to
+   /* Initial matrix pimij */
-      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
-   */
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
-   double s1, lnpijopii;
+   /*  0,                   0                  , 1} */
-   /*double t34;*/
+   /*
-   int i,j, nc, ii, jj;
+    * and after some iteration: */
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
+   /*  0,                   0                  , 1} */
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
+   /* {0.51571254859325999, 0.4842874514067399, */
+   /*  0.51326036147820708, 0.48673963852179264} */
+   /* If we start from prlim again, prlim tends to a constant matrix */
+   int i, ii,j,k, k1;
+   int first=0;
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
+   /* double **matprod2(); */ /* test */
+   double **out, cov[NCOVMAX+1], **bmij();
+   double **newm;
+   double         **dnewm, **doldm, **dsavm;  /* for use */
+   double         **oldm, **savm;  /* for use */
-     for(i=1; i<= nlstate; i++){
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
-       for(j=1; j<i;j++){
+   int ncvloop=0;
-         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           /*lnpijopii += param[i][j][nc]*cov[nc];*/
+   min=vector(1,nlstate);
-           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+   max=vector(1,nlstate);
- /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+   meandiff=vector(1,nlstate);
-         }
-         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+   dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
- /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+   oldm=oldms; savm=savms;
-       }
-       for(j=i+1; j<=nlstate+ndeath;j++){
+   /* Starting with matrix unity */
-         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+     for (j=1;j<=nlstate+ndeath;j++){
-           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-         }
-         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       }
      }
-     for(i=1; i<= nlstate; i++){
+   cov[1]=1.;
-       s1=0;
-       for(j=1; j<i; j++){
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
-         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+   /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
-       }
+   /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
-       for(j=i+1; j<=nlstate+ndeath; j++){
+   for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
-         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+     ncvloop++;
-         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+     newm=savm; /* oldm should be kept from previous iteration or unity at start */
-       }
+                 /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
-       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
+     /* Covariates have to be included here again */
-       ps[i][i]=1./(s1+1.);
+     cov[2]=agefin;
-       /* Computing other pijs */
+     if(nagesqr==1){
-       for(j=1; j<i; j++)
+       cov[3]= agefin*agefin;;
-         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(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
+       if(Typevar[k1]==1){ /* A product with age */
-     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
+         cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
-     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+       }else{
-     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
+         cov[2+nagesqr+k1]=precov[nres][k1];
-     /*   } */
+       }
-     /*   printf("\n "); */
+     }/* End of loop on model equation */
-     /* } */
-     /* printf("\n ");printf("%lf ",cov[2]);*/
-     /*
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-       goto end;*/
-     return ps;
- }
- /**************** Product of 2 matrices ******************/
+ /* Old code */
- double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
+     /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only *\/ */
- {
+     /*                  /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+     /*   cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; */
+     /*   /\* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
+     /* } */
+     /* /\* for (k=1; k<=cptcovn;k++) { *\/ */
+     /* /\*   /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\\/ *\/ */
+     /* /\*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; *\/ */
+     /* /\*   /\\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\\/ *\/ */
+     /* /\* } *\/ */
+     /* for (k=1; k<=nsq;k++) { /\* For single varying covariates only *\/ */
+     /*                  /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
+     /*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];  */
+     /*   /\* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
+     /* } */
+     /* /\* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; *\/ */
+     /* /\* for (k=1; k<=cptcovprod;k++) /\\* Useless *\\/ *\/ */
+     /* /\*   /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\\/ *\/ */
+     /* /\*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
+     /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
+     /*   /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age *\\/ ERROR ???*\/ */
+     /*   if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */
+     /*  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+     /*   } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age *\/ */
+     /*  cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
+     /*   } */
+     /*   /\* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
+     /* } */
+     /* for (k=1; k<=cptcovprod;k++){ /\* For product without age *\/ */
+     /*   /\* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); *\/ */
+     /*   if(Dummy[Tvard[k][1]]==0){ */
+     /*  if(Dummy[Tvard[k][2]]==0){ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+     /*  }else{ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
+     /*  } */
+     /*   }else{ */
+     /*  if(Dummy[Tvard[k][2]]==0){ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
+     /*  }else{ */
+     /*    cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
+     /*  } */
+     /*   } */
+     /* } */
+     /*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 \n",ij, cov[3]);*/
+     /* 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 *\/ */
+                 /* ij should be linked to the correct index of cov */
+                 /* age and covariate values ij are in 'cov', but we need to pass
+                  * ij for the observed prevalence at age and status and covariate
+                  * number:  prevacurrent[(int)agefin][ii][ij]
+                  */
+     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
+     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
+     out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
+     /* if((int)age == 86 || (int)age == 87){ */
+     /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
+     /*   for(i=1; i<=nlstate+ndeath; i++) { */
+     /*  printf("%d newm= ",i); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",newm[i][j]); */
+     /*  } */
+     /*  printf("oldm * "); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",oldm[i][j]); */
+     /*  } */
+     /*  printf(" bmmij "); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",pmmij[i][j]); */
+     /*  } */
+     /*  printf("\n"); */
+     /*   } */
+     /* } */
+     savm=oldm;
+     oldm=newm;
+     for(j=1; j<=nlstate; j++){
+       max[j]=0.;
+       min[j]=1.;
+     }
+     for(j=1; j<=nlstate; j++){
+       for(i=1;i<=nlstate;i++){
+         /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
+         bprlim[i][j]= newm[i][j];
+         max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
+         min[i]=FMIN(min[i],bprlim[i][j]);
+       }
+     }
+     maxmax=0.;
+     for(i=1; i<=nlstate; i++){
+       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column, could be nan! */
+       maxmax=FMAX(maxmax,meandiff[i]);
+       /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
+     } /* i loop */
+     *ncvyear= -( (int)age- (int)agefin);
+     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
+     if(maxmax < ftolpl){
+       /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
+       free_vector(min,1,nlstate);
+       free_vector(max,1,nlstate);
+       free_vector(meandiff,1,nlstate);
+       return bprlim;
+     }
+   } /* agefin loop */
+     /* After some age loop it doesn't converge */
+   if(!first){
+     first=1;
+     printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
+ Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+   }
+   fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
+ Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
+   free_vector(min,1,nlstate);
+   free_vector(max,1,nlstate);
+   free_vector(meandiff,1,nlstate);
+   return bprlim; /* should not reach here */
+ }
+ /*************** transition probabilities ***************/
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+ {
+   /* According to parameters values stored in x and the covariate's values stored in cov,
+      computes the probability to be observed in state j (after stepm years) 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] or probability to be observed in j being in i according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+      Sum on j ps[i][j] should equal to 1.
+   */
+   double s1, lnpijopii;
+   /*double t34;*/
+   int i,j, nc, ii, jj;
+   for(i=1; i<= nlstate; i++){
+     for(j=1; j<i;j++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+         /*lnpijopii += param[i][j][nc]*cov[nc];*/
+         lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+         /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+       }
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       /* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
+     }
+     for(j=i+1; j<=nlstate+ndeath;j++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+         /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+         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]=lnpijopii; /* In fact ln(pij/pii) */
+       /* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
+     }
+   }
+   for(i=1; i<= nlstate; i++){
+     s1=0;
+     for(j=1; j<i; j++){
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+       /* printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+     }
+     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];/* Bug valgrind */
+     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(ii=1; ii<= nlstate+ndeath; ii++){ */
+   /*   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; /* Pointer is unchanged since its call */
+ }
+ /*************** backward transition probabilities ***************/
+  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
+ /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
+  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
+ {
+   /* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
+    * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
+    */
+   int i, ii, j,k;
+   double **out, **pmij();
+   double sumnew=0.;
+   double agefin;
+   double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
+   double **dnewm, **dsavm, **doldm;
+   double **bbmij;
+   doldm=ddoldms; /* global pointers */
+   dnewm=ddnewms;
+   dsavm=ddsavms;
+   /* Debug */
+   /* printf("Bmij ij=%d, cov[2}=%f\n", ij, cov[2]); */
+   agefin=cov[2];
+   /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
+   /* bmij *//* age is cov[2], ij is included in cov, but we need for
+      the observed prevalence (with this covariate ij) at beginning of transition */
+   /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+   /* P_x */
+   pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm *//* Bug valgrind */
+   /* outputs pmmij which is a stochastic matrix in row */
+   /* Diag(w_x) */
+   /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
+   sumnew=0.;
+   /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
+   for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
+     /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
+     sumnew+=prevacurrent[(int)agefin][ii][ij];
+   }
+   if(sumnew >0.01){  /* At least some value in the prevalence */
+     for (ii=1;ii<=nlstate+ndeath;ii++){
+       for (j=1;j<=nlstate+ndeath;j++)
+         doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
+     }
+   }else{
+     for (ii=1;ii<=nlstate+ndeath;ii++){
+       for (j=1;j<=nlstate+ndeath;j++)
+       doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
+     }
+     /* if(sumnew <0.9){ */
+     /*   printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
+     /* } */
+   }
+   k3=0.0;  /* We put the last diagonal to 0 */
+   for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
+       doldm[ii][ii]= k3;
+   }
+   /* End doldm, At the end doldm is diag[(w_i)] */
+   /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
+   bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
+   /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
+   /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
+   for (j=1;j<=nlstate+ndeath;j++){
+     sumnew=0.;
+     for (ii=1;ii<=nlstate;ii++){
+       /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
+       sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
+     } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
+     for (ii=1;ii<=nlstate+ndeath;ii++){
+         /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
+         /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+         /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
+         /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+         /* }else */
+       dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
+     } /*End ii */
+   } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
+   ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
+   /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
+   /* end bmij */
+   return ps; /*pointer is unchanged */
+ }
+ /*************** transition probabilities ***************/
+ double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+ {
+   /* 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, nc, ii, jj;
+   for(i=1; i<= nlstate; i++){
+     for(j=1; j<i;j++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+         /*lnpijopii += param[i][j][nc]*cov[nc];*/
+         lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+         /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+       }
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+     }
+     for(j=i+1; j<=nlstate+ndeath;j++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+         /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+         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]=lnpijopii; /* In fact ln(pij/pii) */
+     }
+   }
+   for(i=1; i<= nlstate; i++){
+     s1=0;
+     for(j=1; j<i; j++){
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+     }
+     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;
+     }
+   }
+   /* Added for prevbcast */ /* Transposed matrix too */
+   for(jj=1; jj<= nlstate+ndeath; jj++){
+     s1=0.;
+     for(ii=1; ii<= nlstate+ndeath; ii++){
+       s1+=ps[ii][jj];
+     }
+     for(ii=1; ii<= nlstate; ii++){
+       ps[ii][jj]=ps[ii][jj]/s1;
+     }
+   }
+   /* Transposition */
+   for(jj=1; jj<= nlstate+ndeath; jj++){
+     for(ii=jj; ii<= nlstate+ndeath; ii++){
+       s1=ps[ii][jj];
+       ps[ii][jj]=ps[jj][ii];
+       ps[jj][ii]=s1;
+     }
+   }
+   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
+   /*   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,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
- Line 1691  double **matprod2(double **out, double *
+ Line 3519  double **matprod2(double **out, double *
  /************* Higher Matrix Product ***************/
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
  {
-   /* Computes the transition matrix starting at age 'age' over
+   /* Already optimized with precov.
+      Computes the transition matrix starting at age 'age' and dummies values in each resultline (loop on ij to find the corresponding combination) to over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
       nhstepm*hstepm matrices.
- Line 1705  double ***hpxij(double ***po, int nhstep
+ Line 3534  double ***hpxij(double ***po, int nhstep
       */
-   int i, j, d, h, k;
+   int i, j, d, h, k, k1;
    double **out, cov[NCOVMAX+1];
    double **newm;
+   double agexact;
+   double agebegin, ageend;
    /* Hstepm could be zero and should return the unit matrix */
    for (i=1;i<=nlstate+ndeath;i++)
- Line 1721  double ***hpxij(double ***po, int nhstep
+ Line 3552  double ***hpxij(double ***po, int nhstep
        newm=savm;
        /* Covariates have to be included here again */
        cov[1]=1.;
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
-       for (k=1; k<=cptcovn;k++)
+       cov[2]=agexact;
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       if(nagesqr==1){
-       for (k=1; k<=cptcovage;k++)
+         cov[3]= agexact*agexact;
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       }
-       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
+       /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
+       for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
+         if(Typevar[k1]==1){ /* A product with age */
+           cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
+         }else{
+           cov[2+nagesqr+k1]=precov[nres][k1];
+         }
+       }/* End of loop on model equation */
+         /* Old code */
+ /*      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /\* Single dummy  *\/ */
+ /* /\*     V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) *\/ */
+ /* /\*       for (k=1; k<=nsd;k++) { /\\* For single dummy covariates only *\\/ *\/ */
+ /* /\* /\\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\\/ *\/ */
+ /*      /\* codtabm(ij,k)  (1 & (ij-1) >> (k-1))+1 *\/ */
+ /* /\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
+ /* /\*    k        1  2   3   4     5    6    7     8    9 *\/ */
+ /* /\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\/ */
+ /* /\*    nsd         1   2                              3 *\/ /\* Counting single dummies covar fixed or tv *\/ */
+ /* /\*TvarsD[nsd]     4   3                              1 *\/ /\* ID of single dummy cova fixed or timevary*\/ */
+ /* /\*TvarsDind[k]    2   3                              9 *\/ /\* position K of single dummy cova *\/ */
+ /*        /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];or [codtabm(ij,TnsdVar[TvarsD[k]] *\/ */
+ /*        cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; */
+ /*        /\* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,TnsdVar[TvarsD[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,TnsdVar[TvarsD[k]])); *\/ */
+ /*        printf("hpxij Dummy combi=%d k1=%d Tvar[%d]=V%d cov[2+%d+%d]=%lf resultmodel[nres][%d]=%d nres/nresult=%d/%d \n",ij,k1,k1, Tvar[k1],nagesqr,k1,cov[2+nagesqr+k1],k1,resultmodel[nres][k1],nres,nresult); */
+ /*        printf("hpxij new Dummy precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
+ /*      }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /\* Single quantitative variables  *\/ */
+ /*        /\* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline *\/ */
+ /*        cov[2+nagesqr+k1]=Tqresult[nres][resultmodel[nres][k1]];  */
+ /*        /\* for (k=1; k<=nsq;k++) { /\\* For single varying covariates only *\\/ *\/ */
+ /*        /\*   /\\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\\/ *\/ */
+ /*        /\*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; *\/ */
+ /*        printf("hPxij Quantitative k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
+ /*        printf("hpxij new Quanti precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
+ /*      }else if( Dummy[k1]==2 ){ /\* For dummy with age product *\/ */
+ /*        /\* Tvar[k1] Variable in the age product age*V1 is 1 *\/ */
+ /*        /\* [Tinvresult[nres][V1] is its value in the resultline nres *\/ */
+ /*        cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvar[k1]]*cov[2]; */
+ /*        printf("DhPxij Dummy with age k1=%d Tvar[%d]=%d TinvDoQresult[nres=%d][%d]=%.f age=%.2f,cov[2+%d+%d]=%.3f\n",k1,k1,Tvar[k1],nres,TinvDoQresult[nres][Tvar[k1]],cov[2],nagesqr,k1,cov[2+nagesqr+k1]); */
+ /*        printf("hpxij new Dummy with age product precov[nres=%d][k1=%d]=%.4f * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
+ /*        /\* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];    *\/ */
+ /*        /\* for (k=1; k<=cptcovage;k++){ /\\* For product with age V1+V1*age +V4 +age*V3 *\\/ *\/ */
+ /*        /\* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*\/ */
+ /*        /\* *\/ */
+ /* /\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
+ /* /\*    k        1  2   3   4     5    6    7     8    9 *\/ */
+ /* /\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\/ */
+ /* /\*cptcovage=2                   1               2      *\/ */
+ /* /\*Tage[k]=                      5               8      *\/   */
+ /*      }else if( Dummy[k1]==3 ){ /\* For quant with age product *\/ */
+ /*        cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];        */
+ /*        printf("QhPxij Quant with age k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
+ /*        printf("hpxij new Quanti with age product precov[nres=%d][k1=%d] * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
+ /*        /\* if(Dummy[Tage[k]]== 2){ /\\* dummy with age *\\/ *\/ */
+ /*        /\* /\\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\\* dummy with age *\\\/ *\\/ *\/ */
+ /*        /\*   /\\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\\/ *\/ */
+ /*        /\*   /\\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; *\\/ *\/ */
+ /*        /\*   cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; *\/ */
+ /*        /\*   printf("hPxij Age combi=%d k=%d cptcovage=%d Tage[%d]=%d Tvar[Tage[%d]]=V%d nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]]])]=%d nres=%d\n",ij,k,cptcovage,k,Tage[k],k,Tvar[Tage[k]], nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]])],nres); *\/ */
+ /*        /\* } else if(Dummy[Tage[k]]== 3){ /\\* quantitative with age *\\/ *\/ */
+ /*        /\*   cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; *\/ */
+ /*        /\* } *\/ */
+ /*        /\* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
+ /*      }else if(Typevar[k1]==2 ){ /\* For product (not with age) *\/ */
+ /* /\*       for (k=1; k<=cptcovprod;k++){ /\\*  For product without age *\\/ *\/ */
+ /* /\* /\\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\\/ *\/ */
+ /* /\* /\\*    k        1  2   3   4     5    6    7     8    9 *\\/ *\/ */
+ /* /\* /\\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\\/ *\/ */
+ /* /\* /\\*cptcovprod=1            1               2            *\\/ *\/ */
+ /* /\* /\\*Tprod[]=                4               7            *\\/ *\/ */
+ /* /\* /\\*Tvard[][1]             4               1             *\\/ *\/ */
+ /* /\* /\\*Tvard[][2]               3               2           *\\/ *\/ */
+ /*        /\* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]=%d nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]=%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2],nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])],nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]); *\/ */
+ /*        /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
+ /*        cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];     */
+ /*        printf("hPxij Prod ij=%d k1=%d  cov[2+%d+%d]=%.5f Tvard[%d][1]=V%d * Tvard[%d][2]=V%d ; TinvDoQresult[nres][Tvardk[k1][1]]=%.4f * TinvDoQresult[nres][Tvardk[k1][1]]=%.4f\n",ij,k1,nagesqr,k1,cov[2+nagesqr+k1],k1,Tvardk[k1][1], k1,Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][1]], TinvDoQresult[nres][Tvardk[k1][2]]); */
+ /*        printf("hpxij new Product no age product precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
+ /*        /\* if(Dummy[Tvardk[k1][1]]==0){ *\/ */
+ /*        /\*   if(Dummy[Tvardk[k1][2]]==0){ /\\* Product of dummies *\\/ *\/ */
+ /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
+ /*            /\* cov[2+nagesqr+k1]=Tinvresult[nres][Tvardk[k1][1]] * Tinvresult[nres][Tvardk[k1][2]];   *\/ */
+ /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])]; *\/ */
+ /*          /\* }else{ /\\* Product of dummy by quantitative *\\/ *\/ */
+ /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * Tqresult[nres][k]; *\/ */
+ /*            /\* cov[2+nagesqr+k1]=Tresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]; *\/ */
+ /*        /\*   } *\/ */
+ /*        /\* }else{ /\\* Product of quantitative by...*\\/ *\/ */
+ /*        /\*   if(Dummy[Tvard[k][2]]==0){  /\\* quant by dummy *\\/ *\/ */
+ /*        /\*     /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][Tvard[k][1]]; *\\/ *\/ */
+ /*        /\*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
+ /*        /\*   }else{ /\\* Product of two quant *\\/ *\/ */
+ /*        /\*     /\\* cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\\/ *\/ */
+ /*        /\*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
+ /*        /\*   } *\/ */
+ /*        /\* }/\\*end of products quantitative *\\/ *\/ */
+ /*      }/\*end of products *\/ */
+       /* } /\* End of loop on model equation *\/ */
+       /* for (k=1; k<=cptcovn;k++)  */
+       /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
+       /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
+       /*        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
+       /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
+       /*        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+       /* right multiplication of oldm by the current matrix */
        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
                     pmij(pmmij,cov,ncovmodel,x,nlstate));
+       /* if((int)age == 70){ */
+       /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
+       /*          printf("%d pmmij ",i); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",pmmij[i][j]); */
+       /*          } */
+       /*          printf(" oldm "); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",oldm[i][j]); */
+       /*          } */
+       /*          printf("\n"); */
+       /*        } */
+       /* } */
        savm=oldm;
        oldm=newm;
      }
- Line 1744  double ***hpxij(double ***po, int nhstep
+ Line 3694  double ***hpxij(double ***po, int nhstep
        }
      /*printf("h=%d ",h);*/
    } /* end h */
- /*     printf("\n H=%d \n",h); */
+   /*     printf("\n H=%d \n",h); */
+   return po;
+ }
+ /************* Higher Back Matrix Product ***************/
+ /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
+ double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
+ {
+   /* For dummy covariates given in each resultline (for historical, computes the corresponding combination ij),
+      computes the transition matrix starting at age 'age' over
+      'nhstepm*hstepm*stepm' months (i.e. until
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+      nhstepm*hstepm matrices.
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+      (typically every 2 years instead of every month which is too big
+      for the memory).
+      Model is determined by parameters x and covariates have to be
+      included manually here. Then we use a call to bmij(x and cov)
+      The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
+   */
+   int i, j, d, h, k, k1;
+   double **out, cov[NCOVMAX+1], **bmij();
+   double **newm, ***newmm;
+   double agexact;
+   double agebegin, ageend;
+   double **oldm, **savm;
+   newmm=po; /* To be saved */
+   oldm=oldms;savm=savms; /* Global pointers */
+   /* Hstepm could be zero and should return the unit matrix */
+   for (i=1;i<=nlstate+ndeath;i++)
+     for (j=1;j<=nlstate+ndeath;j++){
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
+     }
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   for(h=1; h <=nhstepm; h++){
+     for(d=1; d <=hstepm; d++){
+       newm=savm;
+       /* Covariates have to be included here again */
+       cov[1]=1.;
+       agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-1? */
+       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
+         /* Debug */
+       /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */
+       cov[2]=agexact;
+       if(nagesqr==1){
+         cov[3]= agexact*agexact;
+       }
+       /** New code */
+       for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
+         if(Typevar[k1]==1){ /* A product with age */
+           cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
+         }else{
+           cov[2+nagesqr+k1]=precov[nres][k1];
+         }
+       }/* End of loop on model equation */
+       /** End of new code */
+   /** This was old code */
+       /* for (k=1; k<=nsd;k++){ /\* For single dummy covariates only *\//\* cptcovn error *\/ */
+       /* /\*    cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; *\/ */
+       /* /\* /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\\/ *\/ */
+       /*        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])];/\* Bug valgrind *\/ */
+       /*   /\* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
+       /* } */
+       /* for (k=1; k<=nsq;k++) { /\* For single varying covariates only *\/ */
+       /*        /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
+       /*        cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];  */
+       /*        /\* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
+       /* } */
+       /* for (k=1; k<=cptcovage;k++){ /\* Should start at cptcovn+1 *\//\* For product with age *\/ */
+       /*        /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age error!!!*\\/ *\/ */
+       /*        if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */
+       /*          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+       /*        } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age *\/ */
+       /*          cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];  */
+       /*        } */
+       /*        /\* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
+       /* } */
+       /* for (k=1; k<=cptcovprod;k++){ /\* Useless because included in cptcovn *\/ */
+       /*        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+       /*        if(Dummy[Tvard[k][1]]==0){ */
+       /*          if(Dummy[Tvard[k][2]]==0){ */
+       /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]; */
+       /*          }else{ */
+       /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
+       /*          } */
+       /*        }else{ */
+       /*          if(Dummy[Tvard[k][2]]==0){ */
+       /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
+       /*          }else{ */
+       /*            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
+       /*          } */
+       /*        } */
+       /* }                       */
+       /* /\*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*\/ */
+       /* /\*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*\/ */
+ /** End of old code */
+       /* Careful transposed matrix */
+       /* age is in cov[2], prevacurrent at beginning of transition. */
+       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
+       /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
+       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
+,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);/* Bug valgrind */
+       /* if((int)age == 70){ */
+       /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
+       /*          printf("%d pmmij ",i); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",pmmij[i][j]); */
+       /*          } */
+       /*          printf(" oldm "); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",oldm[i][j]); */
+       /*          } */
+       /*          printf("\n"); */
+       /*        } */
+       /* } */
+       savm=oldm;
+       oldm=newm;
+     }
+     for(i=1; i<=nlstate+ndeath; i++)
+       for(j=1;j<=nlstate+ndeath;j++) {
+         po[i][j][h]=newm[i][j];
+         /* if(h==nhstepm) */
+         /*   printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
+       }
+     /* printf("h=%d %.1f ",h, agexact); */
+   } /* end h */
+   /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
    return po;
  }
  #ifdef NLOPT
    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
    double fret;
- Line 1771  double ***hpxij(double ***po, int nhstep
+ Line 3853  double ***hpxij(double ***po, int nhstep
  /*************** log-likelihood *************/
  double func( double *x)
  {
-   int i, ii, j, k, mi, d, kk;
+   int i, ii, j, k, mi, d, kk, kf=0;
+   int ioffset=0;
    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
-   double sw; /* Sum of weights */
    double lli; /* Individual log likelihood */
    int s1, s2;
+   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
    double bbh, survp;
-   long ipmx;
+   double agexact;
+   double agebegin, ageend;
    /*extern weight */
    /* We are differentiating ll according to initial status */
    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
- Line 1791  double func( double *x)
+ Line 3876  double func( double *x)
    cov[1]=1.;
    for(k=1; k<=nlstate; k++) ll[k]=0.;
+   ioffset=0;
    if(mle==1){
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        /* Computes the values of the ncovmodel covariates of the model
-          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+          depending if the covariates are fixed or varying (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 */
+       ioffset=2+nagesqr ;
-         cov[2+k]=covar[Tvar[k]][i];
+    /* Fixed */
+       for (kf=1; kf<=ncovf;kf++){ /* For each fixed covariate dummu or quant or prod */
+         /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
+         /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+         /*  TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
+         /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
+         cov[ioffset+TvarFind[kf]]=covar[Tvar[TvarFind[kf]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/
+         /* V1*V2 (7)  TvarFind[2]=7, TvarFind[3]=9 */
        }
        /* 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]
+          is 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6
           has been calculated etc */
-       for(mi=1; mi<= wav[i]-1; mi++){
+       /* For an individual i, wav[i] gives the number of effective waves */
+       /* We compute the contribution to Likelihood of each effective transition
+          mw[mi][i] is real wave of the mi th effectve wave */
+       /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
+          s2=s[mw[mi+1][i]][i];
+          And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
+          But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
+          meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
+       */
+       for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
+       /* Wave varying (but not age varying) */
+         for(k=1; k <= ncovv ; k++){ /* Varying  covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3)  Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/
+           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */
+           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
+         }
          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);
            }
+         agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
+         ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;  /* Should be changed here */
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
+             if(!FixedV[Tvar[Tage[kk]]])
+               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
+             else
+               cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
            savm=oldm;
            oldm=newm;
          } /* end mult */
          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
          /* But now since version 0.9 we anticipate for bias at large stepm.
           * If stepm is larger than one month (smallest stepm) and if the exact delay
- Line 1831  double func( double *x)
+ Line 3946  double func( double *x)
           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+                                  * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
+                                  * -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 the same as for previous versions of Imach.
-          * For stepm > 1 the results are less biased than in previous versions.
+                                  * 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;
- Line 1850  double func( double *x)
+ Line 3965  double func( double *x)
               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
+              as if date of death was unknown. Death was treated as any other
-         health state: the date of the interview describes the actual state
+              health state: the date of the interview describes the actual state
-         and not the date of a change in health state. The former idea was
+              and not the date of a change in health state. The former idea was
-         to consider that at each interview the state was recorded
+              to consider that at each interview the state was recorded
-         (healthy, disable or death) and IMaCh was corrected; but when we
+              (healthy, disable or death) and IMaCh was corrected; but when we
-         introduced the exact date of death then we should have modified
+              introduced the exact date of death then we should have modified
-         the contribution of an exact death to the likelihood. This new
+              the contribution of an exact death to the likelihood. This new
-         contribution is smaller and very dependent of the step unit
+              contribution is smaller and very dependent of the step unit
-         stepm. It is no more the probability to die between last interview
+              stepm. It is no more the probability to die between last interview
-         and month of death but the probability to survive from last
+              and month of death but the probability to survive from last
-         interview up to one month before death multiplied by the
+              interview up to one month before death multiplied by the
-         probability to die within a month. Thanks to Chris
+              probability to die within a month. Thanks to Chris
-         Jackson for correcting this bug.  Former versions increased
+              Jackson for correcting this bug.  Former versions increased
-         mortality artificially. The bad side is that we add another loop
+              mortality artificially. The bad side is that we add another loop
-         which slows down the processing. The difference can be up to 10%
+              which slows down the processing. The difference can be up to 10%
-         lower mortality.
+              lower mortality.
            */
+           /* If, at the beginning of the maximization mostly, the
+              cumulative probability or probability to be dead is
+              constant (ie = 1) over time d, the difference is equal to
+.  out[s1][3] = savm[s1][3]: probability, being at state
+              s1 at precedent wave, to be dead a month before current
+              wave is equal to probability, being at state s1 at
+              precedent wave, to be dead at mont of the current
+              wave. Then the observed probability (that this person died)
+              is null according to current estimated parameter. In fact,
+              it should be very low but not zero otherwise the log go to
+              infinity.
+           */
+ /* #ifdef INFINITYORIGINAL */
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
+ /* #else */
+ /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
+ /*          lli=log(mytinydouble); */
+ /*        else */
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
+ /* #endif */
            lli=log(out[s1][s2] - savm[s1][s2]);
+         } else if  ( s2==-1 ) { /* alive */
-         } 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) {  */
-         else if  (s2==-4) {
+         /*   for (j=3,survp=0. ; j<=nlstate; j++)   */
-           for (j=3,survp=0. ; j<=nlstate; j++)
+         /*     survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         /*   lli= log(survp);  */
-           lli= log(survp);
+         /* }  */
-         }
+         /* else if  (s2==-5) {  */
+         /*   for (j=1,survp=0. ; j<=2; j++)   */
-         else if  (s2==-5) {
+         /*     survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; */
-           for (j=1,survp=0. ; j<=2; j++)
+         /*   lli= log(survp);  */
-             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 1896  double func( double *x)
+ Line 4027  double func( double *x)
          /*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;
+         /* if (lli < log(mytinydouble)){ */
+         /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
+         /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
+         /* } */
        } /* end of wave */
      } /* end of individual */
    }  else if(mle==2){
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       ioffset=2+nagesqr ;
+       for (k=1; k<=ncovf;k++)
+         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
+         for(k=1; k <= ncovv ; k++){
+           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
+         }
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- Line 1912  double func( double *x)
+ Line 4052  double func( double *x)
            }
          for(d=0; d<=dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 1933  double func( double *x)
+ Line 4076  double func( double *x)
      } /* end of individual */
    }  else if(mle==3){  /* exponential inter-extrapolation */
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+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++){
- Line 1942  double func( double *x)
+ Line 4085  double func( double *x)
            }
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 1963  double func( double *x)
+ Line 4109  double func( double *x)
      } /* end of individual */
    }else if (mle==4){  /* ml=4 no inter-extrapolation */
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+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++){
- Line 1972  double func( double *x)
+ Line 4118  double func( double *x)
            }
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- Line 1987  double func( double *x)
+ Line 4136  double func( double *x)
          s2=s[mw[mi+1][i]][i];
          if( s2 > nlstate){
            lli=log(out[s1][s2] - savm[s1][s2]);
+         } else if  ( s2==-1 ) { /* alive */
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += out[s1][j];
+           lli= log(survp);
          }else{
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
          }
- Line 1998  double func( double *x)
+ Line 4151  double func( double *x)
      } /* 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 (k=1; k<=cptcovn;k++) cov[2+nagesqr+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++){
- Line 2007  double func( double *x)
+ Line 4160  double func( double *x)
            }
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- Line 2037  double func( double *x)
+ Line 4193  double func( double *x)
  /*************** log-likelihood *************/
  double funcone( double *x)
  {
-   /* Same as likeli but slower because of a lot of printf and if */
+   /* Same as func but slower because of a lot of printf and if */
-   int i, ii, j, k, mi, d, kk;
+   int i, ii, j, k, mi, d, kk, kf=0;
+   int ioffset=0;
    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double lli; /* Individual log likelihood */
    double llt;
    int s1, s2;
+   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
    double bbh, survp;
+   double agexact;
+   double agebegin, ageend;
    /*extern weight */
    /* We are differentiating ll according to initial status */
    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
- Line 2054  double funcone( double *x)
+ Line 4215  double funcone( double *x)
    cov[1]=1.;
    for(k=1; k<=nlstate; k++) ll[k]=0.;
+   ioffset=0;
    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
-     for(mi=1; mi<= wav[i]-1; mi++){
+        depending if the covariates are fixed or varying (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.
+     */
+     /* ioffset=2+nagesqr+cptcovage; */
+     ioffset=2+nagesqr;
+     /* Fixed */
+     /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
+     /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
+     for (kf=1; kf<=ncovf;kf++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
+       cov[ioffset+TvarFind[kf]]=covar[Tvar[TvarFind[kf]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
+ /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
+ /*    cov[2+6]=covar[Tvar[6]][i];  */
+ /*    cov[2+6]=covar[2][i]; V2  */
+ /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
+ /*    cov[2+7]=covar[Tvar[7]][i];  */
+ /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
+ /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
+ /*    cov[2+9]=covar[Tvar[9]][i];  */
+ /*    cov[2+9]=covar[1][i]; V1  */
+     }
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
+          is 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6
+          has been calculated etc */
+       /* For an individual i, wav[i] gives the number of effective waves */
+       /* We compute the contribution to Likelihood of each effective transition
+          mw[mi][i] is real wave of the mi th effectve wave */
+       /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
+          s2=s[mw[mi+1][i]][i];
+          And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
+          But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
+          meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
+       */
+     /* This part may be useless now because everythin should be in covar */
+     /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
+     /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
+     /* } */
+     /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
+     /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
+     /* } */
+     for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
+     /* Wave varying (but not age varying) */
+       for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
+         /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
+         cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
+       }
+       /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
+       /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
+       /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
+       /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
+       /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
+       /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
+       /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
+       /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
+       /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
+       /*        cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
+       /* } */
        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++){
+       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
+       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
+       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
+       /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
+         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+           and mw[mi+1][i]. dh depends on stepm.*/
          newm=savm;
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
+         cov[2]=agexact;
+         if(nagesqr==1)
+           cov[3]= agexact*agexact;
          for (kk=1; kk<=cptcovage;kk++) {
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           if(!FixedV[Tvar[Tage[kk]]])
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+           else
+             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
          }
+         /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
          /* 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));
- Line 2077  double funcone( double *x)
+ Line 4309  double funcone( double *x)
          savm=oldm;
          oldm=newm;
        } /* end mult */
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+         /* But now since version 0.9 we anticipate for bias at large stepm.
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
+          * (in months) between two waves is not a multiple of stepm, we rounded to
+          * the nearest (and in case of equal distance, to the lowest) interval but now
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+          * probability in order to take into account the bias as a fraction of the way
+                                  * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+                                  * -stepm/2 to stepm/2 .
+                                  * For stepm=1 the results are the same as for previous versions of Imach.
+                                  * For stepm > 1 the results are less biased than in previous versions.
+                                  */
        s1=s[mw[mi][i]][i];
        s2=s[mw[mi+1][i]][i];
+       /* if(s2==-1){ */
+       /*        printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
+       /*        /\* exit(1); *\/ */
+       /* } */
        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) {
+       } else if  ( s2==-1 ) { /* alive */
          for (j=1,survp=0. ; j<=nlstate; j++)
            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
          lli= log(survp);
- Line 2105  double funcone( double *x)
+ Line 4353  double funcone( double *x)
        ipmx +=1;
        sw += weight[i];
        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       /* printf("Funcone 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],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
        if(globpr){
-         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+         fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
   %11.6f %11.6f %11.6f ", \
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
+  /*     printf("%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\ */
+  /* %11.6f %11.6f %11.6f ", \ */
+  /*             num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw, */
+  /*             2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: 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);
+           /* printf(" %10.6f",-ll[k]*gipmx/gsw); */
          }
          fprintf(ficresilk," %10.6f\n", -llt);
+         /* printf(" %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]); */
+ /* 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;
+ 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 []))
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
  {
    /* This routine should help understanding what is done with
       the selection of individuals/waves and
- Line 2141  void likelione(FILE *ficres,double p[],
+ Line 4395  void likelione(FILE *ficres,double p[],
    int k;
    if(*globpri !=0){ /* Just counts and sums, no printings */
-     strcpy(fileresilk,"ilk");
+     strcpy(fileresilk,"ILK_");
-     strcat(fileresilk,fileres);
+     strcat(fileresilk,fileresu);
      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, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -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 ");
+     fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%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);
+   *fretone=(*func)(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));
+     if (mle ==0)
-     fflush(fichtm);
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
-   }
+     else if(mle >=1)
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
+     fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
+     for (k=1; k<= nlstate ; k++) {
+       fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
+ <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
+     }
+     fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
+ <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+     fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
+ <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+     fflush(fichtm);
+   }
    return;
  }
- Line 2169  void likelione(FILE *ficres,double p[],
+ Line 4437  void likelione(FILE *ficres,double p[],
  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
  {
-   int i,j, iter=0;
+   int i,j,k, jk, jkk=0, iter=0;
    double **xi;
    double fret;
    double fretone; /* Only one call to likelihood */
- Line 2191  void mlikeli(FILE *ficres,double p[], in
+ Line 4459  void mlikeli(FILE *ficres,double p[], in
      for (j=1;j<=npar;j++)
        xi[i][j]=(i==j ? 1.0 : 0.0);
    printf("Powell\n");  fprintf(ficlog,"Powell\n");
-   strcpy(filerespow,"pow");
+   strcpy(filerespow,"POW_");
    strcat(filerespow,fileres);
    if((ficrespow=fopen(filerespow,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", filerespow);
- Line 2203  void mlikeli(FILE *ficres,double p[], in
+ Line 4471  void mlikeli(FILE *ficres,double p[], in
        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
    fprintf(ficrespow,"\n");
  #ifdef POWELL
+ #ifdef LINMINORIGINAL
+ #else /* LINMINORIGINAL */
+   flatdir=ivector(1,npar);
+   for (j=1;j<=npar;j++) flatdir[j]=0;
+ #endif /*LINMINORIGINAL */
+ #ifdef FLATSUP
+   powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
+   /* reorganizing p by suppressing flat directions */
+   for(i=1, jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
+         printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
+         if(flatdir[jk]==1){
+           printf(" To be skipped %d%d flatdir[%d]=%d ",i,k,jk, flatdir[jk]);
+         }
+         for(j=1; j <=ncovmodel; j++){
+           printf("%12.7f ",p[jk]);
+           jk++;
+         }
+         printf("\n");
+       }
+     }
+   }
+ /* skipping */
+   /* for(i=1, jk=1, jkk=1;(flatdir[jk]==0)&& (i <=nlstate); i++){ */
+   for(i=1, jk=1, jkk=1;i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
+         printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
+         if(flatdir[jk]==1){
+           printf(" To be skipped %d%d flatdir[%d]=%d jk=%d p[%d] ",i,k,jk, flatdir[jk],jk, jk);
+           for(j=1; j <=ncovmodel;  jk++,j++){
+             printf(" p[%d]=%12.7f",jk, p[jk]);
+             /*q[jjk]=p[jk];*/
+           }
+         }else{
+           printf(" To be kept %d%d flatdir[%d]=%d jk=%d q[%d]=p[%d] ",i,k,jk, flatdir[jk],jk, jkk, jk);
+           for(j=1; j <=ncovmodel;  jk++,jkk++,j++){
+             printf(" p[%d]=%12.7f=q[%d]",jk, p[jk],jkk);
+             /*q[jjk]=p[jk];*/
+           }
+         }
+         printf("\n");
+       }
+       fflush(stdout);
+     }
+   }
+   powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
+ #else  /* FLATSUP */
    powell(p,xi,npar,ftol,&iter,&fret,func);
- #endif
+ #endif  /* FLATSUP */
+ #ifdef LINMINORIGINAL
+ #else
+       free_ivector(flatdir,1,npar);
+ #endif  /* LINMINORIGINAL*/
+ #endif /* POWELL */
  #ifdef NLOPT
  #ifdef NEWUOA
- Line 2232  void mlikeli(FILE *ficres,double p[], in
+ Line 4557  void mlikeli(FILE *ficres,double p[], in
    }
    nlopt_destroy(opt);
  #endif
+ #ifdef FLATSUP
+   /* npared = npar -flatd/ncovmodel; */
+   /* xired= matrix(1,npared,1,npared); */
+   /* paramred= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */
+   /* powell(pred,xired,npared,ftol,&iter,&fret,flatdir,func); */
+   /* free_matrix(xire,1,npared,1,npared); */
+ #else  /* FLATSUP */
+ #endif /* FLATSUP */
    free_matrix(xi,1,npar,1,npar);
    fclose(ficrespow);
    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
+   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
  }
  /**** Computes Hessian and covariance matrix ***/
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+ void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
  {
    double  **a,**y,*x,pd;
-   double **hess;
+   /* double **hess; */
    int i, j;
    int *indx;
    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 (*func)(double []),int npar);
+   double hessij(double p[], double **hess, 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);
+   /* hess=matrix(1,npar,1,npar); */
    printf("\nCalculation of the hessian matrix. Wait...\n");
    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
    for (i=1;i<=npar;i++){
-     printf("%d",i);fflush(stdout);
+     printf("%d-",i);fflush(stdout);
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+     fprintf(ficlog,"%d-",i);fflush(ficlog);
       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
- Line 2270  void hesscov(double **matcov, double p[]
+ Line 4603  void hesscov(double **matcov, double p[]
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++)  {
        if (j>i) {
-         printf(".%d%d",i,j);fflush(stdout);
+         printf(".%d-%d",i,j);fflush(stdout);
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+         fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+         hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
          hess[j][i]=hess[i][j];
          /*printf(" %lf ",hess[i][j]);*/
- Line 2306  void hesscov(double **matcov, double p[]
+ Line 4639  void hesscov(double **matcov, double p[]
    fprintf(ficlog,"\n#Hessian matrix#\n");
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++) {
-       printf("%.3e ",hess[i][j]);
+       printf("%.6e ",hess[i][j]);
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+       fprintf(ficlog,"%.6e ",hess[i][j]);
      }
      printf("\n");
      fprintf(ficlog,"\n");
    }
+   /* printf("\n#Covariance matrix#\n"); */
+   /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
+   /* for (i=1;i<=npar;i++) {  */
+   /*   for (j=1;j<=npar;j++) {  */
+   /*     printf("%.6e ",matcov[i][j]); */
+   /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
+   /*   } */
+   /*   printf("\n"); */
+   /*   fprintf(ficlog,"\n"); */
+   /* } */
    /* Recompute Inverse */
-   for (i=1;i<=npar;i++)
+   /* for (i=1;i<=npar;i++) */
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+   /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
-   ludcmp(a,npar,indx,&pd);
+   /* ludcmp(a,npar,indx,&pd); */
+   /*  printf("\n#Hessian matrix recomputed#\n"); */
+   /* for (j=1;j<=npar;j++) { */
+   /*   for (i=1;i<=npar;i++) x[i]=0; */
+   /*   x[j]=1; */
+   /*   lubksb(a,npar,indx,x); */
+   /*   for (i=1;i<=npar;i++){  */
+   /*     y[i][j]=x[i]; */
+   /*     printf("%.3e ",y[i][j]); */
+   /*     fprintf(ficlog,"%.3e ",y[i][j]); */
+   /*   } */
+   /*   printf("\n"); */
+   /*   fprintf(ficlog,"\n"); */
+   /* } */
+   /* Verifying the inverse matrix */
+ #ifdef DEBUGHESS
+   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
-   /*  printf("\n#Hessian matrix recomputed#\n");
+    printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
+    fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
    for (j=1;j<=npar;j++) {
-     for (i=1;i<=npar;i++) x[i]=0;
-     x[j]=1;
-     lubksb(a,npar,indx,x);
      for (i=1;i<=npar;i++){
-       y[i][j]=x[i];
+       printf("%.2f ",y[i][j]);
-       printf("%.3e ",y[i][j]);
+       fprintf(ficlog,"%.2f ",y[i][j]);
-       fprintf(ficlog,"%.3e ",y[i][j]);
      }
      printf("\n");
      fprintf(ficlog,"\n");
    }
-   */
+ #endif
    free_matrix(a,1,npar,1,npar);
    free_matrix(y,1,npar,1,npar);
    free_vector(x,1,npar);
    free_ivector(indx,1,npar);
-   free_matrix(hess,1,npar,1,npar);
+   /* free_matrix(hess,1,npar,1,npar); */
  }
  /*************** hessian matrix ****************/
  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
- {
+ { /* Around values of x, computes the function func and returns the scales delti and hessian */
    int i;
    int l=1, lmax=20;
-   double k1,k2;
+   double k1,k2, res, fx;
    double p2[MAXPARM+1]; /* identical to x */
-   double res;
    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   double fx;
    int k=0,kmax=10;
    double l1;
- Line 2368  double hessii(double x[], double delta,
+ Line 4726  double hessii(double x[], double delta,
        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 */
+       res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
- #ifdef DEBUGHESS
+ #ifdef DEBUGHESSII
        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 2384  double hessii(double x[], double delta,
+ Line 4742  double hessii(double x[], double delta,
        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
          delts=delt;
        }
-     }
+     } /* End loop k */
    }
    delti[theta]=delts;
    return res;
  }
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+ double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
  {
    int i;
    int l=1, lmax=20;
    double k1,k2,k3,k4,res,fx;
    double p2[MAXPARM+1];
-   int k;
+   int k, kmax=1;
+   double v1, v2, cv12, lc1, lc2;
+   int firstime=0;
    fx=func(x);
-   for (k=1; k<=2; k++) {
+   for (k=1; k<=kmax; k=k+10) {
      for (i=1;i<=npar;i++) p2[i]=x[i];
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
      k1=func(p2)-fx;
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
      k2=func(p2)-fx;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
      k3=func(p2)-fx;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
      k4=func(p2)-fx;
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
- #ifdef DEBUG
+     if(k1*k2*k3*k4 <0.){
-     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+       firstime=1;
-     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+       kmax=kmax+10;
+     }
+     if(kmax >=10 || firstime ==1){
+       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
+       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
+       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+     }
+ #ifdef DEBUGHESSIJ
+     v1=hess[thetai][thetai];
+     v2=hess[thetaj][thetaj];
+     cv12=res;
+     /* Computing eigen value of Hessian matrix */
+     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     if ((lc2 <0) || (lc1 <0) ){
+       printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
+       fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
+       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+     }
  #endif
    }
    return res;
  }
+     /* Not done yet: Was supposed to fix if not exactly at the maximum */
+ /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
+ /* { */
+ /*   int i; */
+ /*   int l=1, lmax=20; */
+ /*   double k1,k2,k3,k4,res,fx; */
+ /*   double p2[MAXPARM+1]; */
+ /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
+ /*   int k=0,kmax=10; */
+ /*   double l1; */
+ /*   fx=func(x); */
+ /*   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 = delti*(l1*k); */
+ /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
+ /*       k1=func(p2)-fx; */
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
+ /*       k2=func(p2)-fx; */
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
+ /*       k3=func(p2)-fx; */
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
+ /*       k4=func(p2)-fx; */
+ /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
+ /* #ifdef DEBUGHESSIJ */
+ /*       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
+ /*       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
+ /* #endif */
+ /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
+ /*      k=kmax; */
+ /*       } */
+ /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
+ /*      k=kmax; l=lmax*10; */
+ /*       } */
+ /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
+ /*      delts=delt; */
+ /*       } */
+ /*     } /\* End loop k *\/ */
+ /*   } */
+ /*   delti[theta]=delts; */
+ /*   return res;  */
+ /* } */
  /************** Inverse of matrix **************/
  void ludcmp(double **a, int n, int *indx, double *d)
  {
- Line 2439  void ludcmp(double **a, int n, int *indx
+ Line 4874  void ludcmp(double **a, int n, int *indx
      big=0.0;
      for (j=1;j<=n;j++)
        if ((temp=fabs(a[i][j])) > big) big=temp;
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+     if (big == 0.0){
+       printf(" Singular Hessian matrix at row %d:\n",i);
+       for (j=1;j<=n;j++) {
+         printf(" a[%d][%d]=%f,",i,j,a[i][j]);
+         fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
+       }
+       fflush(ficlog);
+       fclose(ficlog);
+       nrerror("Singular matrix in routine ludcmp");
+     }
      vv[i]=1.0/big;
    }
    for (j=1;j<=n;j++) {
- Line 2502  void lubksb(double **a, int n, int *indx
+ Line 4946  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);
+   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
  }
- /************ Frequencies ********************/
+ void date2dmy(double date,double *day, double *month, double *year){
- 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[])
+   double yp=0., yp1=0., yp2=0.;
- {  /* Some frequencies */
-   int i, m, jk, j1, bool, z1,j;
+   yp1=modf(date,&yp);/* extracts integral of date in yp  and
+                         fractional in yp1 */
+   *year=yp;
+   yp2=modf((yp1*12),&yp);
+   *month=yp;
+   yp1=modf((yp2*30.5),&yp);
+   *day=yp;
+   if(*day==0) *day=1;
+   if(*month==0) *month=1;
+ }
+ /************ Frequencies ********************/
+ void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
+                   int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
+                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])
+ {  /* Some frequencies as well as proposing some starting values */
+   /* Frequencies of any combination of dummy covariate used in the model equation */
+   int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
+   int iind=0, iage=0;
+   int mi; /* Effective wave */
    int first;
    double ***freq; /* Frequencies */
-   double *pp, **prop;
+   double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+   int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);
-   char fileresp[FILENAMELENGTH];
+   double *meanq, *stdq, *idq;
+   double **meanqt;
+   double *pp, **prop, *posprop, *pospropt;
+   double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
+   char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
+   double agebegin, ageend;
    pp=vector(1,nlstate);
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
-   strcpy(fileresp,"p");
+   posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
-   strcat(fileresp,fileres);
+   pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
+   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
+   meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
+   stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
+   idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
+   meanqt=matrix(1,lastpass,1,nqtveff);
+   strcpy(fileresp,"P_");
+   strcat(fileresp,fileresu);
+   /*strcat(fileresphtm,fileresu);*/
    if((ficresp=fopen(fileresp,"w"))==NULL) {
      printf("Problem with prevalence resultfile: %s\n", fileresp);
      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      exit(0);
    }
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+   strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
+   if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
+     printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
+     fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
+     fflush(ficlog);
+     exit(70);
+   }
+   else{
+     fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %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=1+age+%s<br>\n",\
+             fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies (weight=%d) and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm, weightopt);
+   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
+   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
+     printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
+     fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
+     fflush(ficlog);
+     exit(70);
+   } else{
+     fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %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=1+age+%s<br>\n",\
+             fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>(weight=%d) frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr,weightopt);
+   y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
+   x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
    j1=0;
-   j=cptcoveff;
+   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
+   j=cptcoveff;  /* Only simple dummy covariates used in the model */
+   /* j=cptcovn;  /\* Only dummy covariates of the model *\/ */
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
+      reference=low_education V1=0,V2=0
+      med_educ                V1=1 V2=0,
+      high_educ               V1=0 V2=1
+      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcovn
+   */
+   dateintsum=0;
+   k2cpt=0;
-   first=1;
+   if(cptcoveff == 0 )
+     nl=1;  /* Constant and age model only */
+   else
+     nl=2;
-   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
+   /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
-   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
+   /* Loop on nj=1 or 2 if dummy covariates j!=0
-   /*    j1++;
+    *   Loop on j1(1 to 2**cptcoveff) covariate combination
- */
+    *     freq[s1][s2][iage] =0.
-   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
+    *     Loop on iind
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+    *       ++freq[s1][s2][iage] weighted
+    *     end iind
+    *     if covariate and j!0
+    *       headers Variable on one line
+    *     endif cov j!=0
+    *     header of frequency table by age
+    *     Loop on age
+    *       pp[s1]+=freq[s1][s2][iage] weighted
+    *       pos+=freq[s1][s2][iage] weighted
+    *       Loop on s1 initial state
+    *         fprintf(ficresp
+    *       end s1
+    *     end age
+    *     if j!=0 computes starting values
+    *     end compute starting values
+    *   end j1
+    * end nl
+    */
+   for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
+     if(nj==1)
+       j=0;  /* First pass for the constant */
+     else{
+       j=cptcoveff; /* Other passes for the covariate values number of simple covariates in the model V2+V1 =2 (simple dummy fixed or time varying) */
+     }
+     first=1;
+     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all dummy covariates combination of the model, ie excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
+       posproptt=0.;
+       /*printf("cptcovn=%d Tvaraff=%d", cptcovn,Tvaraff[1]);
          scanf("%d", i);*/
        for (i=-5; i<=nlstate+ndeath; i++)
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+         for (s2=-5; s2<=nlstate+ndeath; s2++)
            for(m=iagemin; m <= iagemax+3; m++)
-             freq[i][jk][m]=0;
+             freq[i][s2][m]=0;
-       for (i=1; i<=nlstate; i++)
+       for (i=1; i<=nlstate; i++)  {
          for(m=iagemin; m <= iagemax+3; m++)
            prop[i][m]=0;
+         posprop[i]=0;
+         pospropt[i]=0;
+       }
+       for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
+         idq[z1]=0.;
+         meanq[z1]=0.;
+         stdq[z1]=0.;
+       }
+       /* for (z1=1; z1<= nqtveff; z1++) { */
+       /*   for(m=1;m<=lastpass;m++){ */
+       /*          meanqt[m][z1]=0.; */
+       /*        } */
+       /* }       */
+       /* dateintsum=0; */
+       /* k2cpt=0; */
-       dateintsum=0;
+       /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
-       k2cpt=0;
+       for (iind=1; iind<=imx; iind++) { /* For each individual iind */
-       for (i=1; i<=imx; i++) {
          bool=1;
-         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+         if(j !=0){
-           for (z1=1; z1<=cptcoveff; z1++)
+           if(anyvaryingduminmodel==0){ /* If All fixed covariates */
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
+             if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
+               for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
-               bool=0;
+                 /* if(Tvaraff[z1] ==-20){ */
-               /* 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",
+                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
-                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
+                 /* }else  if(Tvaraff[z1] ==-10){ */
-                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
+                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
-               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
+                 /* }else  */ /* TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/
-             }
+                 /* if( iind >=imx-3) printf("Searching error iind=%d Tvaraff[z1]=%d covar[Tvaraff[z1]][iind]=%.f TnsdVar[Tvaraff[z1]]=%d, cptcoveff=%d, cptcovs=%d \n",iind, Tvaraff[z1], covar[Tvaraff[z1]][iind],TnsdVar[Tvaraff[z1]],cptcoveff, cptcovs); */
-         }
+                 if(Tvaraff[z1]<1 || Tvaraff[z1]>=NCOVMAX)
+                   printf("Error Tvaraff[z1]=%d<1 or >=%d, cptcoveff=%d model=%s\n",Tvaraff[z1],NCOVMAX, cptcoveff, model);
-         if (bool==1){
+                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]){ /* for combination j1 of covariates */
-           for(m=firstpass; m<=lastpass; m++){
+                   /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
-             k2=anint[m][i]+(mint[m][i]/12.);
+                   bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+                   /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", */
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+                   /*   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),*/
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+                   /*   j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+                   /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
-               if (m<lastpass) {
+                 } /* Onlyf fixed */
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+               } /* end z1 */
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+             } /* cptcoveff > 0 */
-               }
+           } /* end any */
+         }/* end j==0 */
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+         if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
-                 dateintsum=dateintsum+k2;
+           /* for(m=firstpass; m<=lastpass; m++){ */
+           for(mi=1; mi<wav[iind];mi++){ /* For each wave */
+             m=mw[mi][iind];
+             if(j!=0){
+               if(anyvaryingduminmodel==1){ /* Some are varying covariates */
+                 for (z1=1; z1<=cptcoveff; z1++) {
+                   if( Fixed[Tmodelind[z1]]==1){
+                     iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
+                     if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality. If covariate's
+                                                                                       value is -1, we don't select. It differs from the
+                                                                                       constant and age model which counts them. */
+                       bool=0; /* not selected */
+                   }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
+                     /* i1=Tvaraff[z1]; */
+                     /* i2=TnsdVar[i1]; */
+                     /* i3=nbcode[i1][i2]; */
+                     /* i4=covar[i1][iind]; */
+                     /* if(i4 != i3){ */
+                     if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) { /* Bug valgrind */
+                       bool=0;
+                     }
+                   }
+                 }
+               }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
+             } /* end j==0 */
+             /* bool =0 we keep that guy which corresponds to the combination of dummy values */
+             if(bool==1){ /*Selected */
+               /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
+                  and mw[mi+1][iind]. dh depends on stepm. */
+               agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
+               ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
+               if(m >=firstpass && m <=lastpass){
+                 k2=anint[m][iind]+(mint[m][iind]/12.);
+                 /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+                 if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
+                 if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+                 if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
+                   prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
+                 if (m<lastpass) {
+                   /* if(s[m][iind]==4 && s[m+1][iind]==4) */
+                   /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
+                   if(s[m][iind]==-1)
+                     printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
+                   freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
+                   for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
+                     if(!isnan(covar[ncovcol+z1][iind])){
+                       idq[z1]=idq[z1]+weight[iind];
+                       meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */
+                       /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/
+                       stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
+                     }
+                   }
+                   /* if((int)agev[m][iind] == 55) */
+                   /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
+                   /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
+                   freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
+                 }
+               } /* end if between passes */
+               if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
+                 dateintsum=dateintsum+k2; /* on all covariates ?*/
                  k2cpt++;
+                 /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
                }
-               /*}*/
+             }else{
-           }
+               bool=1;
-         }
+             }/* end bool 2 */
-       } /* end i */
+           } /* end m */
+           /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
+           /*   idq[z1]=idq[z1]+weight[iind]; */
+           /*   meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /\* Computes mean of quantitative with selected filter *\/ */
+           /*   stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/  /\* Computes mean of quantitative with selected filter *\/ */
+           /* } */
+         } /* end bool */
+       } /* end iind = 1 to imx */
+       /* prop[s][age] is fed for any initial and valid live state as well as
+          freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-       pstamp(ficresp);
+       if(cptcoveff==0 && nj==1) /* no covariate and first pass */
-       if  (cptcovn>0) {
+         pstamp(ficresp);
+       if  (cptcoveff>0 && j!=0){
+         pstamp(ficresp);
+         printf( "\n#********** Variable ");
          fprintf(ficresp, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
-         fprintf(ficresp, "**********\n#");
+         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
          fprintf(ficlog, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         for (z1=1; z1<=cptcovs; z1++){
-         fprintf(ficlog, "**********\n#");
+           if(!FixedV[Tvaraff[z1]]){
+             printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+           }else{
+             printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+           }
+         }
+         printf( "**********\n#");
+         fprintf(ficresp, "**********\n#");
+         fprintf(ficresphtm, "**********</h3>\n");
+         fprintf(ficresphtmfr, "**********</h3>\n");
+         fprintf(ficlog, "**********\n");
+       }
+       /*
+         Printing means of quantitative variables if any
+       */
+       for (z1=1; z1<= nqfveff; z1++) {
+         fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
+         fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
+         if(weightopt==1){
+           printf(" Weighted mean and standard deviation of");
+           fprintf(ficlog," Weighted mean and standard deviation of");
+           fprintf(ficresphtmfr," Weighted mean and standard deviation of");
+         }
+         /* mu = \frac{w x}{\sum w}
+            var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2
+         */
+         printf(" fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
+         fprintf(ficlog," fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
+         fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
+       }
+       /* for (z1=1; z1<= nqtveff; z1++) { */
+       /*        for(m=1;m<=lastpass;m++){ */
+       /*          fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
+       /*   } */
+       /* } */
+       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
+       if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
+         fprintf(ficresp, " Age");
+       if(nj==2) for (z1=1; z1<=cptcoveff; z1++) {
+           printf(" V%d=%d, z1=%d, Tvaraff[z1]=%d, j1=%d, TnsdVar[Tvaraff[%d]]=%d |",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])], z1, Tvaraff[z1], j1,z1,TnsdVar[Tvaraff[z1]]);
+           fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+         }
+       for(i=1; i<=nlstate;i++) {
+         if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d)  N(%d)  N  ",i,i);
+         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
        }
-       for(i=1; i<=nlstate;i++)
+       if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       fprintf(ficresphtm, "\n");
-       fprintf(ficresp, "\n");
-       for(i=iagemin; i <= iagemax+3; i++){
+       /* Header of frequency table by age */
-         if(i==iagemax+3){
+       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
+       fprintf(ficresphtmfr,"<th>Age</th> ");
+       for(s2=-1; s2 <=nlstate+ndeath; s2++){
+         for(m=-1; m <=nlstate+ndeath; m++){
+           if(s2!=0 && m!=0)
+             fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
+         }
+       }
+       fprintf(ficresphtmfr, "\n");
+       /* For each age */
+       for(iage=iagemin; iage <= iagemax+3; iage++){
+         fprintf(ficresphtm,"<tr>");
+         if(iage==iagemax+1){
+           fprintf(ficlog,"1");
+           fprintf(ficresphtmfr,"<tr><th>0</th> ");
+         }else if(iage==iagemax+2){
+           fprintf(ficlog,"0");
+           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
+         }else if(iage==iagemax+3){
            fprintf(ficlog,"Total");
+           fprintf(ficresphtmfr,"<tr><th>Total</th> ");
          }else{
            if(first==1){
              first=0;
              printf("See log file for details...\n");
            }
-           fprintf(ficlog,"Age %d", i);
+           fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
+           fprintf(ficlog,"Age %d", iage);
          }
-         for(jk=1; jk <=nlstate ; jk++){
+         for(s1=1; s1 <=nlstate ; s1++){
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+           for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
-             pp[jk] += freq[jk][m][i];
+             pp[s1] += freq[s1][m][iage];
          }
-         for(jk=1; jk <=nlstate ; jk++){
+         for(s1=1; s1 <=nlstate ; s1++){
            for(m=-1, pos=0; m <=0 ; m++)
-             pos += freq[jk][m][i];
+             pos += freq[s1][m][iage];
-           if(pp[jk]>=1.e-10){
+           if(pp[s1]>=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%%",s1,pp[s1],s1,100*pos/pp[s1]);
              }
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
            }else{
              if(first==1)
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
            }
          }
-         for(jk=1; jk <=nlstate ; jk++){
+         for(s1=1; s1 <=nlstate ; s1++){
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+           /* posprop[s1]=0; */
-             pp[jk] += freq[jk][m][i];
+           for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
-         }
+             pp[s1] += freq[s1][m][iage];
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+         }       /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
-           pos += pp[jk];
-           posprop += prop[jk][i];
+         for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
+           pos += pp[s1]; /* pos is the total number of transitions until this age */
+           posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
+                                             from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+           pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
+                                           from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+         }
+         /* Writing ficresp */
+         if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
+           if( iage <= iagemax){
+             fprintf(ficresp," %d",iage);
+           }
+         }else if( nj==2){
+           if( iage <= iagemax){
+             fprintf(ficresp," %d",iage);
+             for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+           }
          }
-         for(jk=1; jk <=nlstate ; jk++){
+         for(s1=1; s1 <=nlstate ; s1++){
            if(pos>=1.e-5){
              if(first==1)
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+               printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
            }else{
              if(first==1)
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
            }
-           if( i <= iagemax){
+           if( iage <= iagemax){
              if(pos>=1.e-5){
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+               if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
-               /*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 if( nj==2){
+                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
+               }
+               fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
+               /*probs[iage][s1][j1]= pp[s1]/pos;*/
+               /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
+             } else{
+               if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
+               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
              }
-             else
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
            }
-         }
+           pospropt[s1] +=posprop[s1];
+         } /* end loop s1 */
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+         /* pospropt=0.; */
-           for(m=-1; m <=nlstate+ndeath; m++)
+         for(s1=-1; s1 <=nlstate+ndeath; s1++){
-             if(freq[jk][m][i] !=0 ) {
+           for(m=-1; m <=nlstate+ndeath; m++){
-             if(first==1)
+             if(freq[s1][m][iage] !=0 ) { /* minimizing output */
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+               if(first==1){
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+                 printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
+               }
+               /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
+               fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
              }
-         if(i <= iagemax)
+             if(s1!=0 && m!=0)
-           fprintf(ficresp,"\n");
+               fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
+           }
+         } /* end loop s1 */
+         posproptt=0.;
+         for(s1=1; s1 <=nlstate; s1++){
+           posproptt += pospropt[s1];
+         }
+         fprintf(ficresphtmfr,"</tr>\n ");
+         fprintf(ficresphtm,"</tr>\n");
+         if((cptcoveff==0 && nj==1)|| nj==2 ) {
+           if(iage <= iagemax)
+             fprintf(ficresp,"\n");
+         }
          if(first==1)
            printf("Others in log...\n");
          fprintf(ficlog,"\n");
+       } /* end loop age iage */
+       fprintf(ficresphtm,"<tr><th>Tot</th>");
+       for(s1=1; s1 <=nlstate ; s1++){
+         if(posproptt < 1.e-5){
+           fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
+         }else{
+           fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
+         }
        }
-       /*}*/
+       fprintf(ficresphtm,"</tr>\n");
-   }
+       fprintf(ficresphtm,"</table>\n");
+       fprintf(ficresphtmfr,"</table>\n");
+       if(posproptt < 1.e-5){
+         fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+         fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+         fprintf(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
+         printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
+         invalidvarcomb[j1]=1;
+       }else{
+         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
+         invalidvarcomb[j1]=0;
+       }
+       fprintf(ficresphtmfr,"</table>\n");
+       fprintf(ficlog,"\n");
+       if(j!=0){
+         printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
+         for(i=1,s1=1; i <=nlstate; i++){
+           for(k=1; k <=(nlstate+ndeath); k++){
+             if (k != i) {
+               for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
+                 if(jj==1){  /* Constant case (in fact cste + age) */
+                   if(j1==1){ /* All dummy covariates to zero */
+                     freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
+                     freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
+                     printf("%d%d ",i,k);
+                     fprintf(ficlog,"%d%d ",i,k);
+                     printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
+                     fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+                     pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
+                   }
+                 }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
+                   for(iage=iagemin; iage <= iagemax+3; iage++){
+                     x[iage]= (double)iage;
+                     y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
+                     /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
+                   }
+                   /* Some are not finite, but linreg will ignore these ages */
+                   no=0;
+                   linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
+                   pstart[s1]=b;
+                   pstart[s1-1]=a;
+                 }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */
+                   printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
+                   printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
+                   pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
+                   printf("%d%d ",i,k);
+                   fprintf(ficlog,"%d%d ",i,k);
+                   printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
+                 }else{ /* Other cases, like quantitative fixed or varying covariates */
+                   ;
+                 }
+                 /* printf("%12.7f )", param[i][jj][k]); */
+                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
+                 s1++;
+               } /* end jj */
+             } /* end k!= i */
+           } /* end k */
+         } /* end i, s1 */
+       } /* end j !=0 */
+     } /* end selected combination of covariate j1 */
+     if(j==0){ /* We can estimate starting values from the occurences in each case */
+       printf("#Freqsummary: Starting values for the constants:\n");
+       fprintf(ficlog,"\n");
+       for(i=1,s1=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);
+             for(jj=1; jj <=ncovmodel; jj++){
+               pstart[s1]=p[s1]; /* Setting pstart to p values by default */
+               if(jj==1){ /* Age has to be done */
+                 pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
+                 printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+                 fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+               }
+               /* printf("%12.7f )", param[i][jj][k]); */
+               /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
+               s1++;
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+       } /* end of state i */
+       printf("#Freqsummary\n");
+       fprintf(ficlog,"\n");
+       for(s1=-1; s1 <=nlstate+ndeath; s1++){
+         for(s2=-1; s2 <=nlstate+ndeath; s2++){
+           /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
+           printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
+           fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
+           /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
+           /*   printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
+           /*   fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
+           /* } */
+         }
+       } /* end loop s1 */
+       printf("\n");
+       fprintf(ficlog,"\n");
+     } /* end j=0 */
+   } /* end j */
+   if(mle == -2){  /* We want to use these values as starting values */
+     for(i=1, jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j!=i){
+           /*ca[0]= k+'a'-1;ca[1]='\0';*/
+           printf("%1d%1d",i,j);
+           fprintf(ficparo,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             /*    printf(" %lf",param[i][j][k]); */
+             /*    fprintf(ficparo," %lf",param[i][j][k]); */
+             p[jk]=pstart[jk];
+             printf(" %f ",pstart[jk]);
+             fprintf(ficparo," %f ",pstart[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficparo,"\n");
+         }
+       }
+     }
+   } /* end mle=-2 */
    dateintmean=dateintsum/k2cpt;
+   date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
    fclose(ficresp);
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+   fclose(ficresphtm);
+   fclose(ficresphtmfr);
+   free_vector(idq,1,nqfveff);
+   free_vector(meanq,1,nqfveff);
+   free_vector(stdq,1,nqfveff);
+   free_matrix(meanqt,1,lastpass,1,nqtveff);
+   free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
+   free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
+   free_vector(pospropt,1,nlstate);
+   free_vector(posprop,1,nlstate);
+   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
    free_vector(pp,1,nlstate);
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+   /* End of freqsummary */
-   /* End of Freq */
+ }
+ /* Simple linear regression */
+ int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
+   /* y=a+bx regression */
+   double   sumx = 0.0;                        /* sum of x                      */
+   double   sumx2 = 0.0;                       /* sum of x**2                   */
+   double   sumxy = 0.0;                       /* sum of x * y                  */
+   double   sumy = 0.0;                        /* sum of y                      */
+   double   sumy2 = 0.0;                       /* sum of y**2                   */
+   double   sume2 = 0.0;                       /* sum of square or residuals */
+   double yhat;
+   double denom=0;
+   int i;
+   int ne=*no;
+   for ( i=ifi, ne=0;i<=ila;i++) {
+     if(!isfinite(x[i]) || !isfinite(y[i])){
+       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
+       continue;
+     }
+     ne=ne+1;
+     sumx  += x[i];
+     sumx2 += x[i]*x[i];
+     sumxy += x[i] * y[i];
+     sumy  += y[i];
+     sumy2 += y[i]*y[i];
+     denom = (ne * sumx2 - sumx*sumx);
+     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
+   }
+   denom = (ne * sumx2 - sumx*sumx);
+   if (denom == 0) {
+     // vertical, slope m is infinity
+     *b = INFINITY;
+     *a = 0;
+     if (r) *r = 0;
+     return 1;
+   }
+   *b = (ne * sumxy  -  sumx * sumy) / denom;
+   *a = (sumy * sumx2  -  sumx * sumxy) / denom;
+   if (r!=NULL) {
+     *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
+       sqrt((sumx2 - sumx*sumx/ne) *
+            (sumy2 - sumy*sumy/ne));
+   }
+   *no=ne;
+   for ( i=ifi, ne=0;i<=ila;i++) {
+     if(!isfinite(x[i]) || !isfinite(y[i])){
+       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
+       continue;
+     }
+     ne=ne+1;
+     yhat = y[i] - *a -*b* x[i];
+     sume2  += yhat * yhat ;
+     denom = (ne * sumx2 - sumx*sumx);
+     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
+   }
+   *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
+   *sa= *sb * sqrt(sumx2/ne);
+   return 0;
  }
  /************ Prevalence ********************/
- Line 2690  void prevalence(double ***probs, double
+ Line 5648  void prevalence(double ***probs, double
       We still use firstpass and lastpass as another selection.
    */
-   int i, m, jk, j1, bool, z1,j;
+   int i, m, jk, j1, bool, z1,j, iv;
+   int mi; /* Effective wave */
+   int iage;
+   double agebegin, ageend;
    double **prop;
    double posprop;
- Line 2701  void prevalence(double ***probs, double
+ Line 5662  void prevalence(double ***probs, double
    iagemin= (int) agemin;
    iagemax= (int) agemax;
    /*pp=vector(1,nlstate);*/
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    j1=0;
    /*j=cptcoveff;*/
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   first=1;
+   first=0;
-   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of simple dummy covariates */
-     /*for(i1=1; i1<=ncodemax[k1];i1++){
+     for (i=1; i<=nlstate; i++)
-       j1++;*/
+       for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
+         prop[i][iage]=0.0;
-       for (i=1; i<=nlstate; i++)
+     printf("Prevalence combination of varying and fixed dummies %d\n",j1);
-         for(m=iagemin; m <= iagemax+3; m++)
+     /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
-           prop[i][m]=0.0;
+     fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
-       for (i=1; i<=imx; i++) { /* Each individual */
+     for (i=1; i<=imx; i++) { /* Each individual */
-         bool=1;
+       bool=1;
-         if  (cptcovn>0) {
+       /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
-           for (z1=1; z1<=cptcoveff; z1++)
+       for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+         m=mw[mi][i];
+         /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
+         /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
+         for (z1=1; z1<=cptcoveff; z1++){
+           if( Fixed[Tmodelind[z1]]==1){
+             iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
+             if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality */
                bool=0;
-         }
+           }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
-         if (bool==1) {
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) {
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+               bool=0;
+             }
+         }
+         if(bool==1){ /* Otherwise we skip that wave/person */
+           agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
+           /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
+           if(m >=firstpass && m <=lastpass){
              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                if(agev[m][i]==1) agev[m][i]=iagemax+2;
-               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
+               if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+                 printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
+                 exit(1);
+               }
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
                  prop[s[m][i]][iagemax+3] += weight[i];
-               }
+               } /* end valid statuses */
-             }
+             } /* end selection of dates */
            } /* end selection of waves */
-         }
+         } /* end bool */
-       }
+       } /* end wave */
-       for(i=iagemin; i <= iagemax+3; i++){
+     } /* end individual */
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+     for(i=iagemin; i <= iagemax+3; i++){
-           posprop += prop[jk][i];
+       for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-         }
+         posprop += prop[jk][i];
+       }
-         for(jk=1; jk <=nlstate ; jk++){
-           if( i <=  iagemax){
+       for(jk=1; jk <=nlstate ; jk++){
-             if(posprop>=1.e-5){
+         if( i <=  iagemax){
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+           if(posprop>=1.e-5){
-             } else{
+             probs[i][jk][j1]= prop[jk][i]/posprop;
-               if(first==1){
+           } else{
-                 first=0;
+             if(!first){
-                 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]);
+               first=1;
-               }
+               printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
+             }else{
+               fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]);
              }
            }
-         }/* end jk */
+         }
-       }/* end i */
+       }/* end jk */
-     /*} *//* end i1 */
+     }/* end i */
+      /*} *//* end i1 */
    } /* end j1 */
    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    /*free_vector(pp,1,nlstate);*/
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
  }  /* End of prevalence */
  /************* Waves Concatenation ***************/
  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
  {
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+   /* Concatenates waves: wav[i] is the number of effective (useful waves in the sense that a non interview is useless) of individual i.
       Death is a valid wave (if date is known).
       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-      and mw[mi+1][i]. dh depends on stepm.
+      and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
-      */
+   */
-   int i, mi, m;
+   int i=0, mi=0, m=0, mli=0;
    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       double sum=0., jmean=0.;*/
-   int first;
+   int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
    int j, k=0,jk, ju, jl;
    double sum=0.;
    first=0;
+   firstwo=0;
+   firsthree=0;
+   firstfour=0;
    jmin=100000;
    jmax=-1;
    jmean=0.;
-   for(i=1; i<=imx; i++){
-     mi=0;
+ /* Treating live states */
-     m=firstpass;
+   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
-     while(s[m][i] <= nlstate){
+     mi=0;  /* First valid wave */
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+     mli=0; /* Last valid wave */
-         mw[++mi][i]=m;
+     m=firstpass;  /* Loop on waves */
-       if(m >=lastpass)
+     while(s[m][i] <= nlstate){  /* a live state or unknown state  */
+       if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
+         mli=m-1;/* mw[++mi][i]=m-1; */
+       }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
+         mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition   */
+         mli=m;
+       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
+       if(m < lastpass){ /* m < lastpass, standard case */
+         m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
+       }
+       else{ /* m = lastpass, eventual special issue with warning */
+ #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
          break;
-       else
+ #else
-         m++;
+         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* no death date and known date of interview, case -2 (vital status unknown is warned later */
+           if(firsthree == 0){
+             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
+             firsthree=1;
+           }else if(firsthree >=1 && firsthree < 10){
+             fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
+             firsthree++;
+           }else if(firsthree == 10){
+             printf("Information, too many Information flags: no more reported to log either\n");
+             fprintf(ficlog,"Information, too many Information flags: no more reported to log either\n");
+             firsthree++;
+           }else{
+             firsthree++;
+           }
+           mw[++mi][i]=m; /* Valid transition with unknown status */
+           mli=m;
+         }
+         if(s[m][i]==-2){ /* Vital status is really unknown */
+           nbwarn++;
+           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified?not a transition */
+             printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
+             fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
+           }
+           break;
+         }
+         break;
+ #endif
+       }/* End m >= lastpass */
      }/* end while */
-     if (s[m][i] > nlstate){
+     /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
+     /* After last pass */
+ /* Treating death states */
+     if (s[m][i] > nlstate){  /* In a death state */
+       /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
+       /* } */
        mi++;     /* Death is another wave */
        /* if(mi==0)  never been interviewed correctly before death */
-          /* Only death is a correct wave */
+       /* Only death is a correct wave */
        mw[mi][i]=m;
-     }
+     } /* else not in a death state */
+ #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
-     wav[i]=mi;
+     else if ((int) andc[i] != 9999) {  /* Date of death is known */
+       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
+         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */
+           nbwarn++;
+           if(firstfiv==0){
+             printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+             firstfiv=1;
+           }else{
+             fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+           }
+             s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
+         }else{ /* Month of Death occured afer last wave month, potential bias */
+           nberr++;
+           if(firstwo==0){
+             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+             firstwo=1;
+           }
+           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+         }
+       }else{ /* if date of interview is unknown */
+         /* death is known but not confirmed by death status at any wave */
+         if(firstfour==0){
+           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+           firstfour=1;
+         }
+         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d  with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+       }
+     } /* end if date of death is known */
+ #endif
+     wav[i]=mi; /* mi should be the last effective wave (or mli),  */
+     /* wav[i]=mw[mi][i];   */
      if(mi==0){
        nbwarn++;
        if(first==0){
- Line 2817  void  concatwav(int wav[], int **dh, int
+ Line 5873  void  concatwav(int wav[], int **dh, int
        }
      } /* end mi==0 */
    } /* End individuals */
+   /* wav and mw are no more changed */
+   printf("Information, you have to check %d informations which haven't been logged!\n",firsthree);
+   fprintf(ficlog,"Information, you have to check %d informations which haven't been logged!\n",firsthree);
    for(i=1; i<=imx; i++){
      for(mi=1; mi<wav[i];mi++){
        if (stepm <=0)
          dh[mi][i]=1;
        else{
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
            if (agedc[i] < 2*AGESUP) {
              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
              if(j==0) j=1;  /* Survives at least one month after exam */
- Line 2852  void  concatwav(int wav[], int **dh, int
+ Line 5913  void  concatwav(int wav[], int **dh, int
          else{
            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
            k=k+1;
            if (j >= jmax) {
              jmax=j;
- Line 2906  void  concatwav(int wav[], int **dh, int
+ Line 5967  void  concatwav(int wav[], int **dh, int
    jmean=sum/k;
    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
-  }
+ }
  /*********** Tricode ****************************/
- void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
+  void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
- {
+  {
-   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
+    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
+    /*     Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
+     * Boring subroutine which should only output nbcode[Tvar[j]][k]
-    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
+     * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
-   /* nbcode[Tvar[j]][1]=
+     * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
-   */
+     */
-   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-   int modmaxcovj=0; /* Modality max of covariates j */
+    int modmaxcovj=0; /* Modality max of covariates j */
-   int cptcode=0; /* Modality max of covariates j */
+    int cptcode=0; /* Modality max of covariates j */
-   int modmincovj=0; /* Modality min of covariates j */
+    int modmincovj=0; /* Modality min of covariates j */
-   cptcoveff=0;
+    /* cptcoveff=0;  */
+    /* *cptcov=0; */
-   for (k=-1; k < maxncov; k++) Ndum[k]=0;
+    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
+    for (k=1; k <= maxncov; k++)
+      for(j=1; j<=2; j++)
-   /* Loop on covariates without age and products */
+        nbcode[k][j]=0; /* Valgrind */
-   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
-     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
+    /* Loop on covariates without age and products and no quantitative variable */
-                                modality of this covariate Vj*/
+    for (k=1; k<=cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
-       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+      for (j=-1; (j < maxncov); j++) Ndum[j]=0;
-                                     * If product of Vn*Vm, still boolean *:
+      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
-                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+        switch(Fixed[k]) {
-                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
+        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
-       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
+          modmaxcovj=0;
-                                       modality of the nth covariate of individual i. */
+          modmincovj=0;
-       if (ij > modmaxcovj)
+          for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
-         modmaxcovj=ij;
+            ij=(int)(covar[Tvar[k]][i]);
-       else if (ij < modmincovj)
+            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-         modmincovj=ij;
+             * If product of Vn*Vm, still boolean *:
-       if ((ij < -1) && (ij > NCOVMAX)){
+             * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
+             * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-         exit(1);
+            /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-       }else
+               modality of the nth covariate of individual i. */
-       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+            if (ij > modmaxcovj)
-       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
+              modmaxcovj=ij;
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+            else if (ij < modmincovj)
-       /* getting the maximum value of the modality of the covariate
+              modmincovj=ij;
-          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+            if (ij <0 || ij >1 ){
-          female is 1, then modmaxcovj=1.*/
+              printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
-     }
+              fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
-     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+              fflush(ficlog);
-     cptcode=modmaxcovj;
+              exit(1);
-     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+            }
-    /*for (i=0; i<=cptcode; i++) {*/
+            if ((ij < -1) || (ij > NCOVMAX)){
-     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
+              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
+              exit(1);
-       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
+            }else
-         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
+              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 */
-       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
+            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+            /* getting the maximum value of the modality of the covariate
-     } /* Ndum[-1] number of undefined modalities */
+               (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+               female ies 1, then modmaxcovj=1.
-     /* 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 */
+          } /* end for loop on individuals i */
-     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
+          printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-        modmincovj=3; modmaxcovj = 7;
+          fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
+          cptcode=modmaxcovj;
-        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
+          /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-        variables V1_1 and V1_2.
+          /*for (i=0; i<=cptcode; i++) {*/
-        nbcode[Tvar[j]][ij]=k;
+          for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
-        nbcode[Tvar[j]][1]=0;
+            printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-        nbcode[Tvar[j]][2]=1;
+            fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-        nbcode[Tvar[j]][3]=2;
+            if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
-     */
+              if( j != -1){
-     ij=1; /* ij is similar to i but can jumps over null modalities */
+                ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
-     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
+                                   covariate for which somebody answered excluding
-       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
+                                   undefined. Usually 2: 0 and 1. */
-         /*recode from 0 */
+              }
-         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
+              ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
-           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
+                                      covariate for which somebody answered including
-                                      k is a modality. If we have model=V1+V1*sex
+                                      undefined. Usually 3: -1, 0 and 1. */
-                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+            }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
-           ij++;
+                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-         }
+          } /* Ndum[-1] number of undefined modalities */
-         if (ij > ncodemax[j]) break;
-       }  /* end of loop on */
+          /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-     } /* end of loop on modality */
+          /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
-   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
+          /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
+          /* modmincovj=3; modmaxcovj = 7; */
-  for (k=-1; k< maxncov; k++) Ndum[k]=0;
+          /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
+          /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
-   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
+          /*              defining two dummy variables: variables V1_1 and V1_2.*/
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+          /* nbcode[Tvar[j]][ij]=k; */
-    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
+          /* nbcode[Tvar[j]][1]=0; */
-    Ndum[ij]++;
+          /* nbcode[Tvar[j]][2]=1; */
-  }
+          /* nbcode[Tvar[j]][3]=2; */
+          /* To be continued (not working yet). */
-  ij=1;
+          ij=0; /* ij is similar to i but can jump over null modalities */
-  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]);*/
+          /* for (i=modmincovj; i<=modmaxcovj; i++) { */ /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+          /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
-      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+          /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
-      Tvaraff[ij]=i; /*For printing (unclear) */
+           * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
-      ij++;
+          /*, could be restored in the future */
-    }else
+          for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
-        Tvaraff[ij]=0;
+            if (Ndum[i] == 0) { /* If nobody responded to this modality k */
+              break;
+            }
+            ij++;
+            nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
+            cptcode = ij; /* New max modality for covar j */
+          } /* end of loop on modality i=-1 to 1 or more */
+          break;
+        case 1: /* Testing on varying covariate, could be simple and
+                 * should look at waves or product of fixed *
+                 * varying. No time to test -1, assuming 0 and 1 only */
+          ij=0;
+          for(i=0; i<=1;i++){
+            nbcode[Tvar[k]][++ij]=i;
+          }
+          break;
+        default:
+          break;
+        } /* end switch */
+      } /* end dummy test */
+      if(Dummy[k]==1 && Typevar[k] !=1){ /* Quantitative covariate and not age product */
+        for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
+          if(Tvar[k]<=0 || Tvar[k]>=NCOVMAX){
+            printf("Error k=%d \n",k);
+            exit(1);
+          }
+          if(isnan(covar[Tvar[k]][i])){
+            printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
+            fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
+            fflush(ficlog);
+            exit(1);
+          }
+        }
+      } /* end Quanti */
+    } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/
+    for (k=-1; k< maxncov; k++) Ndum[k]=0;
+    /* Look at fixed dummy (single or product) covariates to check empty modalities */
+    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
+      /* 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]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */
+      Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
+      /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
+    } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
+    ij=0;
+    /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
+    for (k=1; k<=  cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
+      /* 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)){  /\* Tvar[i] <= ncovmodel ? *\/ */
+      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy simple and non empty in the model */
+        /* Typevar[k] =0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
+        /* Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product*/
+        /* If product not in single variable we don't print results */
+        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+        ++ij;/*    V5 + V4 + V3 + V4*V3 + V5*age + V2 +  V1*V2 + V1*age + V1, *//* V5 quanti, V2 quanti, V4, V3, V1 dummies */
+        /* k=       1    2   3     4       5       6      7       8        9  */
+        /* Tvar[k]= 5    4    3    6       5       2      7       1        1  */
+        /* ij            1    2                                            3  */
+        /* Tvaraff[ij]=  4    3                                            1  */
+        /* Tmodelind[ij]=2    3                                            9  */
+        /* TmodelInvind[ij]=2 1                                            1  */
+        Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
+        Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
+        TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
+        if(Fixed[k]!=0)
+          anyvaryingduminmodel=1;
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
+        /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
+        /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
+        /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
+      }
+    } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
+    /* ij--; */
+    /* cptcoveff=ij; /\*Number of total covariates*\/ */
+    *cptcov=ij; /* cptcov= Number of total real effective simple dummies (fixed or time  arying) effective (used as cptcoveff in other functions)
+                 * because they can be excluded from the model and real
+                 * if in the model but excluded because missing values, but how to get k from ij?*/
+    for(j=ij+1; j<= cptcovt; j++){
+      Tvaraff[j]=0;
+      Tmodelind[j]=0;
+    }
+    for(j=ntveff+1; j<= cptcovt; j++){
+      TmodelInvind[j]=0;
+    }
+    /* To be sorted */
+    ;
   }
-  ij--;
-  cptcoveff=ij; /*Number of total covariates*/
- }
  /*********** Health Expectancies ****************/
- void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres )
  {
    /* Health expectancies, no variances */
+   /* cij is the combination in the list of combination of dummy covariates */
+   /* strstart is a string of time at start of computing */
    int i, j, nhstepm, hstepm, h, nstepm;
    int nhstepma, nstepma; /* Decreasing with age */
    double age, agelim, hf;
    double ***p3mat;
    double eip;
-   pstamp(ficreseij);
+   /* 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++){
- Line 3061  void evsij(double ***eij, double x[], in
+ Line 6210  void evsij(double ***eij, double x[], in
    /* 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 hpijx to understand the reason which relies in memory size consideration
       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
- Line 3092  void evsij(double ***eij, double x[], in
+ Line 6241  void evsij(double ***eij, double x[], in
      /* 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 */
+     /* printf("HELLO evsij Entering hpxij age=%d cij=%d hstepm=%d x[1]=%f nres=%d\n",(int) age, cij, hstepm, x[1], nres); */
-     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
- Line 3128  void evsij(double ***eij, double x[], in
+ Line 6277  void evsij(double ***eij, double x[], in
  }
- 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[] )
+  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[], int nres )
  {
    /* Covariances of health expectancies eij and of total life expectancies according
-    to initial status i, ei. .
+      to initial status i, ei. .
    */
+   /* Very time consuming function, but already optimized with precov */
    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
    int nhstepma, nstepma; /* Decreasing with age */
    double age, agelim, hf;
- Line 3226  void cvevsij(double ***eij, double x[],
+ Line 6376  void cvevsij(double ***eij, double x[],
      /* Typically if 20 years nstepm = 20*12/6=40 stepm */
      /* if (stepm >= YEARM) hstepm=1;*/
      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
      /* If stepm=6 months */
      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      /* Computing  Variances of health expectancies */
      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
         decrease memory allocation */
- Line 3241  void cvevsij(double ***eij, double x[],
+ Line 6391  void cvevsij(double ***eij, double x[],
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
        for(j=1; j<= nlstate; j++){
          for(i=1; i<=nlstate; i++){
            for(h=0; h<=nhstepm-1; h++){
- Line 3252  void cvevsij(double ***eij, double x[],
+ Line 6402  void cvevsij(double ***eij, double x[],
            }
          }
        }
        for(ij=1; ij<= nlstate*nlstate; ij++)
          for(h=0; h<=nhstepm-1; h++){
            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
- Line 3265  void cvevsij(double ***eij, double x[],
+ Line 6415  void cvevsij(double ***eij, double x[],
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+     for(ij=1;ij<=nlstate*nlstate;ij++)
        for(ji=1;ji<=nlstate*nlstate;ji++)
          varhe[ij][ji][(int)age] =0.;
-      printf("%d|",(int)age);fflush(stdout);
+     printf("%d|",(int)age);fflush(stdout);
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-      for(h=0;h<=nhstepm-1;h++){
+     for(h=0;h<=nhstepm-1;h++){
        for(k=0;k<=nhstepm-1;k++){
          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
- Line 3281  void cvevsij(double ***eij, double x[],
+ Line 6431  void cvevsij(double ***eij, double x[],
              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
        }
      }
+     /* if((int)age ==50){ */
+     /*   printf(" age=%d cij=%d nres=%d varhe[%d][%d]=%f ",(int)age, cij, nres, 1,2,varhe[1][2]); */
+     /* } */
      /* Computing expectancies */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
          }
+     /* Standard deviation of expectancies ij */
      fprintf(ficresstdeij,"%3.0f",age );
      for(i=1; i<=nlstate;i++){
        eip=0.;
- Line 3306  void cvevsij(double ***eij, double x[],
+ Line 6459  void cvevsij(double ***eij, double x[],
        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
      }
      fprintf(ficresstdeij,"\n");
+     /* Variance of expectancies ij */
      fprintf(ficrescveij,"%3.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
- Line 3319  void cvevsij(double ***eij, double x[],
+ Line 6473  void cvevsij(double ***eij, double x[],
            }
        }
      fprintf(ficrescveij,"\n");
    }
    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
- Line 3329  void cvevsij(double ***eij, double x[],
+ Line 6483  void cvevsij(double ***eij, double x[],
    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    printf("\n");
    fprintf(ficlog,"\n");
    free_vector(xm,1,npar);
    free_vector(xp,1,npar);
    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  }
  /************ Variance ******************/
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+  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 *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
- {
+  {
-   /* Variance of health expectancies */
+    /** Variance of health expectancies
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+     *  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
-   /* double **newm;*/
+     * double **newm;
-   double **dnewm,**doldm;
+     * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
-   double **dnewmp,**doldmp;
+     */
-   int i, j, nhstepm, hstepm, h, nstepm ;
-   int k;
+    /* int movingaverage(); */
-   double *xp;
+    double **dnewm,**doldm;
-   double **gp, **gm;  /* for var eij */
+    double **dnewmp,**doldmp;
-   double ***gradg, ***trgradg; /*for var eij */
+    int i, j, nhstepm, hstepm, h, nstepm ;
-   double **gradgp, **trgradgp; /* for var p point j */
+    int first=0;
-   double *gpp, *gmp; /* for var p point j */
+    int k;
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+    double *xp;
-   double ***p3mat;
+    double **gp, **gm;  /**< for var eij */
-   double age,agelim, hf;
+    double ***gradg, ***trgradg; /**< for var eij */
-   double ***mobaverage;
+    double **gradgp, **trgradgp; /**< for var p point j */
-   int theta;
+    double *gpp, *gmp; /**< for var p point j */
-   char digit[4];
+    double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
-   char digitp[25];
+    double ***p3mat;
+    double age,agelim, hf;
+    /* double ***mobaverage; */
+    int theta;
+    char digit[4];
+    char digitp[25];
+    char fileresprobmorprev[FILENAMELENGTH];
+    if(popbased==1){
+      if(mobilav!=0)
+        strcpy(digitp,"-POPULBASED-MOBILAV_");
+      else strcpy(digitp,"-POPULBASED-NOMOBIL_");
+    }
+    else
+      strcpy(digitp,"-STABLBASED_");
+    /* if (mobilav!=0) { */
+    /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+    /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
+    /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
+    /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
+    /*   } */
+    /* } */
+    strcpy(fileresprobmorprev,"PRMORPREV-");
+    sprintf(digit,"%-d",ij);
+    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+    strcat(fileresprobmorprev,digit); /* Tvar to be done */
+    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+    strcat(fileresprobmorprev,fileresu);
+    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+      printf("Problem with resultfile: %s\n", fileresprobmorprev);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+    }
+    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+    pstamp(ficresprobmorprev);
+    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
+    fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
+    /* We use TinvDoQresult[nres][resultmodel[nres][j] we sort according to the equation model and the resultline: it is a choice */
+    /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ /\* To be done*\/ */
+    /*   fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+    /* } */
+    for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value */ /* To be done*/
+      fprintf(ficresprobmorprev," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+    }
+    /* for(j=1;j<=cptcoveff;j++)  */
+    /*   fprintf(ficresprobmorprev," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,TnsdVar[Tvaraff[j]])]); */
+    fprintf(ficresprobmorprev,"\n");
+    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+      fprintf(ficresprobmorprev," p.%-d SE",j);
+      for(i=1; i<=nlstate;i++)
+        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+    }
+    fprintf(ficresprobmorprev,"\n");
+    fprintf(ficgp,"\n# Routine varevsij");
+    fprintf(ficgp,"\nunset title \n");
+    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    pstamp(ficresvij);
+    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+    if(popbased==1)
+      fprintf(ficresvij,"the age specific prevalence observed (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,"\n");
+    xp=vector(1,npar);
+    dnewm=matrix(1,nlstate,1,npar);
+    doldm=matrix(1,nlstate,1,nlstate);
+    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+    gpp=vector(nlstate+1,nlstate+ndeath);
+    gmp=vector(nlstate+1,nlstate+ndeath);
+    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+    if(estepm < stepm){
+      printf ("Problem %d lower than %d\n",estepm, stepm);
+    }
+    else  hstepm=estepm;
+    /* 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 agelim.
+       Look at function hpijx to understand why because of memory size limitations,
+       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
+       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;
+    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+      gp=matrix(0,nhstepm,1,nlstate);
+      gm=matrix(0,nhstepm,1,nlstate);
+      for(theta=1; theta <=npar; theta++){
+        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+          xp[i] = x[i] + (i==theta ?delti[theta]:0);
+        }
+        /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
+         * returns into prlim .
+         */
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
+        /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
+        if (popbased==1) {
+          if(mobilav ==0){
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=probs[(int)age][i][ij];
+          }else{ /* mobilav */
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=mobaverage[(int)age][i][ij];
+          }
+        }
+        /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
+         */
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
+        /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
+         * at horizon h in state j including mortality.
+         */
+        for(j=1; j<= nlstate; j++){
+          for(h=0; h<=nhstepm; h++){
+            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+          }
+        }
+        /* Next for computing shifted+ probability of death (h=1 means
+           computed over hstepm matrices product = hstepm*stepm months)
+           as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
+        */
+        for(j=nlstate+1;j<=nlstate+ndeath;j++){
+          for(i=1,gpp[j]=0.; i<= nlstate; i++)
+            gpp[j] += prlim[i][i]*p3mat[i][j][1];
+        }
+        /* Again with minus shift */
+        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+          xp[i] = x[i] - (i==theta ?delti[theta]:0);
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
+        if (popbased==1) {
+          if(mobilav ==0){
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=probs[(int)age][i][ij];
+          }else{ /* mobilav */
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=mobaverage[(int)age][i][ij];
+          }
+        }
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
+        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];
+          }
+        }
+        /* This for computing probability of death (h=1 means
+           computed over hstepm matrices product = hstepm*stepm months)
+           as a weighted average of prlim.
+        */
+        for(j=nlstate+1;j<=nlstate+ndeath;j++){
+          for(i=1,gmp[j]=0.; i<= nlstate; i++)
+            gmp[j] += prlim[i][i]*p3mat[i][j][1];
+        }
+        /* end shifting computations */
+        /**< Computing gradient matrix at horizon h
+         */
+        for(j=1; j<= nlstate; j++) /* vareij */
+          for(h=0; h<=nhstepm; h++){
+            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+          }
+        /**< Gradient of overall mortality p.3 (or p.j)
+         */
+        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
+          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+        }
+      } /* End theta */
+      /* We got the gradient matrix for each theta and state j */
+      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+      for(h=0; h<=nhstepm; h++) /* veij */
+        for(j=1; j<=nlstate;j++)
+          for(theta=1; theta <=npar; theta++)
+            trgradg[h][j][theta]=gradg[h][theta][j];
+      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+        for(theta=1; theta <=npar; theta++)
+          trgradgp[j][theta]=gradgp[theta][j];
+      /**< as well as its transposed matrix
+       */
+      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+      for(i=1;i<=nlstate;i++)
+        for(j=1;j<=nlstate;j++)
+          vareij[i][j][(int)age] =0.;
+      /* Computing trgradg by matcov by gradg at age and summing over h
+       * and k (nhstepm) formula 15 of article
+       * Lievre-Brouard-Heathcote
+       */
+      for(h=0;h<=nhstepm;h++){
+        for(k=0;k<=nhstepm;k++){
+          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+          for(i=1;i<=nlstate;i++)
+            for(j=1;j<=nlstate;j++)
+              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+        }
+      }
+      /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
+       * p.j overall mortality formula 49 but computed directly because
+       * we compute the grad (wix pijx) instead of grad (pijx),even if
+       * wix is independent of theta.
+       */
+      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+      for(j=nlstate+1;j<=nlstate+ndeath;j++)
+        for(i=nlstate+1;i<=nlstate+ndeath;i++)
+          varppt[j][i]=doldmp[j][i];
+      /* end ppptj */
+      /*  x centered again */
+      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
+      if (popbased==1) {
+        if(mobilav ==0){
+          for(i=1; i<=nlstate;i++)
+            prlim[i][i]=probs[(int)age][i][ij];
+        }else{ /* mobilav */
+          for(i=1; i<=nlstate;i++)
+            prlim[i][i]=mobaverage[(int)age][i][ij];
+        }
+      }
+      /* This for computing probability of death (h=1 means
+         computed over hstepm (estepm) matrices product = hstepm*stepm months)
+         as a weighted average of prlim.
+      */
+      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
+      for(j=nlstate+1;j<=nlstate+ndeath;j++){
+        for(i=1,gmp[j]=0.;i<= nlstate; i++)
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+      }
+      /* end probability of death */
+      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+        for(i=1; i<=nlstate;i++){
+          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+        }
+      }
+      fprintf(ficresprobmorprev,"\n");
+      fprintf(ficresvij,"%.0f ",age );
+      for(i=1; i<=nlstate;i++)
+        for(j=1; j<=nlstate;j++){
+          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+        }
+      fprintf(ficresvij,"\n");
+      free_matrix(gp,0,nhstepm,1,nlstate);
+      free_matrix(gm,0,nhstepm,1,nlstate);
+      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+    } /* End age */
+    free_vector(gpp,nlstate+1,nlstate+ndeath);
+    free_vector(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,"\nunset parametric;unset label; set ter png small size 320, 240"); */
+    fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
+    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+    fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
+    /*   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 lt 1 ",subdirf(fileresprobmorprev));
+    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
+    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
+    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <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.svg\"> <br>\n", stepm,YEARM,digitp,digit);
+     */
+    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
+    fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-   char fileresprobmorprev[FILENAMELENGTH];
+    free_vector(xp,1,npar);
+    free_matrix(doldm,1,nlstate,1,nlstate);
+    free_matrix(dnewm,1,nlstate,1,npar);
+    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+    fclose(ficresprobmorprev);
+    fflush(ficgp);
+    fflush(fichtm);
+  }  /* end varevsij */
-   if(popbased==1){
+ /************ Variance of prevlim ******************/
-     if(mobilav!=0)
+  void varprevlim(char fileresvpl[], FILE *ficresvpl, 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 *ncvyearp, int ij, char strstart[], int nres)
-       strcpy(digitp,"-populbased-mobilav-");
+ {
-     else strcpy(digitp,"-populbased-nomobil-");
+   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
-   }
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   else
-     strcpy(digitp,"-stablbased-");
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
-   }
-   strcpy(fileresprobmorprev,"prmorprev");
+   double **dnewmpar,**doldm;
-   sprintf(digit,"%-d",ij);
+   int i, j, nhstepm, hstepm;
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+   double *xp;
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   double *gp, *gm;
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+   double **gradg, **trgradg;
-   strcat(fileresprobmorprev,fileres);
+   double **mgm, **mgp;
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+   double age,agelim;
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+   int theta;
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   }
+   pstamp(ficresvpl);
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
+   fprintf(ficresvpl,"# Age ");
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   if(nresult >=1)
-   pstamp(ficresprobmorprev);
+     fprintf(ficresvpl," Result# ");
-   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-     fprintf(ficresprobmorprev," p.%-d SE",j);
-     for(i=1; i<=nlstate;i++)
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   }
-   fprintf(ficresprobmorprev,"\n");
-   fprintf(ficgp,"\n# Routine varevsij");
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
- /*   } */
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   pstamp(ficresvij);
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   if(popbased==1)
-     fprintf(ficresvij,"the age specific prevalence observed (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(ficresvpl," %1d-%1d",i,i);
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+   fprintf(ficresvpl,"\n");
-   fprintf(ficresvij,"\n");
    xp=vector(1,npar);
-   dnewm=matrix(1,nlstate,1,npar);
+   dnewmpar=matrix(1,nlstate,1,npar);
    doldm=matrix(1,nlstate,1,nlstate);
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-   gpp=vector(nlstate+1,nlstate+ndeath);
-   gmp=vector(nlstate+1,nlstate+ndeath);
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   if(estepm < stepm){
+   hstepm=1*YEARM; /* Every year of age */
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   }
+   agelim = AGESUP;
-   else  hstepm=estepm;
-   /* 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 function hpijx to understand why (it is linked to memory size questions) */
-   /* 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
-      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;
    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+     if (stepm >= YEARM) hstepm=1;
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+     gradg=matrix(1,npar,1,nlstate);
-     gp=matrix(0,nhstepm,1,nlstate);
+     mgp=matrix(1,npar,1,nlstate);
-     gm=matrix(0,nhstepm,1,nlstate);
+     mgm=matrix(1,npar,1,nlstate);
+     gp=vector(1,nlstate);
+     gm=vector(1,nlstate);
      for(theta=1; theta <=npar; theta++){
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+       for(i=1; i<=npar; i++){ /* Computes gradient */
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
+       /* else */
-       if (popbased==1) {
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
-         if(mobilav ==0){
+       for(i=1;i<=nlstate;i++){
-           for(i=1; i<=nlstate;i++)
+         gp[i] = prlim[i][i];
-             prlim[i][i]=probs[(int)age][i][ij];
+         mgp[theta][i] = prlim[i][i];
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
-       }
-       for(j=1; j<= nlstate; j++){
-         for(h=0; h<=nhstepm; h++){
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-         }
        }
-       /* This for computing probability of death (h=1 means
+       for(i=1; i<=npar; i++) /* Computes gradient */
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
-       */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
-       /* end probability of death */
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
+       /* else */
-       if (popbased==1) {
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
-         if(mobilav ==0){
+       for(i=1;i<=nlstate;i++){
-           for(i=1; i<=nlstate;i++)
+         gm[i] = prlim[i][i];
-             prlim[i][i]=probs[(int)age][i][ij];
+         mgm[theta][i] = prlim[i][i];
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
-       }
-       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];
-         }
-       }
-       /* This for computing probability of death (h=1 means
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
-       */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
-       /* end probability of death */
-       for(j=1; j<= nlstate; j++) /* vareij */
-         for(h=0; h<=nhstepm; h++){
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-         }
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
        }
+       for(i=1;i<=nlstate;i++)
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
      } /* End theta */
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+     trgradg =matrix(1,nlstate,1,npar);
-     for(h=0; h<=nhstepm; h++) /* veij */
-       for(j=1; j<=nlstate;j++)
-         for(theta=1; theta <=npar; theta++)
-           trgradg[h][j][theta]=gradg[h][theta][j];
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+     for(j=1; j<=nlstate;j++)
        for(theta=1; theta <=npar; theta++)
-         trgradgp[j][theta]=gradgp[theta][j];
+         trgradg[j][theta]=gradg[theta][j];
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\nmgm mgp %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf(" %d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\n gradg %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf("%d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf("%d %lf ",theta,gradg[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(i=1;i<=nlstate;i++)
-       for(j=1;j<=nlstate;j++)
+       varpl[i][(int)age] =0.;
-         vareij[i][j][(int)age] =0.;
+     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
-     for(h=0;h<=nhstepm;h++){
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
-       for(k=0;k<=nhstepm;k++){
+     }else{
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
-         for(i=1;i<=nlstate;i++)
-           for(j=1;j<=nlstate;j++)
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-       }
-     }
-     /* pptj */
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-         varppt[j][i]=doldmp[j][i];
-     /* end ppptj */
-     /*  x centered again */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-     if (popbased==1) {
-       if(mobilav ==0){
-         for(i=1; i<=nlstate;i++)
-           prlim[i][i]=probs[(int)age][i][ij];
-       }else{ /* mobilav */
-         for(i=1; i<=nlstate;i++)
-           prlim[i][i]=mobaverage[(int)age][i][ij];
-       }
      }
+     for(i=1;i<=nlstate;i++)
-     /* This for computing probability of death (h=1 means
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-        as a weighted average of prlim.
-     */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-     }
-     /* end probability of death */
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-       for(i=1; i<=nlstate;i++){
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-       }
-     }
-     fprintf(ficresprobmorprev,"\n");
-     fprintf(ficresvij,"%.0f ",age );
+     fprintf(ficresvpl,"%.0f ",age );
-     for(i=1; i<=nlstate;i++)
+     if(nresult >=1)
-       for(j=1; j<=nlstate;j++){
+       fprintf(ficresvpl,"%d ",nres );
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+     for(i=1; i<=nlstate;i++){
-       }
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-     fprintf(ficresvij,"\n");
+       /* for(j=1;j<=nlstate;j++) */
-     free_matrix(gp,0,nhstepm,1,nlstate);
+       /*        fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
-     free_matrix(gm,0,nhstepm,1,nlstate);
+     }
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+     fprintf(ficresvpl,"\n");
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+     free_vector(gp,1,nlstate);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     free_vector(gm,1,nlstate);
+     free_matrix(mgm,1,npar,1,nlstate);
+     free_matrix(mgp,1,npar,1,nlstate);
+     free_matrix(gradg,1,npar,1,nlstate);
+     free_matrix(trgradg,1,nlstate,1,npar);
    } /* End age */
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
-   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,"\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; 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 lt 1 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
- */
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    free_vector(xp,1,npar);
-   free_matrix(doldm,1,nlstate,1,nlstate);
+   free_matrix(doldm,1,nlstate,1,npar);
-   free_matrix(dnewm,1,nlstate,1,npar);
+   free_matrix(dnewmpar,1,nlstate,1,nlstate);
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fclose(ficresprobmorprev);
-   fflush(ficgp);
-   fflush(fichtm);
- }  /* end varevsij */
- /************ Variance of prevlim ******************/
+ }
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
+ /************ Variance of backprevalence limit ******************/
+  void varbrevlim(char fileresvbl[], FILE  *ficresvbl, double **varbpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **bprlim, double ftolpl, int mobilavproj, int *ncvyearp, int ij, char strstart[], int nres)
  {
-   /* Variance of prevalence limit */
+   /* Variance of backward prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   double **dnewm,**doldm;
+   double **dnewmpar,**doldm;
    int i, j, nhstepm, hstepm;
    double *xp;
    double *gp, *gm;
    double **gradg, **trgradg;
+   double **mgm, **mgp;
    double age,agelim;
    int theta;
-   pstamp(ficresvpl);
+   pstamp(ficresvbl);
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+   fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
-   fprintf(ficresvpl,"# Age");
+   fprintf(ficresvbl,"# Age ");
+   if(nresult >=1)
+     fprintf(ficresvbl," Result# ");
    for(i=1; i<=nlstate;i++)
-       fprintf(ficresvpl," %1d-%1d",i,i);
+       fprintf(ficresvbl," %1d-%1d",i,i);
-   fprintf(ficresvpl,"\n");
+   fprintf(ficresvbl,"\n");
    xp=vector(1,npar);
-   dnewm=matrix(1,nlstate,1,npar);
+   dnewmpar=matrix(1,nlstate,1,npar);
    doldm=matrix(1,nlstate,1,nlstate);
    hstepm=1*YEARM; /* Every year of age */
    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   agelim = AGESUP;
+   agelim = AGEINF;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   for (age=fage; age>=bage; age --){ /* If stepm=6 months */
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
      if (stepm >= YEARM) hstepm=1;
      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
      gradg=matrix(1,npar,1,nlstate);
+     mgp=matrix(1,npar,1,nlstate);
+     mgm=matrix(1,npar,1,nlstate);
      gp=vector(1,nlstate);
      gm=vector(1,nlstate);
- Line 3681  void varprevlim(char fileres[], double *
+ Line 7015  void varprevlim(char fileres[], double *
        for(i=1; i<=npar; i++){ /* Computes gradient */
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       if(mobilavproj > 0 )
-       for(i=1;i<=nlstate;i++)
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
-         gp[i] = prlim[i][i];
+       else
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
-       for(i=1; i<=npar; i++) /* Computes gradient */
+       for(i=1;i<=nlstate;i++){
+         gp[i] = bprlim[i][i];
+         mgp[theta][i] = bprlim[i][i];
+       }
+      for(i=1; i<=npar; i++) /* Computes gradient */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+        if(mobilavproj > 0 )
-       for(i=1;i<=nlstate;i++)
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
-         gm[i] = prlim[i][i];
+        else
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+       for(i=1;i<=nlstate;i++){
+         gm[i] = bprlim[i][i];
+         mgm[theta][i] = bprlim[i][i];
+       }
        for(i=1;i<=nlstate;i++)
          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
      } /* End theta */
      trgradg =matrix(1,nlstate,1,npar);
- Line 3700  void varprevlim(char fileres[], double *
+ Line 7043  void varprevlim(char fileres[], double *
      for(j=1; j<=nlstate;j++)
        for(theta=1; theta <=npar; theta++)
          trgradg[j][theta]=gradg[theta][j];
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\nmgm mgp %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf(" %d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\n gradg %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf("%d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf("%d %lf ",theta,gradg[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
      for(i=1;i<=nlstate;i++)
-       varpl[i][(int)age] =0.;
+       varbpl[i][(int)age] =0.;
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
+     }else{
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
+     }
      for(i=1;i<=nlstate;i++)
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+       varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-     fprintf(ficresvpl,"%.0f ",age );
+     fprintf(ficresvbl,"%.0f ",age );
+     if(nresult >=1)
+       fprintf(ficresvbl,"%d ",nres );
      for(i=1; i<=nlstate;i++)
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+       fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
-     fprintf(ficresvpl,"\n");
+     fprintf(ficresvbl,"\n");
      free_vector(gp,1,nlstate);
      free_vector(gm,1,nlstate);
+     free_matrix(mgm,1,npar,1,nlstate);
+     free_matrix(mgp,1,npar,1,nlstate);
      free_matrix(gradg,1,npar,1,nlstate);
      free_matrix(trgradg,1,nlstate,1,npar);
    } /* End age */
    free_vector(xp,1,npar);
    free_matrix(doldm,1,nlstate,1,npar);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   free_matrix(dnewmpar,1,nlstate,1,nlstate);
  }
  /************ 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, char strstart[])
- {
+  {
-   int i, j=0,  k1, l1, tj;
+    int i, j=0,  k1, l1, tj;
-   int k2, l2, j1,  z1;
+    int k2, l2, j1,  z1;
-   int k=0, l;
+    int k=0, l;
-   int first=1, first1, first2;
+    int first=1, first1, first2;
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+    int nres=0; /* New */
-   double **dnewm,**doldm;
+    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-   double *xp;
+    double **dnewm,**doldm;
-   double *gp, *gm;
+    double *xp;
-   double **gradg, **trgradg;
+    double *gp, *gm;
-   double **mu;
+    double **gradg, **trgradg;
-   double age, cov[NCOVMAX+1];
+    double **mu;
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+    double age, cov[NCOVMAX+1];
-   int theta;
+    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-   char fileresprob[FILENAMELENGTH];
+    int theta;
-   char fileresprobcov[FILENAMELENGTH];
+    char fileresprob[FILENAMELENGTH];
-   char fileresprobcor[FILENAMELENGTH];
+    char fileresprobcov[FILENAMELENGTH];
-   double ***varpij;
+    char fileresprobcor[FILENAMELENGTH];
+    double ***varpij;
-   strcpy(fileresprob,"prob");
-   strcat(fileresprob,fileres);
+    strcpy(fileresprob,"PROB_");
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+    strcat(fileresprob,fileres);
-     printf("Problem with resultfile: %s\n", fileresprob);
+    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+      printf("Problem with resultfile: %s\n", fileresprob);
-   }
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-   strcpy(fileresprobcov,"probcov");
+    }
-   strcat(fileresprobcov,fileres);
+    strcpy(fileresprobcov,"PROBCOV_");
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+    strcat(fileresprobcov,fileresu);
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+      printf("Problem with resultfile: %s\n", fileresprobcov);
-   }
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-   strcpy(fileresprobcor,"probcor");
+    }
-   strcat(fileresprobcor,fileres);
+    strcpy(fileresprobcor,"PROBCOR_");
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+    strcat(fileresprobcor,fileresu);
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+      printf("Problem with resultfile: %s\n", fileresprobcor);
-   }
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+    }
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+    printf("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,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   pstamp(ficresprob);
+    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+    pstamp(ficresprob);
-   fprintf(ficresprob,"# Age");
+    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-   pstamp(ficresprobcov);
+    fprintf(ficresprob,"# Age");
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+    pstamp(ficresprobcov);
-   fprintf(ficresprobcov,"# Age");
+    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-   pstamp(ficresprobcor);
+    fprintf(ficresprobcov,"# Age");
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+    pstamp(ficresprobcor);
-   fprintf(ficresprobcor,"# Age");
+    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+    fprintf(ficresprobcor,"# Age");
-   for(i=1; i<=nlstate;i++)
-     for(j=1; j<=(nlstate+ndeath);j++){
+    for(i=1; i<=nlstate;i++)
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+      for(j=1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+        fprintf(ficresprobcov," p%1d-%1d ",i,j);
-     }
+        fprintf(ficresprobcor," p%1d-%1d ",i,j);
-  /* fprintf(ficresprob,"\n");
+      }
-   fprintf(ficresprobcov,"\n");
+    /* fprintf(ficresprob,"\n");
-   fprintf(ficresprobcor,"\n");
+       fprintf(ficresprobcov,"\n");
-  */
+       fprintf(ficresprobcor,"\n");
-   xp=vector(1,npar);
+    */
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+    xp=vector(1,npar);
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-   first=1;
+    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-   fprintf(ficgp,"\n# Routine varprob");
+    first=1;
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+    fprintf(ficgp,"\n# Routine varprob");
-   fprintf(fichtm,"\n");
+    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+    fprintf(fichtm,"\n");
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s</li>\n",optionfilehtmcov,optionfilehtmcov);
-   file %s<br>\n",optionfilehtmcov);
+    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
  and drawn. It helps understanding how is the covariance between two incidences.\
   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
  standard deviations wide on each axis. <br>\
- Line 3814  standard deviations wide on each axis. <
+ Line 7184  standard deviations wide on each axis. <
   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");
-   cov[1]=1;
+    cov[1]=1;
-   /* tj=cptcoveff; */
+    /* tj=cptcoveff; */
-   tj = (int) pow(2,cptcoveff);
+    tj = (int) pow(2,cptcoveff);
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-   j1=0;
+    j1=0;
-   for(j1=1; j1<=tj;j1++){
-     /*for(i1=1; i1<=ncodemax[t];i1++){ */
+    for(nres=1;nres <=nresult; nres++){ /* For each resultline */
-     /*j1++;*/
+    for(j1=1; j1<=tj;j1++){ /* For any combination of dummy covariates, fixed and varying */
-       if  (cptcovn>0) {
+      printf("Varprob  TKresult[nres]=%d j1=%d, nres=%d, cptcovn=%d, cptcoveff=%d tj=%d cptcovs=%d\n",  TKresult[nres], j1, nres, cptcovn, cptcoveff, tj, cptcovs);
-         fprintf(ficresprob, "\n#********** Variable ");
+      if(tj != 1 && TKresult[nres]!= j1)
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+        continue;
-         fprintf(ficresprob, "**********\n#\n");
-         fprintf(ficresprobcov, "\n#********** Variable ");
+    /* for(j1=1; j1<=tj;j1++){  /\* For each valid combination of covariates or only once*\/ */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+      /* for(nres=1;nres <=1; nres++){ /\* For each resultline *\/ */
-         fprintf(ficresprobcov, "**********\n#\n");
+      /* /\* for(nres=1;nres <=nresult; nres++){ /\\* For each resultline *\\/ *\/ */
+      if  (cptcovn>0) {
-         fprintf(ficgp, "\n#********** Variable ");
+        fprintf(ficresprob, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+        fprintf(ficresprobcov, "\n#********** Variable ");
-         fprintf(ficgp, "**********\n#\n");
+        fprintf(ficgp, "\n#********** Variable ");
+        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+        fprintf(ficresprobcor, "\n#********** 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]]);
+        /* Including quantitative variables of the resultline to be done */
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+        for (z1=1; z1<=cptcovs; z1++){ /* Loop on each variable of this resultline  */
+          printf("Varprob modelresult[%d][%d]=%d model=%s \n",nres, z1, modelresult[nres][z1], model);
-         fprintf(ficresprobcor, "\n#********** Variable ");
+          fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=%s \n",nres, z1, modelresult[nres][z1], model);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+          /* fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=%s resultline[%d]=%s \n",nres, z1, modelresult[nres][z1], model, nres, resultline[nres]); */
-         fprintf(ficresprobcor, "**********\n#");
+          if(Dummy[modelresult[nres][z1]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to z1 in resultline  */
-       }
+            if(Fixed[modelresult[nres][z1]]==0){ /* Fixed referenced to model equation */
+              fprintf(ficresprob,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
-       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+              fprintf(ficresprobcov,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
-       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+              fprintf(ficgp,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
-       gp=vector(1,(nlstate)*(nlstate+ndeath));
+              fprintf(fichtmcov,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
-       gm=vector(1,(nlstate)*(nlstate+ndeath));
+              fprintf(ficresprobcor,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
-       for (age=bage; age<=fage; age ++){
+              fprintf(ficresprob,"fixed ");
-         cov[2]=age;
+              fprintf(ficresprobcov,"fixed ");
-         for (k=1; k<=cptcovn;k++) {
+              fprintf(ficgp,"fixed ");
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
+              fprintf(fichtmcov,"fixed ");
-                                                          * 1  1 1 1 1
+              fprintf(ficresprobcor,"fixed ");
-                                                          * 2  2 1 1 1
+            }else{
-                                                          * 3  1 2 1 1
+              fprintf(ficresprob,"varyi ");
-                                                          */
+              fprintf(ficresprobcov,"varyi ");
-           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
+              fprintf(ficgp,"varyi ");
-         }
+              fprintf(fichtmcov,"varyi ");
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+              fprintf(ficresprobcor,"varyi ");
-         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]]];
+          }else if(Dummy[modelresult[nres][z1]]==1){ /* Quanti variable */
+            /* For each selected (single) quantitative value */
+            fprintf(ficresprob," V%d=%lg ",Tvqresult[nres][z1],Tqresult[nres][z1]);
-         for(theta=1; theta <=npar; theta++){
+            if(Fixed[modelresult[nres][z1]]==0){ /* Fixed */
-           for(i=1; i<=npar; i++)
+              fprintf(ficresprob,"fixed ");
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+              fprintf(ficresprobcov,"fixed ");
+              fprintf(ficgp,"fixed ");
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+              fprintf(fichtmcov,"fixed ");
+              fprintf(ficresprobcor,"fixed ");
-           k=0;
+            }else{
-           for(i=1; i<= (nlstate); i++){
+              fprintf(ficresprob,"varyi ");
-             for(j=1; j<=(nlstate+ndeath);j++){
+              fprintf(ficresprobcov,"varyi ");
-               k=k+1;
+              fprintf(ficgp,"varyi ");
-               gp[k]=pmmij[i][j];
+              fprintf(fichtmcov,"varyi ");
-             }
+              fprintf(ficresprobcor,"varyi ");
-           }
+            }
+          }else{
-           for(i=1; i<=npar; i++)
+            printf("Error in varprob() Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=V%d cptcovs=%d, cptcoveff=%d \n", nres, z1, Dummy[modelresult[nres][z1]],nres,z1,modelresult[nres][z1],cptcovs, cptcoveff);  /* end if dummy  or quanti */
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+            fprintf(ficlog,"Error in varprob() Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=V%d cptcovs=%d, cptcoveff=%d \n", nres, z1, Dummy[modelresult[nres][z1]],nres,z1,modelresult[nres][z1],cptcovs, cptcoveff);  /* end if dummy  or quanti */
+            exit(1);
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+          }
-           k=0;
+        } /* End loop on variable of this resultline */
-           for(i=1; i<=(nlstate); i++){
+        /* for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); */
-             for(j=1; j<=(nlstate+ndeath);j++){
+        fprintf(ficresprob, "**********\n#\n");
-               k=k+1;
+        fprintf(ficresprobcov, "**********\n#\n");
-               gm[k]=pmmij[i][j];
+        fprintf(ficgp, "**********\n#\n");
-             }
+        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-           }
+        fprintf(ficresprobcor, "**********\n#");
+        if(invalidvarcomb[j1]){
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+          fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+          fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
-         }
+          continue;
+        }
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+      }
-           for(theta=1; theta <=npar; theta++)
+      gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-             trgradg[j][theta]=gradg[theta][j];
+      trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+      gp=vector(1,(nlstate)*(nlstate+ndeath));
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+      gm=vector(1,(nlstate)*(nlstate+ndeath));
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+      for (age=bage; age<=fage; age ++){ /* Fo each age we feed the model equation with covariates, using precov as in hpxij() ? */
+        cov[2]=age;
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+        if(nagesqr==1)
+          cov[3]= age*age;
-         k=0;
+        /* New code end of combination but for each resultline */
-         for(i=1; i<=(nlstate); i++){
+        for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
-           for(j=1; j<=(nlstate+ndeath);j++){
+          if(Typevar[k1]==1){ /* A product with age */
-             k=k+1;
+            cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
-             mu[k][(int) age]=pmmij[i][j];
+          }else{
-           }
+            cov[2+nagesqr+k1]=precov[nres][k1];
-         }
+          }
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+        }/* End of loop on model equation */
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+ /* Old code */
-             varpij[i][j][(int)age] = doldm[i][j];
+        /* /\* for (k=1; k<=cptcovn;k++) { *\/ */
+        /* /\*    cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; *\/ */
-         /*printf("\n%d ",(int)age);
+        /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only *\/ */
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+        /*        /\* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates *\/ */
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+        /*        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,TnsdVar[TvarsD[k]])]; */
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+        /*        /\*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*\//\* j1 1 2 3 4 */
-           }*/
+        /*                                                                   * 1  1 1 1 1 */
+        /*                                                                   * 2  2 1 1 1 */
-         fprintf(ficresprob,"\n%d ",(int)age);
+        /*                                                                   * 3  1 2 1 1 */
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+        /*                                                                   *\/ */
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+        /*        /\* nbcode[1][1]=0 nbcode[1][2]=1;*\/ */
+        /* } */
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+        /* /\* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 *\/ */
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+        /* /\* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] *\/ */
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+        /* /\*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; *\/ */
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+        /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+        /*        if(Dummy[Tage[k]]==2){ /\* dummy with age *\/ */
-         }
+        /*          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,TnsdVar[Tvar[Tage[k]]])]*cov[2]; */
-         i=0;
+        /*          /\* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
-         for (k=1; k<=(nlstate);k++){
+        /*        } else if(Dummy[Tage[k]]==3){ /\* quantitative with age *\/ */
-           for (l=1; l<=(nlstate+ndeath);l++){
+        /*          printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]); */
-             i++;
+        /*          /\* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\\* Using the mean of quantitative variable Tvar[Tage[k]] /\\* Tqresult[nres][k]; *\\/ *\/ */
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+        /*          /\* exit(1); *\/ */
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+        /*          /\* cov[++k1]=Tqresult[nres][k];  *\/ */
-             for (j=1; j<=i;j++){
+        /*        } */
-               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
+        /*        /\* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
-               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]));
+        /* for (k=1; k<=cptcovprod;k++){/\* For product without age *\/ */
-             }
+        /*        if(Dummy[Tvard[k][1]]==0){ */
-           }
+        /*          if(Dummy[Tvard[k][2]]==0){ */
-         }/* end of loop for state */
+        /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])]; */
-       } /* end of loop for age */
+        /*            /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
-       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+        /*          }else{ /\* Should we use the mean of the quantitative variables? *\/ */
-       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+        /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * Tqresult[nres][resultmodel[nres][k]]; */
-       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+        /*            /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; *\/ */
-       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+        /*          } */
+        /*        }else{ */
-       /* Confidence intervalle of pij  */
+        /*          if(Dummy[Tvard[k][2]]==0){ */
-       /*
+        /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][TnsdVar[Tvard[k][1]]]; */
-         fprintf(ficgp,"\nunset parametric;unset label");
+        /*            /\* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; *\/ */
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+        /*          }else{ */
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+        /*            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][TnsdVar[Tvard[k][1]]]*  Tqinvresult[nres][TnsdVar[Tvard[k][2]]]; */
-         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);
+        /*            /\* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\/ */
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+        /*          } */
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+        /*        } */
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+        /*        /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
-       */
+        /* } */
+ /* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+        for(theta=1; theta <=npar; theta++){
-       first1=1;first2=2;
+          for(i=1; i<=npar; i++)
-       for (k2=1; k2<=(nlstate);k2++){
+            xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
-           if(l2==k2) continue;
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-           j=(k2-1)*(nlstate+ndeath)+l2;
-           for (k1=1; k1<=(nlstate);k1++){
+          k=0;
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+          for(i=1; i<= (nlstate); i++){
-               if(l1==k1) continue;
+            for(j=1; j<=(nlstate+ndeath);j++){
-               i=(k1-1)*(nlstate+ndeath)+l1;
+              k=k+1;
-               if(i<=j) continue;
+              gp[k]=pmmij[i][j];
-               for (age=bage; age<=fage; age ++){
+            }
-                 if ((int)age %5==0){
+          }
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+          for(i=1; i<=npar; i++)
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+            xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-                   c12=cv12/sqrt(v1*v2);
+          k=0;
-                   /* Computing eigen value of matrix of covariance */
+          for(i=1; i<=(nlstate); i++){
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+            for(j=1; j<=(nlstate+ndeath);j++){
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+              k=k+1;
-                   if ((lc2 <0) || (lc1 <0) ){
+              gm[k]=pmmij[i][j];
-                     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);
-                     }
+          for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-                     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);
+            gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
+        }
-                     /* lc2=fabs(lc2); */
-                   }
-                   /* Eigen vectors */
+        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+          for(theta=1; theta <=npar; theta++)
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+            trgradg[j][theta]=gradg[theta][j];
-                   v21=(lc1-v1)/cv12*v11;
-                   v12=-v21;
+        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-                   v22=v11;
+        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-                   tnalp=v21/v11;
-                   if(first1==1){
+        pmij(pmmij,cov,ncovmodel,x,nlstate);
-                     first1=0;
-                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+        k=0;
-                   }
+        for(i=1; i<=(nlstate); i++){
-                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+          for(j=1; j<=(nlstate+ndeath);j++){
-                   /*printf(fignu*/
+            k=k+1;
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+            mu[k][(int) age]=pmmij[i][j];
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+          }
-                   if(first==1){
+        }
-                     first=0;
+        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-                     fprintf(ficgp,"\nset parametric;unset label");
+          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-                     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);
+            varpij[i][j][(int)age] = doldm[i][j];
-                     fprintf(ficgp,"\nset ter png small size 320, 240");
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+        /*printf("\n%d ",(int)age);
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+          printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+          fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-                             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(ficresprob,"\n%d ",(int)age);
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+        fprintf(ficresprobcov,"\n%d ",(int)age);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+        fprintf(ficresprobcor,"\n%d ",(int)age);
-                     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",\
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+          fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-                   }else{
+          fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-                     first=0;
+          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+        }
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+        i=0;
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+        for (k=1; k<=(nlstate);k++){
-                     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",\
+          for (l=1; l<=(nlstate+ndeath);l++){
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+            i++;
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-                   }/* if first */
+            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-                 } /* age mod 5 */
+            for (j=1; j<=i;j++){
-               } /* end loop age */
+              /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+              fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-               first=1;
+              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-             } /*l12 */
+            }
-           } /* k12 */
+          }
-         } /*l1 */
+        }/* end of loop for state */
-       }/* k1 */
+      } /* end of loop for age */
-       /* } /* loop covariates */
+      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-   }
+      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+      /* Confidence intervalle of pij  */
-   free_vector(xp,1,npar);
+      /*
-   fclose(ficresprob);
+        fprintf(ficgp,"\nunset parametric;unset label");
-   fclose(ficresprobcov);
+        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-   fclose(ficresprobcor);
+        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-   fflush(ficgp);
+        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);
-   fflush(fichtmcov);
+        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
- }
+        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+      */
+      /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+      first1=1;first2=2;
+      for (k2=1; k2<=(nlstate);k2++){
+        for (l2=1; l2<=(nlstate+ndeath);l2++){
+          if(l2==k2) continue;
+          j=(k2-1)*(nlstate+ndeath)+l2;
+          for (k1=1; k1<=(nlstate);k1++){
+            for (l1=1; l1<=(nlstate+ndeath);l1++){
+              if(l1==k1) continue;
+              i=(k1-1)*(nlstate+ndeath)+l1;
+              if(i<=j) continue;
+              for (age=bage; age<=fage; age ++){
+                if ((int)age %5==0){
+                  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+                  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                  mu1=mu[i][(int) age]/stepm*YEARM ;
+                  mu2=mu[j][(int) age]/stepm*YEARM;
+                  c12=cv12/sqrt(v1*v2);
+                  /* Computing eigen value of matrix of covariance */
+                  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                  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 */
+                  if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
+                    printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+                    fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+                    v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
+                  }else
+                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                  /*v21=sqrt(1.-v11*v11); *//* error */
+                  v21=(lc1-v1)/cv12*v11;
+                  v12=-v21;
+                  v22=v11;
+                  tnalp=v21/v11;
+                  if(first1==1){
+                    first1=0;
+                    printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                  }
+                  fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                  /*printf(fignu*/
+                  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+                  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+                  if(first==1){
+                    first=0;
+                    fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
+                    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 svg size 640, 480");
+                    fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
+ %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
+                            subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
+                            subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+                    fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",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.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
+                            mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
+                            mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
+                  }else{
+                    first=0;
+                    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                    fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
+                            mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)),   \
+                            mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
+                  }/* if first */
+                } /* age mod 5 */
+              } /* end loop age */
+              fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+              first=1;
+            } /*l12 */
+          } /* k12 */
+        } /*l1 */
+      }/* k1 */
+    }  /* loop on combination of covariates j1 */
+    } /* loop on nres */
+    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+    free_vector(xp,1,npar);
+    fclose(ficresprob);
+    fclose(ficresprobcov);
+    fclose(ficresprobcor);
+    fflush(ficgp);
+    fflush(fichtmcov);
+  }
  /******************* Printing html file ***********/
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+ void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-                   int popforecast, int estepm ,\
+                   int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
-                   double jprev1, double mprev1,double anprev1, \
+                   double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
-                   double jprev2, double mprev2,double anprev2){
+                   double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
-   int jj1, k1, i1, cpt;
+   int jj1, k1, i1, cpt, k4, nres;
+   /* In fact some results are already printed in fichtm which is open */
     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
  </ul>");
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+ /*    fprintf(fichtm,"<ul><li> model=1+age+%s\n \ */
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+ /* </ul>", model); */
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
+    fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
+    fprintf(fichtm,"<li> - Observed prevalence (cross-sectional prevalence) in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
+    fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
     fprintf(fichtm,"\
   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+            stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
     fprintf(fichtm,"\
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+            stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
     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): \
+  - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-    <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     fprintf(fichtm,"\
-  - Population projections by age and states: \
+  - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+            subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
+    fprintf(fichtm,"\
+  - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . 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(fileresu,"E_"),subdirf2(fileresu,"E_"));
+    if(prevfcast==1){
+      fprintf(fichtm,"\
+  - Prevalence projections by age and states:                            \
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
+    }
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-  m=pow(2,cptcoveff);
+    m=pow(2,cptcoveff);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-  jj1=0;
+    fprintf(fichtm," \n<ul><li><b>Graphs (first order)</b></li><p>");
-  for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+    jj1=0;
+    fprintf(fichtm," \n<ul>");
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+      /* k1=nres; */
+      k1= TKresult[nres];
+    /* for(k1=1; k1<=m;k1++){ /\* For each combination of covariate *\/ */
+    /*   if(m != 1 && TKresult[nres]!= k1) */
+    /*     continue; */
       jj1++;
       if (cptcovn > 0) {
+        fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
+        for (cpt=1; cpt<=cptcovs;cpt++){ /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
+          fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
+        }
+        /* for (cpt=1; cpt<=cptcoveff;cpt++){  */
+        /*        fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]); */
+        /* } */
+        /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+        /*        fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+        /* } */
+        fprintf(fichtm,"\">");
+        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
+        fprintf(fichtm,"************ Results for covariates");
+        for (cpt=1; cpt<=cptcovs;cpt++){
+          fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
+        }
+        /* fprintf(fichtm,"************ Results for covariates"); */
+        /* for (cpt=1; cpt<=cptcoveff;cpt++){  */
+        /*        fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]); */
+        /* } */
+        /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+        /*        fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+        /* } */
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
+          continue;
+        }
+        fprintf(fichtm,"</a></li>");
+      } /* cptcovn >0 */
+    }
+    fprintf(fichtm," \n</ul>");
+    jj1=0;
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+      /* k1=nres; */
+      k1= TKresult[nres];
+    /* for(k1=1; k1<=m;k1++){ /\* For each combination of covariate *\/ */
+    /*   if(m != 1 && TKresult[nres]!= k1) */
+    /*     continue; */
+      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
+      jj1++;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"\n<p><a name=\"rescov");
+        for (cpt=1; cpt<=cptcovs;cpt++){
+          fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
+        }
+        /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+        /*        fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+        /* } */
+        fprintf(fichtm,"\"</a>");
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+        for (cpt=1; cpt<=cptcovs;cpt++){
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+          fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+          printf(" V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
+          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
+          /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
+        }
+        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
+        fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
+          printf("\nCombination (%d) ignored because no cases \n",k1);
+          continue;
+        }
       }
+      /* aij, bij */
+      fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
+ <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
       /* Pij */
-      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> \
+      fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
- <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ <img src=\"%s_%d-2-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
       /* Quasi-incidences */
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+      fprintf(fichtm,"<br>\n- I<sub>ij</sub> 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: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
- <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
-        /* Period (stable) prevalence in each health state */
+ divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-%d.svg</a><br> \
+ <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
+      /* Survival functions (period) in state j */
+      for(cpt=1; cpt<=nlstate;cpt++){
+        fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
+      }
+      /* State specific survival functions (period) */
+      for(cpt=1; cpt<=nlstate;cpt++){
+        fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
+  And probability to be observed in various states (up to %d) being in state %d at different ages.       \
+  <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> ", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
+      }
+      /* Period (forward stable) prevalence in each health state */
+      for(cpt=1; cpt<=nlstate;cpt++){
+        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"P_"),subdirf2(optionfilefiname,"P_"));
+       fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
+      }
+      if(prevbcast==1){
+        /* Backward prevalence in each health state */
         for(cpt=1; cpt<=nlstate;cpt++){
-          fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
+          fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
- <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+ <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
         }
+      }
+      if(prevfcast==1){
+        /* Projection of prevalence up to period (forward stable) prevalence in each health state */
+        for(cpt=1; cpt<=nlstate;cpt++){
+          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+          fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
+          fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",
+                  subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+        }
+      }
+      if(prevbcast==1){
+       /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
+        for(cpt=1; cpt<=nlstate;cpt++){
+          fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
+  from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
+  account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
+ with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+          fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
+          fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+        }
+      }
       for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
- <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\"> %s.txt</a>)\n<br>",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
       }
-    } /* end i1 */
+      /* } /\* end i1 *\/ */
-  }/* End k1 */
+    }/* End k1=nres */
-  fprintf(fichtm,"</ul>");
+    fprintf(fichtm,"</ul>");
+    fprintf(fichtm,"\
-  fprintf(fichtm,"\
  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
+  - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
+ But because parameters are usually highly correlated (a higher incidence of disability \
+ and a higher incidence of recovery can give very close observed transition) it might \
+ be very useful to look not only at linear confidence intervals estimated from the \
+ variances but at the covariance matrix. And instead of looking at the estimated coefficients \
+ (parameters) of the logistic regression, it might be more meaningful to visualize the \
+ covariance matrix of the one-step probabilities. \
+ See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+    fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+            subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+            subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+            subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
-  fprintf(fichtm,"\
+    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"));
+            estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
-  fprintf(fichtm,"\
+    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"));
+            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
-  fprintf(fichtm,"\
+    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",
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the forward (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"));
+            estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
-  fprintf(fichtm,"\
+    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"));
+            estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+  - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+            subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
- Line 4158  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 7770  fprintf(fichtm," \n<ul><li><b>Graphs</b>
  /*      <br>",fileres,fileres,fileres,fileres); */
  /*  else  */
  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
-  fflush(fichtm);
+    fflush(fichtm);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+    m=pow(2,cptcoveff);
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    fprintf(fichtm," <ul><li><b>Graphs (second order)</b></li><p>");
-  m=pow(2,cptcoveff);
+   jj1=0;
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-  jj1=0;
+    fprintf(fichtm," \n<ul>");
-  for(k1=1; k1<=m;k1++){
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-    for(i1=1; i1<=ncodemax[k1];i1++){
+      /* k1=nres; */
+      k1= TKresult[nres];
+      /* for(k1=1; k1<=m;k1++){ /\* For each combination of covariate *\/ */
+      /* if(m != 1 && TKresult[nres]!= k1) */
+      /*   continue; */
       jj1++;
       if (cptcovn > 0) {
+        fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescovsecond");
+        for (cpt=1; cpt<=cptcovs;cpt++){
+          fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
+        }
+        fprintf(fichtm,"\">");
+        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
+        fprintf(fichtm,"************ Results for covariates");
+        for (cpt=1; cpt<=cptcovs;cpt++){
+          fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
+        }
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
+          continue;
+        }
+        fprintf(fichtm,"</a></li>");
+      } /* cptcovn >0 */
+    } /* End nres */
+    fprintf(fichtm," \n</ul>");
+    jj1=0;
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+      /* k1=nres; */
+      k1= TKresult[nres];
+      /* for(k1=1; k1<=m;k1++){ */
+      /* if(m != 1 && TKresult[nres]!= k1) */
+      /*   continue; */
+      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
+      jj1++;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"\n<p><a name=\"rescovsecond");
+        for (cpt=1; cpt<=cptcovs;cpt++){
+          fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
+        }
+        fprintf(fichtm,"\"</a>");
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+        for (cpt=1; cpt<=cptcovs;cpt++){  /**< cptcoveff number of variables */
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+          fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+          printf(" V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
-      }
+          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
+        }
+        fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
+          continue;
+        }
+      } /* If cptcovn >0 */
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+        fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
- prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
+ prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
- <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+        fprintf(fichtm," (data from text file  <a href=\"%s\">%s</a>)\n <br>",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
       }
       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) \
+ health expectancies in each live states (1 to %d). 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>\
+  observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+      fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
-    } /* end i1 */
+      fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);
-  }/* End k1 */
+      /* } /\* end i1 *\/ */
-  fprintf(fichtm,"</ul>");
+   }/* End nres */
-  fflush(fichtm);
+    fprintf(fichtm,"</ul>");
+    fflush(fichtm);
  }
  /******************* Gnuplot file **************/
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+ void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){
    char dirfileres[132],optfileres[132];
-   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+   char gplotcondition[132], gplotlabel[132];
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
+   int lv=0, vlv=0, kl=0;
    int ng=0;
+   int vpopbased;
+   int ioffset; /* variable offset for columns */
+   int iyearc=1; /* variable column for year of projection  */
+   int iagec=1; /* variable column for age of projection  */
+   int nres=0; /* Index of resultline */
+   int istart=1; /* For starting graphs in projections */
  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
- Line 4204  void printinggnuplot(char fileres[], cha
+ Line 7880  void printinggnuplot(char fileres[], cha
    /*#ifdef windows */
    fprintf(ficgp,"cd \"%s\" \n",pathc);
-     /*#endif */
+   /*#endif */
    m=pow(2,cptcoveff);
+   /* diagram of the model */
+   fprintf(ficgp,"\n#Diagram of the model \n");
+   fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
+   fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
+   fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+   fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0)  ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+   fprintf(ficgp,"\n#show arrow\nunset label\n");
+   fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+   fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0.  font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
+   fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
+   fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
+   fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
+   /* Contribution to likelihood */
+   /* Plot the probability implied in the likelihood */
+   fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
+   /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
+   fprintf(ficgp,"\nset ter pngcairo size 640, 480");
+ /* nice for mle=4 plot by number of matrix products.
+    replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
+ /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
+   /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
+   fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
+   fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
+   fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
+   fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
+   for (i=1; i<= nlstate ; i ++) {
+     fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
+     fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
+     fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
+     for (j=2; j<= nlstate+ndeath ; j ++) {
+       fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
+     }
+     fprintf(ficgp,";\nset out; unset ylabel;\n");
+   }
+   /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
+   /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
+   /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
+   fprintf(ficgp,"\nset out;unset log\n");
+   /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
-  /* 1eme*/
+   /* 1eme*/
-   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
+   for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+     /* for (k1=1; k1<= m ; k1 ++){ /\* For each valid combination of covariate *\/ */
-     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+         k1=TKresult[nres];
-      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
+         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+         /* if(m != 1 && TKresult[nres]!= k1) */
- set ylabel \"Probability\" \n\
+         /*   continue; */
- set ter png small size 320, 240\n\
+         /* We are interested in selected combination by the resultline */
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
+         fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
-      for (i=1; i<= nlstate ; i ++) {
+         strcpy(gplotlabel,"(");
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-        else        fprintf(ficgp," \%%*lf (\%%*lf)");
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-      }
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-      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 ++) {
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate k get corresponding value lv for combination k1 *\/ */
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the value of the covariate corresponding to k1 combination *\\/ *\/ */
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+         /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
-      }
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
-      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+         /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
-      for (i=1; i<= nlstate ; i ++) {
+         /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         /*   vlv= nbcode[Tvaraff[k]][lv]; /\* vlv is the value of the covariate lv, 0 or 1 *\/ */
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+         /*   /\* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv *\/ */
-      }
+         /*   /\* printf(" V%d=%d ",Tvaraff[k],vlv); *\/ */
-      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+         /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
-    }
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
-   }
+         /* } */
-   /*2 eme*/
+         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
-   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
+         /*   /\* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); *\/ */
-   for (k1=1; k1<= m ; k1 ++) {
+         /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
-     for (i=1; i<= nlstate+1 ; i ++) {
+         /* printf("\n#\n"); */
-       k=2*i;
+         fprintf(ficgp,"\n#\n");
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+         if(invalidvarcomb[k1]){
-       for (j=1; j<= nlstate+1 ; j ++) {
+           /*k1=k1-1;*/ /* To be checked */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+           continue;
-       }
+         }
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+         fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
-       for (j=1; j<= nlstate+1 ; j ++) {
+         /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
-       }
+         /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
-       fprintf(ficgp,"\" t\"\" w l lt 0,");
+       /* k1-1 error should be nres-1*/
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+         for (i=1; i<= nlstate ; i ++) {
-       for (j=1; j<= nlstate+1 ; j ++) {
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+           else        fprintf(ficgp," %%*lf (%%*lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         }
-       }
+         fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+         for (i=1; i<= nlstate ; i ++) {
-       else fprintf(ficgp,"\" t\"\" w l lt 0,");
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-     }
+           else fprintf(ficgp," %%*lf (%%*lf)");
-   }
+         }
+         fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
-   /*3eme*/
+         for (i=1; i<= nlstate ; i ++) {
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
+         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
+         if(cptcoveff ==0){
+           fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3",      2+3*(cpt-1),  cpt );
+         }else{
+           kl=0;
+           for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
+             /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
+             lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
+             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+             vlv= nbcode[Tvaraff[k]][lv];
+             kl++;
+             /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+             if(k==cptcoveff){
+               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
++cptcoveff*2+3*(cpt-1),  cpt );  /* 4 or 6 ?*/
+             }else{
+               fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
+               kl++;
+             }
+           } /* end covariate */
+         } /* end if no covariate */
+         if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
+           fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
+           if(cptcoveff ==0){
+             fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3",    2+(cpt-1),  cpt );
+           }else{
+             kl=0;
+             for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
+               /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
+               lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
+               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+               /* vlv= nbcode[Tvaraff[k]][lv]; */
+               vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
+               kl++;
+               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+               if(k==cptcoveff){
+                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
++cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
+               }else{
+                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]);
+                 kl++;
+               }
+             } /* end covariate */
+           } /* end if no covariate */
+           if(prevbcast == 1){
+             fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+             /* k1-1 error should be nres-1*/
+             for (i=1; i<= nlstate ; i ++) {
+               if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+               else        fprintf(ficgp," %%*lf (%%*lf)");
+             }
+             fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+             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 lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+             for (i=1; i<= nlstate ; i ++) {
+               if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+               else fprintf(ficgp," %%*lf (%%*lf)");
+             }
+             fprintf(ficgp,"\" t\"\" w l lt 4");
+           } /* end if backprojcast */
+         } /* end if prevbcast */
+         /* fprintf(ficgp,"\nset out ;unset label;\n"); */
+         fprintf(ficgp,"\nset out ;unset title;\n");
+       } /* nres */
+     /* } /\* k1 *\/ */
+   } /* cpt */
-   for (k1=1; k1<= m ; k1 ++) {
+   /*2 eme*/
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+   /* for (k1=1; k1<= m ; k1 ++){   */
-       /*       k=2+nlstate*(2*cpt-2); */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       k=2+(nlstate+1)*(cpt-1);
+       k1=TKresult[nres];
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+       /* if(m != 1 && TKresult[nres]!= k1) */
-       fprintf(ficgp,"set ter png small size 320, 240\n\
+       /*        continue; */
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+       strcpy(gplotlabel,"(");
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+       for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+         fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+       /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+       /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
+       /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
+       /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
+       /*        /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
+       /*        /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
+       /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
+       /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
+       /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
+       /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
+       /* } */
+       /* /\* for(k=1; k <= ncovds; k++){ *\/ */
+       /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+       /*        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+       /*        fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+       /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+       }
+       strcpy(gplotlabel+strlen(gplotlabel),")");
+       fprintf(ficgp,"\n#\n");
+       if(invalidvarcomb[k1]){
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         continue;
+       }
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
+       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+         fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
+         if(vpopbased==0){
+           fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
+         }else
+           fprintf(ficgp,"\nreplot ");
+         for (i=1; i<= nlstate+1 ; i ++) {
+           k=2*i;
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
+           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 lt %d, \\\n",i);
+           else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
+           for (j=1; j<= nlstate+1 ; j ++) {
+             if (j==i) fprintf(ficgp," %%lf (%%lf)");
+             else fprintf(ficgp," %%*lf (%%*lf)");
+           }
+           fprintf(ficgp,"\" t\"\" w l lt 0,");
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
+           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 lt 0");
+           else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
+         } /* state */
+       } /* vpopbased */
+       fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
+     } /* end nres */
+   /* } /\* k1 end 2 eme*\/ */
-       */
-       for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+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);*/
-       }
+   /*3eme*/
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+   /* for (k1=1; k1<= m ; k1 ++){ */
-     }
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-   }
+       k1=TKresult[nres];
+       /* if(m != 1 && TKresult[nres]!= k1) */
-   /* CV preval stable (period) */
+       /*        continue; */
-   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+       for (cpt=1; cpt<= nlstate ; cpt ++) { /* Fragile no verification of covariate values */
-       k=3;
+         fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
-       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
+         strcpy(gplotlabel,"(");
-       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
+         /*   lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
+         /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
+         /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
+         /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
+         /* } */
+         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+         /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]); */
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         /*       k=2+nlstate*(2*cpt-2); */
+         k=2+(nlstate+1)*(cpt-1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
+         fprintf(ficgp,"set ter svg size 640, 480\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
+         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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);
+         */
+         for (i=1; i< nlstate ; i ++) {
+           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-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(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
+       }
+       fprintf(ficgp,"\nunset label;\n");
+     } /* end nres */
+   /* } /\* end kl 3eme *\/ */
+   /* 4eme */
+   /* Survival functions (period) from state i in state j by initial state i */
+   /* for (k1=1; k1<=m; k1++){    /\* For each covariate and each value *\/ */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       k1=TKresult[nres];
+       /* if(m != 1 && TKresult[nres]!= k1) */
+       /*        continue; */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n# Survival functions in state %d : 'LIJ_' files, cov=%d state=%d", cpt, k1, cpt);
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
+         /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
+         /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
+         /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
+         /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
+         /* } */
+         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+         /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3;
+         for (i=1; i<= nlstate ; i ++){
+           if(i==1){
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           }else{
+             fprintf(ficgp,", '' ");
+           }
+           l=(nlstate+ndeath)*(i-1)+1;
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+           for (j=2; j<= nlstate+ndeath ; j ++)
+             fprintf(ficgp,"+$%d",k+l+j-1);
+           fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+         } /* nlstate */
+         fprintf(ficgp,"\nset out; unset label;\n");
+       } /* end cpt state*/
+     } /* end nres */
+   /* } /\* end covariate k1 *\/   */
+ /* 5eme */
+   /* Survival functions (period) from state i in state j by final state j */
+   /* for (k1=1; k1<= m ; k1++){ /\* For each covariate combination if any *\/ */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       k1=TKresult[nres];
+       /* if(m != 1 && TKresult[nres]!= k1) */
+       /*        continue; */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
+         /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
+         /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
+         /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
+         /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
+         /* } */
+         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+         /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3;
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           if(j==1)
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           else
+             fprintf(ficgp,", '' ");
+           l=(nlstate+ndeath)*(cpt-1) +j;
+           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+           /* for (i=2; i<= nlstate+ndeath ; i ++) */
+           /*   fprintf(ficgp,"+$%d",k+l+i-1); */
+           fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+         } /* nlstate */
+         fprintf(ficgp,", '' ");
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           l=(nlstate+ndeath)*(cpt-1) +j;
+           if(j < nlstate)
+             fprintf(ficgp,"$%d +",k+l);
+           else
+             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+         }
+         fprintf(ficgp,"\nset out; unset label;\n");
+       } /* end cpt state*/
+     /* } /\* end covariate *\/   */
+   } /* end nres */
+ /* 6eme */
+   /* CV preval stable (period) for each covariate */
+   /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+      k1=TKresult[nres];
+      /* if(m != 1 && TKresult[nres]!= k1) */
+      /*  continue; */
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
+       strcpy(gplotlabel,"(");
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
+       for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+         fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+       /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
+       /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
+       /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
+       /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
+       /*        /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
+       /*        /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
+       /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
+       /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
+       /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
+       /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
+       /* } */
+       /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+       /*        fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+       /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+       }
+       strcpy(gplotlabel+strlen(gplotlabel),")");
+       fprintf(ficgp,"\n#\n");
+       if(invalidvarcomb[k1]){
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         continue;
+       }
+       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
+       fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- set ter png small size 320, 240\n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- unset log y\n\
+       k=3; /* Offset */
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+       for (i=1; i<= nlstate ; i ++){ /* State of origin */
-       for (i=1; i<= nlstate ; i ++){
          if(i==1)
-           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
          else
            fprintf(ficgp,", '' ");
-         l=(nlstate+ndeath)*(i-1)+1;
+         l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-         for (j=1; j<= (nlstate-1) ; j ++)
+         for (j=2; j<= nlstate ; j ++)
-           fprintf(ficgp,"+$%d",k+l+j);
+           fprintf(ficgp,"+$%d",k+l+j-1);
          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
        } /* nlstate */
-       fprintf(ficgp,"\n");
+       fprintf(ficgp,"\nset out; unset label;\n");
      } /* end cpt state*/
    } /* end covariate */
-   /* proba elementaires */
+ /* 7eme */
+   if(prevbcast == 1){
+     /* CV backward prevalence  for each covariate */
+     /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       k1=TKresult[nres];
+       /* if(m != 1 && TKresult[nres]!= k1) */
+       /*        continue; */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
+         /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
+         /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
+         /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
+         /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
+         /* } */
+         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+         /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3; /* Offset */
+         for (i=1; i<= nlstate ; i ++){ /* State of arrival */
+           if(i==1)
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
+           else
+             fprintf(ficgp,", '' ");
+           /* l=(nlstate+ndeath)*(i-1)+1; */
+           l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
+           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
+           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
+           /* for (j=2; j<= nlstate ; j ++) */
+           /*    fprintf(ficgp,"+$%d",k+l+j-1); */
+           /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
+           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
+         } /* nlstate */
+         fprintf(ficgp,"\nset out; unset label;\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if prevbcast */
+   /* 8eme */
+   if(prevfcast==1){
+     /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
+     /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       k1=TKresult[nres];
+       /* if(m != 1 && TKresult[nres]!= k1) */
+       /*        continue; */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
+         /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
+         /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
+         /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
+         /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
+         /* } */
+         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+         /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+         /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
+         istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
+         /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
+         for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
+           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           if(i==istart){
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
+           }else{
+             fprintf(ficgp,",\\\n '' ");
+           }
+           if(cptcoveff ==0){ /* No covariate */
+             ioffset=2; /* Age is in 2 */
+             /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             fprintf(ficgp," u %d:(", ioffset);
+             if(i==nlstate+1){
+               fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ",        \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",ioffset);
+               fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
+                      offyear,                           \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate );
+             }else
+               fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+           }else{ /* more than 2 covariates */
+             ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
+             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+             iyearc=ioffset-1;
+             iagec=ioffset;
+             fprintf(ficgp," u %d:(",ioffset);
+             kl=0;
+             strcpy(gplotcondition,"(");
+             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
+               /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
+               lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
+               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+               /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
+               vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
+               kl++;
+               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+               kl++;
+               if(k <cptcoveff && cptcoveff>1)
+                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
+             }
+             strcpy(gplotcondition+strlen(gplotcondition),")");
+             /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+             if(i==nlstate+1){
+               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",iagec);
+               fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
+                       iyearc, iagec, offyear,                           \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
+ /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
+             }else{
+               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+             }
+           } /* end if covariate */
+         } /* nlstate */
+         fprintf(ficgp,"\nset out; unset label;\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if prevfcast */
+   if(prevbcast==1){
+     /* Back projection from cross-sectional to stable (mixed) for each covariate */
+     /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+      k1=TKresult[nres];
+        /* if(m != 1 && TKresult[nres]!= k1) */
+        /*       continue; */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
+         /*   lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
+         /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
+         /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
+         /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
+         /* } */
+         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+         /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+         /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
+         istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
+         /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
+         for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
+           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           if(i==istart){
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
+           }else{
+             fprintf(ficgp,",\\\n '' ");
+           }
+           if(cptcoveff ==0){ /* No covariate */
+             ioffset=2; /* Age is in 2 */
+             /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             fprintf(ficgp," u %d:(", ioffset);
+             if(i==nlstate+1){
+               fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",ioffset);
+               fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
+                      offbyear,                          \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
+             }else
+               fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ",      \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
+           }else{ /* more than 2 covariates */
+             ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
+             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+             iyearc=ioffset-1;
+             iagec=ioffset;
+             fprintf(ficgp," u %d:(",ioffset);
+             kl=0;
+             strcpy(gplotcondition,"(");
+             for (k=1; k<=cptcovs; k++){    /* For each covariate k of the resultline, get corresponding value lv for combination k1 */
+               if(Dummy[Tvresult[nres][k]]==0){  /* To be verified */
+                 /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate writing the chain of conditions *\/ */
+                 /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
+                 /* lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
+                 lv=Tvresult[nres][k];
+                 vlv=TinvDoQresult[nres][Tvresult[nres][k]];
+                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+                 /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
+                 /* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
+                 kl++;
+                 /* sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); */
+                 sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%lg " ,kl,Tvresult[nres][k], kl+1,TinvDoQresult[nres][Tvresult[nres][k]]);
+                 kl++;
+                 if(k <cptcoveff && cptcoveff>1)
+                   sprintf(gplotcondition+strlen(gplotcondition)," && ");
+               }
+             }
+             strcpy(gplotcondition+strlen(gplotcondition),")");
+             /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+             if(i==nlstate+1){
+               fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",iagec);
+               /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
+               fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
+                       iyearc,iagec,offbyear,                            \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
+ /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
+             }else{
+               /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
+               fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
+             }
+           } /* end if covariate */
+         } /* nlstate */
+         fprintf(ficgp,"\nset out; unset label;\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if prevbcast */
+   /* 9eme writing MLE parameters */
+   fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
    for(i=1,jk=1; i <=nlstate; i++){
+     fprintf(ficgp,"# initial state %d\n",i);
      for(k=1; k <=(nlstate+ndeath); k++){
        if (k != i) {
+         fprintf(ficgp,"#   current state %d\n",k);
          for(j=1; j <=ncovmodel; j++){
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
            jk++;
-           fprintf(ficgp,"\n");
          }
+         fprintf(ficgp,"\n");
        }
      }
-    }
+   }
+   fprintf(ficgp,"##############\n#\n");
    /*goto avoid;*/
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+   /* 10eme Graphics of probabilities or incidences using written MLE parameters */
-      for(jk=1; jk <=m; jk++) {
+   fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
-        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
-        if (ng==2)
+   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
-        else
+   fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+   fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
-        i=1;
+   fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-        for(k2=1; k2<=nlstate; k2++) {
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
-          k3=i;
+   fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
-          for(k=1; k<=(nlstate+ndeath); k++) {
+   fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-            if (k != k2){
+   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
-              if(ng==2)
+   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+   fprintf(ficgp,"#\n");
-              else
+   for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
-              ij=1;/* To be checked else nbcode[0][0] wrong */
+     fprintf(ficgp,"#model=%s \n",model);
-              for(j=3; j <=ncovmodel; j++) {
+     fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
-                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
+     fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
-                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
+     /* for(k1=1; k1 <=m; k1++)  /\* For each combination of covariate *\/ */
-                /*        ij++; */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-                /* } */
+      /* k1=nres; */
-                /* else */
+       k1= TKresult[nres];
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+       fprintf(ficgp,"\n\n# Resultline k1=%d ",k1);
-              }
+       strcpy(gplotlabel,"(");
-              fprintf(ficgp,")/(1");
+       /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
+       for (k=1; k<=cptcovs; k++){  /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
-              for(k1=1; k1 <=nlstate; k1++){
+         /* for each resultline nres, and position k, Tvresult[nres][k] gives the name of the variable and
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+            TinvDoQresult[nres][Tvresult[nres][k]] gives its value double or integer) */
-                ij=1;
+         fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-                for(j=3; j <=ncovmodel; j++){
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-                  /* 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]]]); */
+       /* if(m != 1 && TKresult[nres]!= k1) */
-                  /*   ij++; */
+       /*        continue; */
-                  /* } */
+       /* fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1); */
-                  /* else */
+       /* strcpy(gplotlabel,"("); */
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+       /* /\*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*\/ */
-                }
+       /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
-                fprintf(ficgp,")");
+       /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
-              }
+       /*        lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+       /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+       /*        /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
-              i=i+ncovmodel;
+       /*        /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
-            }
+       /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
-          } /* end k */
+       /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
-        } /* end k2 */
+       /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
-      } /* end jk */
+       /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
-    } /* end ng */
+       /* } */
-  /* avoid: */
+       /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
-    fflush(ficgp);
+       /*        fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+       /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+       /* }       */
+       strcpy(gplotlabel+strlen(gplotlabel),")");
+       fprintf(ficgp,"\n#\n");
+       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
+       fprintf(ficgp,"\nset key outside ");
+       /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
+       fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
+       fprintf(ficgp,"\nset ter svg size 640, 480 ");
+       if (ng==1){
+         fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
+         fprintf(ficgp,"\nunset log y");
+       }else if (ng==2){
+         fprintf(ficgp,"\nset ylabel \"Probability\"\n");
+         fprintf(ficgp,"\nset log y");
+       }else if (ng==3){
+         fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+         fprintf(ficgp,"\nset log y");
+       }else
+         fprintf(ficgp,"\nunset title ");
+       fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+       i=1;
+       for(k2=1; k2<=nlstate; k2++) {
+         k3=i;
+         for(k=1; k<=(nlstate+ndeath); k++) {
+           if (k != k2){
+             switch( ng) {
+             case 1:
+               if(nagesqr==0)
+                 fprintf(ficgp," p%d+p%d*x",i,i+1);
+               else /* nagesqr =1 */
+                 fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
+               break;
+             case 2: /* ng=2 */
+               if(nagesqr==0)
+                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+               else /* nagesqr =1 */
+                 fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
+               break;
+             case 3:
+               if(nagesqr==0)
+                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+               else /* nagesqr =1 */
+                 fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
+               break;
+             }
+             ij=1;/* To be checked else nbcode[0][0] wrong */
+             ijp=1; /* product no age */
+             /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
+             for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
+               /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
+               switch(Typevar[j]){
+               case 1:
+                 if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
+                   if(j==Tage[ij]) { /* Product by age  To be looked at!!*//* Bug valgrind */
+                     if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
+                       if(DummyV[j]==0){/* Bug valgrind */
+                         fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
+                       }else{ /* quantitative */
+                         fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
+                         /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                       }
+                       ij++;
+                     }
+                   }
+                 }
+                 break;
+               case 2:
+                 if(cptcovprod >0){
+                   if(j==Tprod[ijp]) { /* */
+                     /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
+                     if(ijp <=cptcovprod) { /* Product */
+                       if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
+                         if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
+                           /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
+                           fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
+                         }else{ /* Vn is dummy and Vm is quanti */
+                           /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
+                           fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                         }
+                       }else{ /* Vn*Vm Vn is quanti */
+                         if(DummyV[Tvard[ijp][2]]==0){
+                           fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
+                         }else{ /* Both quanti */
+                           fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                         }
+                       }
+                       ijp++;
+                     }
+                   } /* end Tprod */
+                 }
+                 break;
+               case 0:
+                 /* simple covariate */
+                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
+                 if(Dummy[j]==0){
+                   fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
+                 }else{ /* quantitative */
+                   fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
+                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                 }
+                /* end simple */
+                 break;
+               default:
+                 break;
+               } /* end switch */
+             } /* end j */
+           }else{ /* k=k2 */
+             if(ng !=1 ){ /* For logit formula of log p11 is more difficult to get */
+               fprintf(ficgp," (1.");i=i-ncovmodel;
+             }else
+               i=i-ncovmodel;
+           }
+           if(ng != 1){
+             fprintf(ficgp,")/(1");
+             for(cpt=1; cpt <=nlstate; cpt++){
+               if(nagesqr==0)
+                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
+               else /* nagesqr =1 */
+                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
+               ij=1;
+               ijp=1;
+               /* for(j=3; j <=ncovmodel-nagesqr; j++){ */
+               for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
+                 switch(Typevar[j]){
+                 case 1:
+                   if(cptcovage >0){
+                     if(j==Tage[ij]) { /* Bug valgrind */
+                       if(ij <=cptcovage) { /* Bug valgrind */
+                         if(DummyV[j]==0){/* Bug valgrind */
+                           /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); */
+                           /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,nbcode[Tvar[j]][codtabm(k1,j)]); */
+                           fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]);
+                           /* fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; */
+                           /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                         }else{ /* quantitative */
+                           /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */
+                           fprintf(ficgp,"+p%d*%f*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
+                           /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */
+                           /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                         }
+                         ij++;
+                       }
+                     }
+                   }
+                   break;
+                 case 2:
+                   if(cptcovprod >0){
+                     if(j==Tprod[ijp]) { /* */
+                       /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
+                       if(ijp <=cptcovprod) { /* Product */
+                         if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
+                           if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
+                             /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
+                             fprintf(ficgp,"+p%d*%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
+                             /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); */
+                           }else{ /* Vn is dummy and Vm is quanti */
+                             /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
+                             fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                             /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
+                           }
+                         }else{ /* Vn*Vm Vn is quanti */
+                           if(DummyV[Tvard[ijp][2]]==0){
+                             fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
+                             /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); */
+                           }else{ /* Both quanti */
+                             fprintf(ficgp,"+p%d*%f*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                             /* fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
+                           }
+                         }
+                         ijp++;
+                       }
+                     } /* end Tprod */
+                   } /* end if */
+                   break;
+                 case 0:
+                   /* simple covariate */
+                   /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
+                   if(Dummy[j]==0){
+                     /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\*  *\/ */
+                     fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]); /*  */
+                     /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\*  *\/ */
+                   }else{ /* quantitative */
+                     fprintf(ficgp,"+p%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* */
+                     /* fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* *\/ */
+                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                   }
+                   /* end simple */
+                   /* fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/\* Valgrind bug nbcode *\/ */
+                   break;
+                 default:
+                   break;
+                 } /* end switch */
+               }
+               fprintf(ficgp,")");
+             }
+             fprintf(ficgp,")");
+             if(ng ==2)
+               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
+             else /* ng= 3 */
+               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
+           }else{ /* end ng <> 1 */
+             if( k !=k2) /* logit p11 is hard to draw */
+               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
+           }
+           if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
+             fprintf(ficgp,",");
+           if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
+             fprintf(ficgp,",");
+           i=i+ncovmodel;
+         } /* end k */
+       } /* end k2 */
+       /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
+       fprintf(ficgp,"\n set out; unset title;set key default;\n");
+     } /* end resultline */
+   } /* end ng */
+   /* avoid: */
+   fflush(ficgp);
  }  /* end gnuplot */
  /*************** Moving average **************/
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+ /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
+  int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
+    int i, cpt, cptcod;
+    int modcovmax =1;
+    int mobilavrange, mob;
+    int iage=0;
+    int firstA1=0, firstA2=0;
+    double sum=0., sumr=0.;
+    double age;
+    double *sumnewp, *sumnewm, *sumnewmr;
+    double *agemingood, *agemaxgood;
+    double *agemingoodr, *agemaxgoodr;
+    /* modcovmax=2*cptcoveff;  Max number of modalities. We suppose  */
+    /*              a covariate has 2 modalities, should be equal to ncovcombmax   */
+    sumnewp = vector(1,ncovcombmax);
+    sumnewm = vector(1,ncovcombmax);
+    sumnewmr = vector(1,ncovcombmax);
+    agemingood = vector(1,ncovcombmax);
+    agemingoodr = vector(1,ncovcombmax);
+    agemaxgood = vector(1,ncovcombmax);
+    agemaxgoodr = vector(1,ncovcombmax);
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+      sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
+      sumnewp[cptcod]=0.;
+      agemingood[cptcod]=0, agemingoodr[cptcod]=0;
+      agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
+    }
+    if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
+    if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+      if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
+      else mobilavrange=mobilav;
+      for (age=bage; age<=fage; age++)
+        for (i=1; i<=nlstate;i++)
+          for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
+            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+      /* We keep the original values on the extreme ages bage, fage and for
+         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+         we use a 5 terms etc. until the borders are no more concerned.
+      */
+      for (mob=3;mob <=mobilavrange;mob=mob+2){
+        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+          for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+            sumnewm[cptcod]=0.;
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+              for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+              }
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+              sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+            } /* end i */
+            if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
+          } /* end cptcod */
+        }/* end age */
+      }/* end mob */
+    }else{
+      printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
+      return -1;
+    }
-   int i, cpt, cptcod;
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
-   int modcovmax =1;
+      /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
-   int mobilavrange, mob;
+      if(invalidvarcomb[cptcod]){
-   double age;
+        printf("\nCombination (%d) ignored because no cases \n",cptcod);
+        continue;
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+      }
-                            a covariate has 2 modalities */
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+      for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
+        sumnewm[cptcod]=0.;
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+        sumnewmr[cptcod]=0.;
-     if(mobilav==1) mobilavrange=5; /* default */
+        for (i=1; i<=nlstate;i++){
-     else mobilavrange=mobilav;
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
-     for (age=bage; age<=fage; age++)
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
-       for (i=1; i<=nlstate;i++)
+        }
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+        if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+          agemingoodr[cptcod]=age;
-     /* We keep the original values on the extreme ages bage, fage and for
+        }
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
-        we use a 5 terms etc. until the borders are no more concerned.
+            agemingood[cptcod]=age;
-     */
+        }
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+      } /* age */
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+      for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
-         for (i=1; i<=nlstate;i++){
+        sumnewm[cptcod]=0.;
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+        sumnewmr[cptcod]=0.;
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+        for (i=1; i<=nlstate;i++){
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+        }
-               }
+        if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+          agemaxgoodr[cptcod]=age;
-           }
+        }
-         }
+        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
-       }/* end age */
+          agemaxgood[cptcod]=age;
-     }/* end mob */
+        }
-   }else return -1;
+      } /* age */
-   return 0;
+      /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
- }/* End movingaverage */
+      /* but they will change */
+      firstA1=0;firstA2=0;
+      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
+        sumnewm[cptcod]=0.;
+        sumnewmr[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
+        }
+        if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
+          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
+            agemaxgoodr[cptcod]=age;  /* age min */
+            for (i=1; i<=nlstate;i++)
+              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+          }else{ /* bad we change the value with the values of good ages */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }else{
+          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+            agemaxgood[cptcod]=age;
+          }else{ /* bad we change the value with the values of good ages */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }/* end else */
+        sum=0.;sumr=0.;
+        for (i=1; i<=nlstate;i++){
+          sum+=mobaverage[(int)age][i][cptcod];
+          sumr+=probs[(int)age][i][cptcod];
+        }
+        if(fabs(sum - 1.) > 1.e-3) { /* bad */
+          if(!firstA1){
+            firstA1=1;
+            printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
+          }
+          fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
+        } /* end bad */
+        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
+        if(fabs(sumr - 1.) > 1.e-3) { /* bad */
+          if(!firstA2){
+            firstA2=1;
+            printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
+          }
+          fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
+        } /* end bad */
+      }/* age */
+      for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
+        sumnewm[cptcod]=0.;
+        sumnewmr[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
+        }
+        if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
+          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
+            agemingoodr[cptcod]=age;
+            for (i=1; i<=nlstate;i++)
+              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+          }else{ /* bad we change the value with the values of good ages */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }else{
+          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+            agemingood[cptcod]=age;
+          }else{ /* bad */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }/* end else */
+        sum=0.;sumr=0.;
+        for (i=1; i<=nlstate;i++){
+          sum+=mobaverage[(int)age][i][cptcod];
+          sumr+=mobaverage[(int)age][i][cptcod];
+        }
+        if(fabs(sum - 1.) > 1.e-3) { /* bad */
+          printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
+        } /* end bad */
+        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
+        if(fabs(sumr - 1.) > 1.e-3) { /* bad */
+          printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage);
+        } /* end bad */
+      }/* age */
+      for (age=bage; age<=fage; age++){
+        /* printf("%d %d ", cptcod, (int)age); */
+        sumnewp[cptcod]=0.;
+        sumnewm[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewp[cptcod]+=probs[(int)age][i][cptcod];
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
+        }
+        /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
+      }
+      /* printf("\n"); */
+      /* } */
+      /* brutal averaging */
+      /* for (i=1; i<=nlstate;i++){ */
+      /*   for (age=1; age<=bage; age++){ */
+      /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+      /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
+      /*   }      */
+      /*   for (age=fage; age<=AGESUP; age++){ */
+      /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
+      /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
+      /*   } */
+      /* } /\* end i status *\/ */
+      /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
+      /*   for (age=1; age<=AGESUP; age++){ */
+      /*          /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
+      /*          mobaverage[(int)age][i][cptcod]=0.; */
+      /*   } */
+      /* } */
+    }/* end cptcod */
+    free_vector(agemaxgoodr,1, ncovcombmax);
+    free_vector(agemaxgood,1, ncovcombmax);
+    free_vector(agemingood,1, ncovcombmax);
+    free_vector(agemingoodr,1, ncovcombmax);
+    free_vector(sumnewmr,1, ncovcombmax);
+    free_vector(sumnewm,1, ncovcombmax);
+    free_vector(sumnewp,1, ncovcombmax);
+    return 0;
+  }/* End movingaverage */
  /************** Forecasting ******************/
- prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+ /* void prevforecast(char fileres[], double dateintmean, double anprojd, double mprojd, double jprojd, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anprojf, double p[], int cptcoveff)*/
-   /* proj1, year, month, day of starting projection
+ void prevforecast(char fileres[], double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
+   /* dateintemean, mean date of interviews
+      dateprojd, year, month, day of starting projection
+      dateprojf date of end of projection;year of end of projection (same day and month as proj1).
       agemin, agemax range of age
       dateprev1 dateprev2 range of dates during which prevalence is computed
-      anproj2 year of en of projection (same day and month as proj1).
    */
-   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
+   /* double anprojd, mprojd, jprojd; */
+   /* double anprojf, mprojf, jprojf; */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
    double agec; /* generic age */
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double agelim, ppij, yp,yp1,yp2;
    double *popeffectif,*popcount;
    double ***p3mat;
-   double ***mobaverage;
+   /* double ***mobaverage; */
    char fileresf[FILENAMELENGTH];
    agelim=AGESUP;
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, 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.
+   */
+   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
+   /*          firstpass, lastpass,  stepm,  weightopt, model); */
-   strcpy(fileresf,"f");
+   strcpy(fileresf,"F_");
-   strcat(fileresf,fileres);
+   strcat(fileresf,fileresu);
    if((ficresf=fopen(fileresf,"w"))==NULL) {
      printf("Problem with forecast resultfile: %s\n", fileresf);
      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
    }
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+   fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
    if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
-   }
    stepsize=(int) (stepm+YEARM-1)/YEARM;
    if (stepm<=12) stepsize=1;
    if(estepm < stepm){
      printf ("Problem %d lower than %d\n",estepm, stepm);
    }
-   else  hstepm=estepm;
+   else{
+     hstepm=estepm;
+   }
+   if(estepm > stepm){ /* Yes every two year */
+     stepsize=2;
+   }
+   hstepm=hstepm/stepm;
-   hstepm=hstepm/stepm;
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+   /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
-                                fractional in yp1 */
+   /*                              fractional in yp1 *\/ */
-   anprojmean=yp;
+   /* aintmean=yp; */
-   yp2=modf((yp1*12),&yp);
+   /* yp2=modf((yp1*12),&yp); */
-   mprojmean=yp;
+   /* mintmean=yp; */
-   yp1=modf((yp2*30.5),&yp);
+   /* yp1=modf((yp2*30.5),&yp); */
-   jprojmean=yp;
+   /* jintmean=yp; */
-   if(jprojmean==0) jprojmean=1;
+   /* if(jintmean==0) jintmean=1; */
-   if(mprojmean==0) jprojmean=1;
+   /* if(mintmean==0) mintmean=1; */
+   /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
+   /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
+   /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
+   i1=pow(2,cptcoveff);
+   if (cptcovn < 1){i1=1;}
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
+ /*            if (h==(int)(YEARM*yearp)){ */
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){ /* We want to find the combination k corresponding to the values of the dummies given in this resut line (to be cleaned one day) */
+     if(i1 != 1 && TKresult[nres]!= k)
+       continue;
+     if(invalidvarcomb[k]){
+       printf("\nCombination (%d) projection ignored because no cases \n",k);
+       continue;
+     }
+     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
+     for(j=1;j<=cptcoveff;j++) {
+       /* fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); */
+       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+     }
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+     }
+     fprintf(ficresf," yearproj age");
+     for(j=1; j<=nlstate+ndeath;j++){
+       for(i=1; i<=nlstate;i++)
+         fprintf(ficresf," p%d%d",i,j);
+       fprintf(ficresf," wp.%d",j);
+     }
+     for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
+       fprintf(ficresf,"\n");
+       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
+       /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
+       for (agec=fage; agec>=(bage); agec--){
+         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+         nhstepm = nhstepm/hstepm;
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
+         /* We compute pii at age agec over nhstepm);*/
+         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
+         /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
+         for (h=0; h<=nhstepm; h++){
+           if (h*hstepm/YEARM*stepm ==yearp) {
+             break;
+           }
+         }
+         fprintf(ficresf,"\n");
+         for(j=1;j<=cptcoveff;j++)
+           /* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Tvaraff not correct *\/ */
+           fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /* TnsdVar[Tvaraff]  correct */
+         fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
+         for(j=1; j<=nlstate+ndeath;j++) {
+           ppij=0.;
+           for(i=1; i<=nlstate;i++) {
+             if (mobilav>=1)
+              ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
+             else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
+                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
+             }
+             fprintf(ficresf," %.3f", p3mat[i][j][h]);
+           } /* end i */
+           fprintf(ficresf," %.3f", ppij);
+         }/* end j */
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       } /* end agec */
+       /* diffyear=(int) anproj1+yearp-ageminpar-1; */
+       /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
+     } /* end yearp */
+   } /* end  k */
+   fclose(ficresf);
+   printf("End of Computing forecasting \n");
+   fprintf(ficlog,"End of Computing forecasting\n");
+ }
+ /************** Back Forecasting ******************/
+  /* void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
+  void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
+   /* back1, year, month, day of starting backprojection
+      agemin, agemax range of age
+      dateprev1 dateprev2 range of dates during which prevalence is computed
+      anback2 year of end of backprojection (same day and month as back1).
+      prevacurrent and prev are prevalences.
+   */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
+   double agec; /* generic age */
+   double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
+   double *popeffectif,*popcount;
+   double ***p3mat;
+   /* double ***mobaverage; */
+   char fileresfb[FILENAMELENGTH];
+   agelim=AGEINF;
+   /* 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.
+   */
+   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
+   /*          firstpass, lastpass,  stepm,  weightopt, model); */
+   /*Do we need to compute prevalence again?*/
-   i1=cptcoveff;
+   /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+   strcpy(fileresfb,"FB_");
+   strcat(fileresfb,fileresu);
+   if((ficresfb=fopen(fileresfb,"w"))==NULL) {
+     printf("Problem with back forecast resultfile: %s\n", fileresfb);
+     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
+   }
+   printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
+   fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else{
+     hstepm=estepm;
+   }
+   if(estepm >= stepm){ /* Yes every two year */
+     stepsize=2;
+   }
+   hstepm=hstepm/stepm;
+   /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
+   /*                              fractional in yp1 *\/ */
+   /* aintmean=yp; */
+   /* yp2=modf((yp1*12),&yp); */
+   /* mintmean=yp; */
+   /* yp1=modf((yp2*30.5),&yp); */
+   /* jintmean=yp; */
+   /* if(jintmean==0) jintmean=1; */
+   /* if(mintmean==0) jintmean=1; */
+   i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
+   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
+   for(k=1; k<=i1;k++){
+     if(i1 != 1 && TKresult[nres]!= k)
+       continue;
+     if(invalidvarcomb[k]){
+       printf("\nCombination (%d) projection ignored because no cases \n",k);
+       continue;
+     }
+     fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
+     for(j=1;j<=cptcoveff;j++) {
+       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+     }
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+     }
+     fprintf(ficresfb," yearbproj age");
+     for(j=1; j<=nlstate+ndeath;j++){
+       for(i=1; i<=nlstate;i++)
+         fprintf(ficresfb," b%d%d",i,j);
+       fprintf(ficresfb," b.%d",j);
+     }
+     for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
+       /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
+       fprintf(ficresfb,"\n");
+       fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
+       /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
+       /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */
+       for (agec=bage; agec<=fage; agec++){  /* testing */
+         /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
+         nhstepm=(int) (agec-agelim) *YEARM/stepm;/*     nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
+         nhstepm = nhstepm/hstepm;
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
+         /* computes hbxij at age agec over 1 to nhstepm */
+         /* printf("####prevbackforecast debug  agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
+         hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
+         /* hpxij(p3mat,nhstepm,agec,hstepm,p,             nlstate,stepm,oldm,savm, k,nres); */
+         /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
+         /* printf(" agec=%.2f\n",agec);fflush(stdout); */
+         for (h=0; h<=nhstepm; h++){
+           if (h*hstepm/YEARM*stepm ==-yearp) {
+             break;
+           }
+         }
+         fprintf(ficresfb,"\n");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+         fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
+         for(i=1; i<=nlstate+ndeath;i++) {
+           ppij=0.;ppi=0.;
+           for(j=1; j<=nlstate;j++) {
+             /* if (mobilav==1) */
+             ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
+             ppi=ppi+prevacurrent[(int)agec][j][k];
+             /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
+             /* ppi=ppi+mobaverage[(int)agec][j][k]; */
+               /* else { */
+               /*        ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
+               /* } */
+             fprintf(ficresfb," %.3f", p3mat[i][j][h]);
+           } /* end j */
+           if(ppi <0.99){
+             printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
+             fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
+           }
+           fprintf(ficresfb," %.3f", ppij);
+         }/* end j */
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       } /* end agec */
+     } /* end yearp */
+   } /* end k */
+   /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+   fclose(ficresfb);
+   printf("End of Computing Back forecasting \n");
+   fprintf(ficlog,"End of Computing Back forecasting\n");
+ }
- /*            if (h==(int)(YEARM*yearp)){ */
+ /* Variance of prevalence limit: varprlim */
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+  void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+     /*------- Variance of forward period (stable) prevalence------*/
-       k=k+1;
-       fprintf(ficresf,"\n#******");
+    char fileresvpl[FILENAMELENGTH];
-       for(j=1;j<=cptcoveff;j++) {
+    FILE *ficresvpl;
-         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+    double **oldm, **savm;
-       }
+    double **varpl; /* Variances of prevalence limits by age */
-       fprintf(ficresf,"******\n");
+    int i1, k, nres, j ;
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-       for(j=1; j<=nlstate+ndeath;j++){
+     strcpy(fileresvpl,"VPL_");
-         for(i=1; i<=nlstate;i++)
+     strcat(fileresvpl,fileresu);
-           fprintf(ficresf," p%d%d",i,j);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-         fprintf(ficresf," p.%d",j);
+       printf("Problem with variance of forward period (stable) prevalence  resultfile: %s\n", fileresvpl);
-       }
+       exit(0);
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+     }
-         fprintf(ficresf,"\n");
+     printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+     fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     i1=pow(2,cptcoveff);
+     if (cptcovn < 1){i1=1;}
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+        k=TKresult[nres];
-           nhstepm = nhstepm/hstepm;
+      /* for(k=1; k<=i1;k++){ /\* We find the combination equivalent to result line values of dummies *\/ */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       if(i1 != 1 && TKresult[nres]!= k)
-           oldm=oldms;savm=savms;
+         continue;
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+       fprintf(ficresvpl,"\n#****** ");
+       printf("\n#****** ");
-           for (h=0; h<=nhstepm; h++){
+       fprintf(ficlog,"\n#****** ");
-             if (h*hstepm/YEARM*stepm ==yearp) {
+       for(j=1;j<=cptcovs;j++) {
-               fprintf(ficresf,"\n");
+         fprintf(ficresvpl,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-               for(j=1;j<=cptcoveff;j++)
+         fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+         /* fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-             }
+         /* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-             for(j=1; j<=nlstate+ndeath;j++) {
+       }
-               ppij=0.;
+       /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
-               for(i=1; i<=nlstate;i++) {
+       /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
-                 if (mobilav==1)
+       /*        fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+       /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
-                 else {
+       /* }       */
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+       fprintf(ficresvpl,"******\n");
-                 }
+       printf("******\n");
-                 if (h*hstepm/YEARM*stepm== yearp) {
+       fprintf(ficlog,"******\n");
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-                 }
+       varpl=matrix(1,nlstate,(int) bage, (int) fage);
-               } /* end i */
+       oldm=oldms;savm=savms;
-               if (h*hstepm/YEARM*stepm==yearp) {
+       varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
-                 fprintf(ficresf," %.3f", ppij);
+       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
-               }
+       /*}*/
-             }/* end j */
+     }
-           } /* end h */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     fclose(ficresvpl);
-         } /* end agec */
+     printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
-       } /* end yearp */
+     fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
-     } /* end cptcod */
-   } /* end  cptcov */
+  }
+ /* Variance of back prevalence: varbprlim */
+  void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
+       /*------- Variance of back (stable) prevalence------*/
+    char fileresvbl[FILENAMELENGTH];
+    FILE  *ficresvbl;
+    double **oldm, **savm;
+    double **varbpl; /* Variances of back prevalence limits by age */
+    int i1, k, nres, j ;
+    strcpy(fileresvbl,"VBL_");
+    strcat(fileresvbl,fileresu);
+    if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
+      printf("Problem with variance of back (stable) prevalence  resultfile: %s\n", fileresvbl);
+      exit(0);
+    }
+    printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
+    fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
+    i1=pow(2,cptcoveff);
+    if (cptcovn < 1){i1=1;}
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+      k=TKresult[nres];
+     /* for(k=1; k<=i1;k++){ */
+     /*    if(i1 != 1 && TKresult[nres]!= k) */
+     /*   continue; */
+        fprintf(ficresvbl,"\n#****** ");
+        printf("\n#****** ");
+        fprintf(ficlog,"\n#****** ");
+        for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value */
+          printf(" V%d=%lg ",Tvqresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
+          fprintf(ficresvbl," V%d=%lg ",Tvqresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
+          fprintf(ficlog," V%d=%lg ",Tvqresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
+        /* for(j=1;j<=cptcoveff;j++) { */
+        /*        fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+        /*        fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+        /*        printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+        /* } */
+        /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
+        /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+        /*        fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+        /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+        }
+        fprintf(ficresvbl,"******\n");
+        printf("******\n");
+        fprintf(ficlog,"******\n");
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+        varbpl=matrix(1,nlstate,(int) bage, (int) fage);
+        oldm=oldms;savm=savms;
+        varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
+        free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
+        /*}*/
+      }
+    fclose(ficresvbl);
+    printf("done variance-covariance of back prevalence\n");fflush(stdout);
+    fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
-   fclose(ficresf);
+  } /* End of varbprlim */
- }
  /************** Forecasting *****not tested NB*************/
- populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+ /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-   int *popage;
-   double calagedatem, agelim, kk1, kk2;
-   double *popeffectif,*popcount;
-   double ***p3mat,***tabpop,***tabpopprev;
-   double ***mobaverage;
-   char filerespop[FILENAMELENGTH];
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   agelim=AGESUP;
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
-   strcpy(filerespop,"pop");
+ /*   int *popage; */
-   strcat(filerespop,fileres);
+ /*   double calagedatem, agelim, kk1, kk2; */
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+ /*   double *popeffectif,*popcount; */
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+ /*   double ***p3mat,***tabpop,***tabpopprev; */
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+ /*   /\* double ***mobaverage; *\/ */
-   }
+ /*   char filerespop[FILENAMELENGTH]; */
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+ /*   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   agelim=AGESUP; */
+ /*   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
+ /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+ /*   strcpy(filerespop,"POP_");  */
+ /*   strcat(filerespop,fileresu); */
+ /*   if((ficrespop=fopen(filerespop,"w"))==NULL) { */
+ /*     printf("Problem with forecast resultfile: %s\n", filerespop); */
+ /*     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
+ /*   } */
+ /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
+ /*   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+ /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
-   if (mobilav!=0) {
+ /*   /\* if (mobilav!=0) { *\/ */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+ /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+ /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
-     }
+ /*   /\*   } *\/ */
-   }
+ /*   /\* } *\/ */
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+ /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
-   if (stepm<=12) stepsize=1;
+ /*   if (stepm<=12) stepsize=1; */
-   agelim=AGESUP;
-   hstepm=1;
+ /*   agelim=AGESUP; */
-   hstepm=hstepm/stepm;
-   if (popforecast==1) {
+ /*   hstepm=1; */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+ /*   hstepm=hstepm/stepm;  */
-       printf("Problem with population file : %s\n",popfile);exit(0);
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+ /*   if (popforecast==1) { */
-     }
+ /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
-     popage=ivector(0,AGESUP);
+ /*       printf("Problem with population file : %s\n",popfile);exit(0); */
-     popeffectif=vector(0,AGESUP);
+ /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
-     popcount=vector(0,AGESUP);
+ /*     }  */
+ /*     popage=ivector(0,AGESUP); */
+ /*     popeffectif=vector(0,AGESUP); */
+ /*     popcount=vector(0,AGESUP); */
-     i=1;
+ /*     i=1;    */
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+ /*     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
-     imx=i;
+ /*     imx=i; */
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+ /*     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
-   }
+ /*   } */
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+ /*   for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+ /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
-       k=k+1;
+ /*       k=k+1; */
-       fprintf(ficrespop,"\n#******");
+ /*       fprintf(ficrespop,"\n#******"); */
-       for(j=1;j<=cptcoveff;j++) {
+ /*       for(j=1;j<=cptcoveff;j++) { */
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ /*      fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
-       }
+ /*       } */
-       fprintf(ficrespop,"******\n");
+ /*       fprintf(ficrespop,"******\n"); */
-       fprintf(ficrespop,"# Age");
+ /*       fprintf(ficrespop,"# Age"); */
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+ /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+ /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
-       for (cpt=0; cpt<=0;cpt++) {
+ /*       for (cpt=0; cpt<=0;cpt++) {  */
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+ /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+ /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
-           nhstepm = nhstepm/hstepm;
+ /*        nhstepm = nhstepm/hstepm;  */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
-           oldm=oldms;savm=savms;
+ /*        oldm=oldms;savm=savms; */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+ /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
-           for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedatem+YEARM*cpt)) {
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-             }
-             for(j=1; j<=nlstate+ndeath;j++) {
-               kk1=0.;kk2=0;
-               for(i=1; i<=nlstate;i++) {
-                 if (mobilav==1)
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-                 else {
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-                 }
-               }
-               if (h==(int)(calagedatem+12*cpt)){
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-                   /*fprintf(ficrespop," %.3f", kk1);
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-               }
-             }
-             for(i=1; i<=nlstate;i++){
-               kk1=0.;
-                 for(j=1; j<=nlstate;j++){
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-                 }
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-             }
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
-       }
-   /******/
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-           nhstepm = nhstepm/hstepm;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        for (h=0; h<=nhstepm; h++){ */
-           oldm=oldms;savm=savms;
+ /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+ /*            fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
-           for (h=0; h<=nhstepm; h++){
+ /*          }  */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+ /*          for(j=1; j<=nlstate+ndeath;j++) { */
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+ /*            kk1=0.;kk2=0; */
-             }
+ /*            for(i=1; i<=nlstate;i++) {               */
-             for(j=1; j<=nlstate+ndeath;j++) {
+ /*              if (mobilav==1)  */
-               kk1=0.;kk2=0;
+ /*                kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
-               for(i=1; i<=nlstate;i++) {
+ /*              else { */
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+ /*                kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
-               }
+ /*              } */
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+ /*            } */
-             }
+ /*            if (h==(int)(calagedatem+12*cpt)){ */
-           }
+ /*              tabpop[(int)(agedeb)][j][cptcod]=kk1; */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*              /\*fprintf(ficrespop," %.3f", kk1); */
-         }
+ /*                if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
-       }
+ /*            } */
-    }
+ /*          } */
-   }
+ /*          for(i=1; i<=nlstate;i++){ */
+ /*            kk1=0.; */
+ /*            for(j=1; j<=nlstate;j++){ */
+ /*              kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  */
+ /*            } */
+ /*            tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
+ /*          } */
+ /*          if (h==(int)(calagedatem+12*cpt)) */
+ /*            for(j=1; j<=nlstate;j++)  */
+ /*              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
+ /*        } */
+ /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+ /*      } */
+ /*       } */
+ /*       /\******\/ */
+ /*       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  */
+ /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
+ /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
+ /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
+ /*        nhstepm = nhstepm/hstepm;  */
+ /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+ /*        oldm=oldms;savm=savms; */
+ /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
+ /*        for (h=0; h<=nhstepm; h++){ */
+ /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
+ /*            fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
+ /*          }  */
+ /*          for(j=1; j<=nlstate+ndeath;j++) { */
+ /*            kk1=0.;kk2=0; */
+ /*            for(i=1; i<=nlstate;i++) {               */
+ /*              kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
+ /*            } */
+ /*            if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
+ /*          } */
+ /*        } */
+ /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+ /*      } */
+ /*       } */
+ /*     }  */
+ /*   } */
+ /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
+ /*   if (popforecast==1) { */
+ /*     free_ivector(popage,0,AGESUP); */
+ /*     free_vector(popeffectif,0,AGESUP); */
+ /*     free_vector(popcount,0,AGESUP); */
+ /*   } */
+ /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   fclose(ficrespop); */
+ /* } /\* End of popforecast *\/ */
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   if (popforecast==1) {
-     free_ivector(popage,0,AGESUP);
-     free_vector(popeffectif,0,AGESUP);
-     free_vector(popcount,0,AGESUP);
-   }
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fclose(ficrespop);
- } /* End of popforecast */
  int fileappend(FILE *fichier, char *optionfich)
  {
    if((fichier=fopen(optionfich,"a"))==NULL) {
- Line 4848  void prwizard(int ncovmodel, int nlstate
+ Line 9951  void prwizard(int ncovmodel, int nlstate
  /******************* Gompertz Likelihood ******************************/
  double gompertz(double x[])
  {
-   double A,B,L=0.0,sump=0.,num=0.;
+   double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
    int i,n=0; /* n is the size of the sample */
-   for (i=0;i<=imx-1 ; i++) {
+   for (i=1;i<=imx ; i++) {
      sump=sump+weight[i];
      /*    sump=sump+1;*/
      num=num+1;
    }
+   L=0.0;
+   /* agegomp=AGEGOMP; */
    /* for (i=0; i<=imx; i++)
       if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-   for (i=1;i<=imx ; i++)
+   for (i=1;i<=imx ; i++) {
-     {
+     /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
-       if (cens[i] == 1 && wav[i]>1)
+        mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+      * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month)
+      *   and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
-       if (cens[i] == 0 && wav[i]>1)
+      * +
+      * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
+      */
+      if (wav[i] > 1 || agedc[i] < AGESUP) {
+        if (cens[i] == 1){
+          A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+        } else if (cens[i] == 0){
          A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+           +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
+       } else
+          printf("Gompertz cens[%d] neither 1 nor 0\n",i);
        /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-       if (wav[i] > 1 ) { /* ??? */
+        L=L+A*weight[i];
-         L=L+A*weight[i];
          /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-       }
+      }
-     }
+   }
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   /*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;
  }
- Line 4886  double gompertz(double x[])
+ Line 9995  double gompertz(double x[])
  /******************* Gompertz_f Likelihood ******************************/
  double gompertz_f(const gsl_vector *v, void *params)
  {
-   double A,B,LL=0.0,sump=0.,num=0.;
+   double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
    double *x= (double *) v->data;
    int i,n=0; /* n is the size of the sample */
- Line 4924  double gompertz_f(const gsl_vector *v, v
+ Line 10033  double gompertz_f(const gsl_vector *v, v
  #endif
  /******************* Printing html file ***********/
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+ void printinghtmlmort(char fileresu[], 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;
- Line 4933  void printinghtmlmort(char fileres[], ch
+ Line 10042  void printinghtmlmort(char fileres[], ch
    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,"<br><br><img src=\"graphmort.svg\">");
    fprintf(fichtm,"</ul>");
  fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
- Line 4948  fprintf(fichtm,"<ul><li><h4>Life table</
+ Line 10057  fprintf(fichtm,"<ul><li><h4>Life table</
  }
  /******************* Gnuplot file **************/
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+ void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    char dirfileres[132],optfileres[132];
- Line 4962  void printinggnuplotmort(char fileres[],
+ Line 10071  void printinggnuplotmort(char fileres[],
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+   fprintf(ficgp,"set out \"graphmort.svg\"\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 ter svg size 640, 480\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);
- Line 4976  int readdata(char datafile[], int firsto
+ Line 10085  int readdata(char datafile[], int firsto
    /*-------- data file ----------*/
    FILE *fic;
    char dummy[]="                         ";
-   int i=0, j=0, n=0;
+   int i=0, j=0, n=0, iv=0, v;
+   int lstra;
    int linei, month, year,iout;
+   int noffset=0; /* This is the offset if BOM data file */
    char line[MAXLINE], linetmp[MAXLINE];
    char stra[MAXLINE], strb[MAXLINE];
    char *stratrunc;
-   int lstra;
+   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
+   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
+   for(v=1;v<NCOVMAX;v++){
+     DummyV[v]=0;
+     FixedV[v]=0;
+   }
+   for(v=1; v <=ncovcol;v++){
+     DummyV[v]=0;
+     FixedV[v]=0;
+   }
+   for(v=ncovcol+1; v <=ncovcol+nqv;v++){
+     DummyV[v]=1;
+     FixedV[v]=0;
+   }
+   for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
+     DummyV[v]=0;
+     FixedV[v]=1;
+   }
+   for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
+     DummyV[v]=1;
+     FixedV[v]=1;
+   }
+   for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
+     printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
+     fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
+   }
    if((fic=fopen(datafile,"r"))==NULL)    {
-     printf("Problem while opening datafile: %s\n", datafile);return 1;
+     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
    }
-   i=1;
+     /* Is it a BOM UTF-8 Windows file? */
+   /* First data line */
    linei=0;
+   while(fgets(line, MAXLINE, fic)) {
+     noffset=0;
+     if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
+     {
+       noffset=noffset+3;
+       printf("# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
+       fprintf(ficlog,"# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
+       fflush(ficlog); return 1;
+     }
+     /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
+     else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
+     {
+       noffset=noffset+2;
+       printf("# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
+       fprintf(ficlog,"# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
+       fflush(ficlog); return 1;
+     }
+     else if( line[0] == 0 && line[1] == 0)
+     {
+       if( line[2] == (char)0xFE && line[3] == (char)0xFF){
+         noffset=noffset+4;
+         printf("# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
+         fprintf(ficlog,"# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
+         fflush(ficlog); return 1;
+       }
+     } else{
+       ;/*printf(" Not a BOM file\n");*/
+     }
+         /* If line starts with a # it is a comment */
+     if (line[noffset] == '#') {
+       linei=linei+1;
+       break;
+     }else{
+       break;
+     }
+   }
+   fclose(fic);
+   if((fic=fopen(datafile,"r"))==NULL)    {
+     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
+     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
+   }
+   /* Not a Bom file */
+   i=1;
    while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
      linei=linei+1;
      for(j=strlen(line); j>=0;j--){  /* Untabifies line */
- Line 5008  int readdata(char datafile[], int firsto
+ Line 10190  int readdata(char datafile[], int firsto
      }
      trimbb(linetmp,line); /* Trims multiple blanks in line */
      strcpy(line, linetmp);
+     /* Loops on waves */
      for (j=maxwav;j>=1;j--){
+       for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
+         cutv(stra, strb, line, ' ');
+         if(strb[0]=='.') { /* Missing value */
+           lval=-1;
+           cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
+           cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
+           if(isalpha(strb[1])) { /* .m or .d Really Missing value */
+             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
+             return 1;
+           }
+         }else{
+           errno=0;
+           /* what_kind_of_number(strb); */
+           dval=strtod(strb,&endptr);
+           /* if( strb[0]=='\0' || (*endptr != '\0')){ */
+           /* if(strb != endptr && *endptr == '\0') */
+           /*    dval=dlval; */
+           /* 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 the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
+             return 1;
+           }
+           cotqvar[j][iv][i]=dval;
+           cotvar[j][ntv+iv][i]=dval;
+         }
+         strcpy(line,stra);
+       }/* end loop ntqv */
+       for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
+         cutv(stra, strb, line, ' ');
+         if(strb[0]=='.') { /* Missing value */
+           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 the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);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 of wave %d (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,iv,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 of wave %d (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,iv,j);fflush(ficlog);
+           return 1;
+         }
+         cotvar[j][iv][i]=(double)(lval);
+         strcpy(line,stra);
+       }/* end loop ntv */
+       /* Statuses  at wave */
        cutv(stra, strb, line, ' ');
-       if(strb[0]=='.') { /* Missing status */
+       if(strb[0]=='.') { /* Missing value */
          lval=-1;
        }else{
          errno=0;
          lval=strtol(strb,&endptr,10);
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+         /*      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;
+       /* Date of Interview */
        strcpy(line,stra);
        cutv(stra, strb,line,' ');
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
        }
-       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
          month=99;
          year=9999;
        }else{
- Line 5039  int readdata(char datafile[], int firsto
+ Line 10293  int readdata(char datafile[], int firsto
          return 1;
        }
        anint[j][i]= (double) year;
        mint[j][i]= (double)month;
+       /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
+       /*        printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
+       /*        fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
+       /* } */
        strcpy(line,stra);
-     } /* ENd Waves */
+     } /* End loop on waves */
+     /* Date of death */
      cutv(stra, strb,line,' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
      }
-     else  if(iout=sscanf(strb,"%s.",dummy) != 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);
+       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;
+       return 1;
      }
      andc[i]=(double) year;
      moisdc[i]=(double) month;
      strcpy(line,stra);
+     /* Date of birth */
      cutv(stra, strb,line,' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
      }
-     else  if(iout=sscanf(strb,"%s.", dummy) != 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;
+       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;
+       return 1;
      }
      annais[i]=(double)(year);
      moisnais[i]=(double)(month);
+     for (j=1;j<=maxwav;j++){
+       if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
+         printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j,(int)moisnais[i],(int)annais[i]);
+         fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j, (int)moisnais[i],(int)annais[i]);
+       }
+     }
      strcpy(line,stra);
+     /* Sample weight */
      cutv(stra, strb,line,' ');
      errno=0;
      dval=strtod(strb,&endptr);
- Line 5091  int readdata(char datafile[], int firsto
+ Line 10359  int readdata(char datafile[], int firsto
      weight[i]=dval;
      strcpy(line,stra);
+     for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing value */
+         lval=-1;
+         coqvar[iv][i]=NAN;
+         covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */
+       }else{
+         errno=0;
+         /* what_kind_of_number(strb); */
+         dval=strtod(strb,&endptr);
+         /* if(strb != endptr && *endptr == '\0') */
+         /*   dval=dlval; */
+         /* 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 the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
+           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
+           return 1;
+         }
+         coqvar[iv][i]=dval;
+         covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
+       }
+       strcpy(line,stra);
+     }/* end loop nqv */
+     /* Covariate values */
      for (j=ncovcol;j>=1;j--){
        cutv(stra, strb,line,' ');
-       if(strb[0]=='.') { /* Missing status */
+       if(strb[0]=='.') { /* Missing covariate value */
          lval=-1;
        }else{
          errno=0;
- Line 5108  int readdata(char datafile[], int firsto
+ Line 10401  int readdata(char datafile[], int firsto
          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 \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
-  build V1=0 V2=0 for the reference value (1),\n \
+  build V1=0 V2=0 for the reference value (1),\n                         \
-         V1=1 V2=0 for (2) \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 \
+  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 \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
-  build V1=0 V2=0 for the reference value (1),\n \
+  build V1=0 V2=0 for the reference value (1),\n                         \
-         V1=1 V2=0 for (2) \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 \
+  output of IMaCh is often meaningless.\n                                \
   Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
          return 1;
        }
- Line 5129  int readdata(char datafile[], int firsto
+ Line 10422  int readdata(char datafile[], int firsto
        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);
- Line 5141  int readdata(char datafile[], int firsto
+ Line 10434  int readdata(char datafile[], int firsto
      i=i+1;
    } /* End loop reading  data */
    *imax=i-1; /* Number of individuals */
    fclose(fic);
    return (0);
    /* endread: */
-     printf("Exiting readdata: ");
+   printf("Exiting readdata: ");
-     fclose(fic);
+   fclose(fic);
-     return (1);
+   return (1);
+ }
+ void removefirstspace(char **stri){/*, char stro[]) {*/
+   char *p1 = *stri, *p2 = *stri;
+   while (*p2 == ' ')
+     p2++;
+   /* while ((*p1++ = *p2++) !=0) */
+   /*   ; */
+   /* do */
+   /*   while (*p2 == ' ') */
+   /*     p2++; */
+   /* while (*p1++ == *p2++); */
+   *stri=p2;
+ }
+ int decoderesult( char resultline[], int nres)
+ /**< This routine decode one result line and returns the combination # of dummy covariates only **/
+ {
+   int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
+   char resultsav[MAXLINE];
+   /* int resultmodel[MAXLINE]; */
+   /* int modelresult[MAXLINE]; */
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
+   removefirstspace(&resultline);
+   printf("decoderesult:%s\n",resultline);
+   strcpy(resultsav,resultline);
+   printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline);
+   if (strlen(resultsav) >1){
+     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' in this resultline */
+   }
+   if(j == 0){ /* Resultline but no = */
+     TKresult[nres]=0; /* Combination for the nresult and the model */
+     return (0);
+   }
+   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
+     printf("ERROR: the number of variables in the resultline which is %d, differs from the number %d of single variables used in the model line, %s.\n",j, cptcovs, model);
+     fprintf(ficlog,"ERROR: the number of variables in the resultline which is %d, differs from the number %d of single variables used in the model line, %s.\n",j, cptcovs, model);
+     /* return 1;*/
+   }
+   for(k=1; k<=j;k++){ /* Loop on any covariate of the RESULT LINE */
+     if(nbocc(resultsav,'=') >1){
+       cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop *//*     resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */
+       /* If resultsav= "V4= 1 V5=25.1 V3=0" with a blank then strb="V4=" and stra="1 V5=25.1 V3=0" */
+       cutl(strc,strd,strb,'=');  /* strb:"V4=1" strc="1" strd="V4" */
+       /* If a blank, then strc="V4=" and strd='\0' */
+       if(strc[0]=='\0'){
+       printf("Error in resultline, probably a blank after the \"%s\", \"result:%s\", stra=\"%s\" resultsav=\"%s\"\n",strb,resultline, stra, resultsav);
+         fprintf(ficlog,"Error in resultline, probably a blank after the \"V%s=\", resultline=%s\n",strb,resultline);
+         return 1;
+       }
+     }else
+       cutl(strc,strd,resultsav,'=');
+     Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */
+     cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
+     Tvarsel[k]=atoi(strc);  /* 4 */ /* Tvarsel is the id of the kth covariate in the result line Tvarsel[1] in "V4=1.." is 4.*/
+     /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
+     /* cptcovsel++;     */
+     if (nbocc(stra,'=') >0)
+       strcpy(resultsav,stra); /* and analyzes it */
+   }
+   /* Checking for missing or useless values in comparison of current model needs */
+   /* Feeds resultmodel[nres][k1]=k2 for k1th product covariate with age in the model equation fed by the index k2 of the resutline*/
+   for(k1=1; k1<= cptcovt ;k1++){ /* Loop on MODEL LINE V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     if(Typevar[k1]==0){ /* Single covariate in model */
+       /* 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
+       match=0;
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
+           modelresult[nres][k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
+           break;
+         }
+       }
+       if(match == 0){
+         printf("Error in result line (Dummy single): V%d is missing in result: %s according to model=%s. Tvar[k1=%d]=%d is different from Tvarsel[k2=%d]=%d.\n",Tvar[k1], resultline, model,k1, Tvar[k1], k2, Tvarsel[k2]);
+         fprintf(ficlog,"Error in result line (Dummy single): V%d is missing in result: %s according to model=%s\n",Tvar[k1], resultline, model);
+         return 1;
+       }
+     }else if(Typevar[k1]==1){ /* Product with age We want to get the position k2 in the resultline of the product k1 in the model line*/
+       /* We feed resultmodel[k1]=k2; */
+       match=0;
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline.  jth occurence of = signs in the result line. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
+           modelresult[nres][k2]=k1;/* we found a Vn=1 corrresponding to Vn*age in the model modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
+           resultmodel[nres][k1]=k2; /* Added here */
+           printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%d*AGE\n",k2,k1,Tvar[k1]);
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
+           break;
+         }
+       }
+       if(match == 0){
+         printf("Error in result line (Product with age): V%d is missing in result: %s according to model=%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
+         fprintf(ficlog,"Error in result line (Product with age): V%d is missing in result: %s according to model=%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
+       return 1;
+       }
+     }else if(Typevar[k1]==2){ /* Product No age We want to get the position in the resultline of the product in the model line*/
+       /* resultmodel[nres][of such a Vn * Vm product k1] is not unique, so can't exist, we feed Tvard[k1][1] and [2] */
+       match=0;
+       printf("Decoderesult very first Product Tvardk[k1=%d][1]=%d Tvardk[k1=%d][2]=%d V%d * V%d\n",k1,Tvardk[k1][1],k1,Tvardk[k1][2],Tvardk[k1][1],Tvardk[k1][2]);
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvardk[k1][1]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
+           /* modelresult[k2]=k1; */
+           printf("Decoderesult first Product modelresult[k2=%d]=%d (k1) V%d * \n",k2,k1,Tvarsel[k2]);
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
+         }
+       }
+       if(match == 0){
+         printf("Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][1], resultline, model);
+         fprintf(ficlog,"Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][1], resultline, model);
+         return 1;
+       }
+       match=0;
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvardk[k1][2]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
+           /* modelresult[k2]=k1;*/
+           printf("Decoderesult second Product modelresult[k2=%d]=%d (k1) * V%d \n ",k2,k1,Tvarsel[k2]);
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
+           break;
+         }
+       }
+       if(match == 0){
+         printf("Error in result line (Product without age second variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][2], resultline, model);
+         fprintf(ficlog,"Error in result line (Product without age second variable): V%d is missing in result : %s according to model=%s\n",Tvardk[k1][2], resultline, model);
+         return 1;
+       }
+     }/* End of testing */
+   }/* End loop cptcovt */
+   /* Checking for missing or useless values in comparison of current model needs */
+   /* Feeds resultmodel[nres][k1]=k2 for single covariate (k1) in the model equation */
+   for(k2=1; k2 <=j;k2++){ /* j or cptcovs is the number of single covariates used either in the model line as well as in the result line (dummy or quantitative)
+                            * Loop on resultline variables: result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+     match=0;
+     for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       if(Typevar[k1]==0){ /* Single only */
+         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
+           resultmodel[nres][k1]=k2;  /* k1th position in the model equation corresponds to k2th position in the result line. resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
+           modelresult[nres][k2]=k1; /* k1th position in the model equation corresponds to k2th position in the result line. modelresult[1]=2 modelresult[2]=1  modelresult[3]=3  remodelresult[4]=6 modelresult[5]=9 */
+           ++match;
+         }
+       }
+     }
+     if(match == 0){
+       printf("Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], resultline, model);
+       fprintf(ficlog,"Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], resultline, model);
+       return 1;
+     }else if(match > 1){
+       printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
+       fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
+       return 1;
+     }
+   }
+   /* cptcovres=j /\* Number of variables in the resultline is equal to cptcovs and thus useless *\/     */
+   /* We need to deduce which combination number is chosen and save quantitative values */
+   /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+   /* nres=1st result line: V4=1 V5=25.1 V3=0  V2=8 V1=1 */
+   /* should correspond to the combination 6 of dummy: V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 1*1 + 0*2 + 1*4 = 5 + (1offset) = 6*/
+   /* nres=2nd result line: V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+   /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
+   /*    1 0 0 0 */
+   /*    2 1 0 0 */
+   /*    3 0 1 0 */
+   /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 (nres=2)*/
+   /*    5 0 0 1 */
+   /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 (nres=1)*/
+   /*    7 0 1 1 */
+   /*    8 1 1 1 */
+   /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
+   /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
+   /* V5*age V5 known which value for nres?  */
+   /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
+   for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* cptcovt number of covariates (excluding 1 and age or age*age) in the MODEL equation.
+                                                    * loop on position k1 in the MODEL LINE */
+     /* k counting number of combination of single dummies in the equation model */
+     /* k4 counting single dummies in the equation model */
+     /* k4q counting single quantitatives in the equation model */
+     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, k1 is sorting according to MODEL, but k3 to resultline */
+        /* k4+1= (not always if quant in model) position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */
+       /* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/
+       /* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */
+       /* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline                        */
+       /*      k3 is the position in the nres result line of the k1th variable of the model equation                                  */
+       /* Tvarsel[k3]: Name of the variable at the k3th position in the result line.                                                  */
+       /* Tvalsel[k3]: Value of the variable at the k3th position in the result line.                                                 */
+       /* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline                   */
+       /* Tvresult[nres][result_position]= name of the dummy variable at the result_position in the nres resultline                     */
+       /* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line                                        */
+       /* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line                                                      */
+       k3= resultmodel[nres][k1]; /* From position k1 in model get position k3 in result line */
+       /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
+       k2=(int)Tvarsel[k3]; /* from position k3 in resultline get name k2: nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
+       k+=Tvalsel[k3]*pow(2,k4);  /* nres=1 k1=2 Tvalsel[1]=1 (V4=1); k1=3 k3=2 Tvalsel[2]=0 (V3=0) */
+       TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][Name]=Value; stores the value into the name of the variable. */
+       /* Tinvresult[nres][4]=1 */
+       /* Tresult[nres][k4+1]=Tvalsel[k3];/\* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) *\/ */
+       Tresult[nres][k3]=Tvalsel[k3];/* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) */
+       /* Tvresult[nres][k4+1]=(int)Tvarsel[k3];/\* Tvresult[nres][1]=4 Tvresult[nres][3]=1 *\/ */
+       Tvresult[nres][k3]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
+       Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
+       precov[nres][k1]=Tvalsel[k3]; /* Value from resultline of the variable at the k1 position in the model */
+       printf("Decoderesult Dummy k=%d, k1=%d precov[nres=%d][k1=%d]=%.f V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k1, nres, k1,precov[nres][k1], k2, k3, (int)Tvalsel[k3], k4);
+       k4++;;
+     }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */
+       /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 */
+       /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline                                 */
+       /* Tqinvresult[nres][Name of a quantitative variable]= value of the variable in the result line                                                      */
+       k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 5 =k3q */
+       k2q=(int)Tvarsel[k3q]; /*  Name of variable at k3q th position in the resultline */
+       /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
+       /* Tqresult[nres][k4q+1]=Tvalsel[k3q]; /\* Tqresult[nres][1]=25.1 *\/ */
+       /* Tvresult[nres][k4q+1]=(int)Tvarsel[k3q];/\* Tvresult[nres][1]=4 Tvresult[nres][3]=1 *\/ */
+       /* Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /\* Tvqresult[nres][1]=5 *\/ */
+       Tqresult[nres][k3q]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
+       Tvresult[nres][k3q]=(int)Tvarsel[k3q];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
+       Tvqresult[nres][k3q]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
+       Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
+       TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
+       precov[nres][k1]=Tvalsel[k3q];
+       printf("Decoderesult Quantitative nres=%d,precov[nres=%d][k1=%d]=%.f V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, nres, k1,precov[nres][k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
+       k4q++;;
+     }else if( Dummy[k1]==2 ){ /* For dummy with age product */
+       /* Tvar[k1]; */ /* Age variable */
+       /* Wrong we want the value of variable name Tvar[k1] */
+       k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
+       k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
+       TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][4]=1 */
+       precov[nres][k1]=Tvalsel[k3];
+       printf("Decoderesult Dummy with age k=%d, k1=%d precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]);
+     }else if( Dummy[k1]==3 ){ /* For quant with age product */
+       k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
+       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
+       TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */
+       precov[nres][k1]=Tvalsel[k3q];
+       printf("Decoderesult Quantitative with age nres=%d, k1=%d, precov[nres=%d][k1=%d]=%f Tvar[%d]=V%d V(k2q=%d)= Tvarsel[%d]=%d, Tvalsel[%d]=%f\n",nres, k1, nres, k1,precov[nres][k1], k1,  Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
+     }else if(Typevar[k1]==2 ){ /* For product quant or dummy (not with age) */
+       precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];
+       printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]);
+     }else{
+       printf("Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
+       fprintf(ficlog,"Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
+     }
+   }
+   TKresult[nres]=++k; /* Number of combinations of dummies for the nresult and the model =Tvalsel[k3]*pow(2,k4) + 1*/
+   return (0);
  }
- void removespace(char *str) {
-   char *p1 = str, *p2 = str;
+ int decodemodel( char model[], int lastobs)
-   do
+  /**< This routine decodes the model and returns:
-     while (*p2 == ' ')
+         * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
-       p2++;
+         * - nagesqr = 1 if age*age in the model, otherwise 0.
-   while (*p1++ = *p2++);
+         * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
- }
+         * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
+         * - cptcovage number of covariates with age*products =2
- int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
+         * - cptcovs number of simple covariates
-    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
+         * - 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
-    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
+         *     which is a new column after the 9 (ncovcol) variables.
-    * - cptcovn or number of covariates k of the models excluding age*products =6
+         * - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual
-    * - cptcovage number of covariates with age*products =2
+         * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
-    * - cptcovs number of simple covariates
+         *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
-    * - 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
+         * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
-    *     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
+ /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
-    * - 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 i, j, k, ks, v;
-   int  j1, k1, k2;
+   int  j1, k1, k2, k3, k4;
    char modelsav[80];
    char stra[80], strb[80], strc[80], strd[80],stre[80];
+   char *strpt;
    /*removespace(model);*/
    if (strlen(model) >1){ /* If there is at least 1 covariate */
      j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-     j=nbocc(model,'+'); /**< j=Number of '+' */
-     j1=nbocc(model,'*'); /**< j1=Number of '*' */
-     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
-                   /* including age products which are counted in cptcovage.
-                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-     strcpy(modelsav,model);
      if (strstr(model,"AGE") !=0){
-       printf("Error. AGE must be in lower case 'age' model=%s ",model);
+       printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
-       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
+       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
        return 1;
      }
      if (strstr(model,"v") !=0){
- Line 5203  int decodemodel ( char model[], int last
+ Line 10729  int decodemodel ( char model[], int last
        fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
        return 1;
      }
+     strcpy(modelsav,model);
-     /*   Design
+     if ((strpt=strstr(model,"age*age")) !=0){
-      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
+       printf(" strpt=%s, model=%s\n",strpt, model);
-      *  <          ncovcol=8                >
+       if(strpt != model){
-      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
+         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
-      *   k=  1    2      3       4     5       6      7        8
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
+  corresponding column of parameters.\n",model);
-      *  covar[k,i], value of kth covariate if not including age for individual i:
+         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
-      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
+  corresponding column of parameters.\n",model); fflush(ficlog);
-      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
+         return 1;
-      *  Tage[++cptcovage]=k
+       }
-      *       if products, new covar are created after ncovcol with k1
+       nagesqr=1;
-      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
+       if (strstr(model,"+age*age") !=0)
-      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
+         substrchaine(modelsav, model, "+age*age");
-      *  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
+       else if (strstr(model,"age*age+") !=0)
-      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
+         substrchaine(modelsav, model, "age*age+");
-      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
+       else
-      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
+         substrchaine(modelsav, model, "age*age");
-      *  <          ncovcol=8                >
+     }else
-      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
+       nagesqr=0;
-      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
+     if (strlen(modelsav) >1){
-      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
+       j=nbocc(modelsav,'+'); /**< j=Number of '+' */
-      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
-      * p Tprod[1]@2={                         6, 5}
+       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
-      *p Tvard[1][1]@4= {7, 8, 5, 6}
+       cptcovt= j+1; /* Number of total covariates in the model, not including
-      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
+                      * cst, age and age*age
-      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+                      * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
-      *How to reorganize?
+       /* including age products which are counted in cptcovage.
-      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
+        * but the covariates which are products must be treated
-      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+        * separately: ncovn=4- 2=2 (V1+V3). */
-      *       {2,   1,     4,      8,    5,      6,     3,       7}
+       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-      * Struct []
+       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-      */
-     /* This loop fills the array Tvar from the string 'model'.*/
+       /*   Design
-     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+        *  <          ncovcol=8                >
-     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
+        *   k=  1    2      3       4     5       6      7        8
-     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
+        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-     /*  k=1 Tvar[1]=2 (from V2) */
+        *  covar[k,i], value of kth covariate if not including age for individual i:
-     /*  k=5 Tvar[5] */
+        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
-     /* for (k=1; k<=cptcovn;k++) { */
+        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
-     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-     /*  } */
+        *  Tage[++cptcovage]=k
-     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+        *       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
-      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
+        *  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[k]=0;
+        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-     cptcovage=0;
+        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+        *  <          ncovcol=8                >
-                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-       /*scanf("%d",i);*/
+        * p Tvar[1]@12={2,   1,     3,      3,  11,     10,     8,       8,   7,   8,   5,  6}
-       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+        * p Tprod[1]@2={                         6, 5}
-         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+        *p Tvard[1][1]@4= {7, 8, 5, 6}
-         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-           /* covar is not filled and then is empty */
+        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           cptcovprod--;
+        *How to reorganize? Tvars(orted)
-           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
+        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-           cptcovage++; /* Sums the number of covariates which include age as a product */
+        *       {2,   1,     4,      8,    5,      6,     3,       7}
-           Tage[cptcovage]=k;  /* Tage[1] = 4 */
+        * Struct []
-           /*printf("stre=%s ", stre);*/
+        */
-         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-           cptcovprod--;
+       /* This loop fills the array Tvar from the string 'model'.*/
-           cutl(stre,strb,strc,'V');
+       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-           Tvar[k]=atoi(stre);
+       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-           cptcovage++;
+       /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-           Tage[cptcovage]=k;
+       /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
-         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+       /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
-           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+       /*        k=1 Tvar[1]=2 (from V2) */
-           cptcovn++;
+       /*        k=5 Tvar[5] */
-           cptcovprodnoage++;k1++;
+       /* for (k=1; k<=cptcovn;k++) { */
-           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+       /*        cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
+       /*        } */
-                                   because this model-covariate is a construction we invent a new column
+       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
-                                   ncovcol + k1
+       /*
-                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+       for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
-           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+         Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
-           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+       }
-           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+       cptcovage=0;
-           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
-           k2=k2+2;
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
-           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
+                                          modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */    /* <model> "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */
-           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
+         if (nbocc(modelsav,'+')==0)
-           for (i=1; i<=lastobs;i++){
+           strcpy(strb,modelsav); /* and analyzes it */
-             /* Computes the new covariate which is a product of
+         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
+         /*scanf("%d",i);*/
-             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V5*age+ V4+V3*age strb=V3*age */
-           }
+           cutl(strc,strd,strb,'*'); /**< k=1 strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-         } /* End age is not in the model */
+           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-       } /* End if model includes a product */
+             /* covar is not filled and then is empty */
-       else { /* no more sum */
+             cptcovprod--;
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-        /*  scanf("%d",i);*/
+             Tvar[k]=atoi(stre);  /* V2+V1+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
-         cutl(strd,strc,strb,'V');
+             Typevar[k]=1;  /* 1 for age product */
-         ks++; /**< Number of simple covariates */
+             cptcovage++; /* Counts the number of covariates which include age as a product */
-         cptcovn++;
+             Tage[cptcovage]=k;  /*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
-         Tvar[k]=atoi(strd);
+             /*printf("stre=%s ", stre);*/
-       }
+           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+             cptcovprod--;
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+             cutl(stre,strb,strc,'V');
-         scanf("%d",i);*/
+             Tvar[k]=atoi(stre);
-     } /* end of loop + */
+             Typevar[k]=1;  /* 1 for age product */
-   } /* end model */
+             cptcovage++;
+             Tage[cptcovage]=k;
+           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+             cptcovn++;
+             cptcovprodnoage++;k1++;
+             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+             Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
+                                                 because this model-covariate is a construction we invent a new column
+                                                 which is after existing variables ncovcol+nqv+ntv+nqtv + k1
+                                                 If already ncovcol=4 and model= V2 + V1 + V1*V4 + age*V3 + V3*V2
+                                                 thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
+                                                 Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=4 etc */
+             /* Please remark that the new variables are model dependent */
+             /* If we have 4 variable but the model uses only 3, like in
+              * model= V1 + age*V1 + V2 + V3 + age*V2 + age*V3 + V1*V2 + V1*V3
+              *  k=     1     2       3   4     5        6        7       8
+              * Tvar[k]=1     1       2   3     2        3       (5       6) (and not 4 5 because of V4 missing)
+              * Tage[kk]    [1]= 2           [2]=5      [3]=6                  kk=1 to cptcovage=3
+              * Tvar[Tage[kk]][1]=2          [2]=2      [3]=3
+              */
+             Typevar[k]=2;  /* 2 for double fixed dummy covariates */
+             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+             Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
+             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+             Tvardk[k][1] =atoi(strc); /* m 1 for V1*/
+             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+             Tvardk[k][2] =atoi(stre); /* n 4 for V4*/
+             k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
+             /* 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) *\/ */
+             /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
+             /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
+             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 { /* not a product */
+           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+           /*  scanf("%d",i);*/
+           cutl(strd,strc,strb,'V');
+           ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
+           cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
+           Tvar[k]=atoi(strd);
+           Typevar[k]=0;  /* 0 for simple covariates */
+         }
+         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 + on total covariates */
+     } /* end if strlen(modelsave == 0) age*age might exist */
+   } /* end if strlen(model == 0) */
    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-   printf("cptcovprod=%d ", cptcovprod);
+      printf("cptcovprod=%d ", cptcovprod);
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+      fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+      scanf("%d ",i);*/
-   scanf("%d ",i);*/
+ /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
+    of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
+ /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1  = 5 possible variables data: 2 fixed 3, varying
+    model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
+    k =           1    2   3     4       5       6      7      8        9
+    Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5
+    Typevar[k]=   0    0   0     2       1       0      2      1        0
+    Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
+    Dummy[k]      1    0   0     0       3       1      1      2        3
+           Tmodelind[combination of covar]=k;
+ */
+ /* Dispatching between quantitative and time varying covariates */
+   /* If Tvar[k] >ncovcol it is a product */
+   /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
+         /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
+   printf("Model=1+age+%s\n\
+ Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
+ Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
+ Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
+   fprintf(ficlog,"Model=1+age+%s\n\
+ Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
+ Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
+ Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
+   for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
+   for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
+     if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
+       Fixed[k]= 0;
+       Dummy[k]= 0;
+       ncoveff++;
+       ncovf++;
+       nsd++;
+       modell[k].maintype= FTYPE;
+       TvarsD[nsd]=Tvar[k];
+       TvarsDind[nsd]=k;
+       TnsdVar[Tvar[k]]=nsd;
+       TvarF[ncovf]=Tvar[k];
+       TvarFind[ncovf]=k;
+       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
+       Fixed[k]= 0;
+       Dummy[k]= 0;
+       ncoveff++;
+       ncovf++;
+       modell[k].maintype= FTYPE;
+       TvarF[ncovf]=Tvar[k];
+       /* TnsdVar[Tvar[k]]=nsd; */ /* To be done */
+       TvarFind[ncovf]=k;
+       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
+       Fixed[k]= 0;
+       Dummy[k]= 1;
+       nqfveff++;
+       modell[k].maintype= FTYPE;
+       modell[k].subtype= FQ;
+       nsq++;
+       TvarsQ[nsq]=Tvar[k]; /* Gives the variable name (extended to products) of first nsq simple quantitative covariates (fixed or time vary see below */
+       TvarsQind[nsq]=k;    /* Gives the position in the model equation of the first nsq simple quantitative covariates (fixed or time vary) */
+       ncovf++;
+       TvarF[ncovf]=Tvar[k];
+       TvarFind[ncovf]=k;
+       TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+       TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
+       Fixed[k]= 1;
+       Dummy[k]= 0;
+       ntveff++; /* Only simple time varying dummy variable */
+       modell[k].maintype= VTYPE;
+       modell[k].subtype= VD;
+       nsd++;
+       TvarsD[nsd]=Tvar[k];
+       TvarsDind[nsd]=k;
+       TnsdVar[Tvar[k]]=nsd; /* To be verified */
+       ncovv++; /* Only simple time varying variables */
+       TvarV[ncovv]=Tvar[k];
+       TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
+       TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4  TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
+       TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
+       printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
+       printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
+     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
+       Fixed[k]= 1;
+       Dummy[k]= 1;
+       nqtveff++;
+       modell[k].maintype= VTYPE;
+       modell[k].subtype= VQ;
+       ncovv++; /* Only simple time varying variables */
+       nsq++;
+       TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */ /* Gives the variable name (extended to products) of first nsq simple quantitative covariates (fixed or time vary here) */
+       TvarsQind[nsq]=k; /* For single quantitative covariate gives the model position of each single quantitative covariate *//* Gives the position in the model equation of the first nsq simple quantitative covariates (fixed or time vary) */
+       TvarV[ncovv]=Tvar[k];
+       TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
+       TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+       TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+       TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
+       /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
+       printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
+       printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
+     }else if (Typevar[k] == 1) {  /* product with age */
+       ncova++;
+       TvarA[ncova]=Tvar[k];
+       TvarAind[ncova]=k;
+       if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
+         Fixed[k]= 2;
+         Dummy[k]= 2;
+         modell[k].maintype= ATYPE;
+         modell[k].subtype= APFD;
+         /* ncoveff++; */
+       }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
+         Fixed[k]= 2;
+         Dummy[k]= 3;
+         modell[k].maintype= ATYPE;
+         modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
+         /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
+       }else if( Tvar[k] <=ncovcol+nqv+ntv ){
+         Fixed[k]= 3;
+         Dummy[k]= 2;
+         modell[k].maintype= ATYPE;
+         modell[k].subtype= APVD;                /*      Product age * varying dummy */
+         /* ntveff++; /\* Only simple time varying dummy variable *\/ */
+       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
+         Fixed[k]= 3;
+         Dummy[k]= 3;
+         modell[k].maintype= ATYPE;
+         modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
+         /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
+       }
+     }else if (Typevar[k] == 2) {  /* product without age */
+       k1=Tposprod[k];
+       if(Tvard[k1][1] <=ncovcol){
+         if(Tvard[k1][2] <=ncovcol){
+           Fixed[k]= 1;
+           Dummy[k]= 0;
+           modell[k].maintype= FTYPE;
+           modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
+           ncovf++; /* Fixed variables without age */
+           TvarF[ncovf]=Tvar[k];
+           TvarFind[ncovf]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           Fixed[k]= 0;  /* or 2 ?*/
+           Dummy[k]= 1;
+           modell[k].maintype= FTYPE;
+           modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
+           ncovf++; /* Varying variables without age */
+           TvarF[ncovf]=Tvar[k];
+           TvarFind[ncovf]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 0;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else if(Tvard[k1][1] <=ncovcol+nqv){
+         if(Tvard[k1][2] <=ncovcol){
+           Fixed[k]= 0;  /* or 2 ?*/
+           Dummy[k]= 1;
+           modell[k].maintype= FTYPE;
+           modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
+           ncovf++; /* Fixed variables without age */
+           TvarF[ncovf]=Tvar[k];
+           TvarFind[ncovf]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
+         if(Tvard[k1][2] <=ncovcol){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 0;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
+         if(Tvard[k1][2] <=ncovcol){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else{
+         printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
+         fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
+       } /*end k1*/
+     }else{
+       printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
+       fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
+     }
+     printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
+     printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
+     fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
+   }
+   /* Searching for doublons in the model */
+   for(k1=1; k1<= cptcovt;k1++){
+     for(k2=1; k2 <k1;k2++){
+       /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
+       if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
+         if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
+           if(Tvar[k1]==Tvar[k2]){
+             printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
+             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);
+             return(1);
+           }
+         }else if (Typevar[k1] ==2){
+           k3=Tposprod[k1];
+           k4=Tposprod[k2];
+           if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
+             printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
+             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
+             return(1);
+           }
+         }
+       }
+     }
+   }
+   printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
+   fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
+   printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
+   fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
    return (0); /* with covar[new additional covariate if product] and Tage if age */
    /*endread:*/
-     printf("Exiting decodemodel: ");
+   printf("Exiting decodemodel: ");
-     return (1);
+   return (1);
  }
- calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+ int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
- {
+ {/* Check ages at death */
    int i, m;
+   int firstone=0;
    for (i=1; i<=imx; i++) {
      for(m=2; (m<= maxwav); m++) {
        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
          anint[m][i]=9999;
-         s[m][i]=-1;
+         if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
+           s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         *nberr++;
+         *nberr = *nberr + 1;
-         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);
+         if(firstone == 0){
-         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);
+           firstone=1;
-         s[m][i]=-1;
+         printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
+         }
+         fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
+         s[m][i]=-1;  /* Droping the death status */
        }
        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-         *nberr++;
+         (*nberr)++;
-         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+         printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
-         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]);
+         fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+         s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
        }
      }
    }
- Line 5359  calandcheckages(int imx, int maxwav, dou
+ Line 11244  calandcheckages(int imx, int maxwav, dou
    for (i=1; i<=imx; i++)  {
      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
      for(m=firstpass; (m<= lastpass); m++){
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+       if(s[m][i] >0  || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
          if (s[m][i] >= nlstate+1) {
-           if(agedc[i]>0)
+           if(agedc[i]>0){
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                agev[m][i]=agedc[i];
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+               /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-             else {
+             }else {
                if ((int)andc[i]!=9999){
                  nbwarn++;
                  printf("Warning negative age at death: %ld line:%d\n",num[i],i);
- Line 5373  calandcheckages(int imx, int maxwav, dou
+ Line 11258  calandcheckages(int imx, int maxwav, dou
                  agev[m][i]=-1;
                }
              }
-         }
+           } /* agedc > 0 */
+         } /* end if */
          else if(s[m][i] !=9){ /* Standard case, age in fractional
                                   years but with the precision of a month */
            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
- Line 5389  calandcheckages(int imx, int maxwav, dou
+ Line 11275  calandcheckages(int imx, int maxwav, dou
            }
            /*agev[m][i]=anint[m][i]-annais[i];*/
            /*     agev[m][i] = age[i]+2*m;*/
-         }
+         } /* en if 9*/
          else { /* =9 */
+           /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
            agev[m][i]=1;
            s[m][i]=-1;
          }
        }
-       else /*= 0 Unknown */
+       else if(s[m][i]==0) /*= 0 Unknown */
          agev[m][i]=1;
-     }
+       else{
+         printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
+         fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
+         agev[m][i]=0;
+       }
+     } /* End for lastpass */
    }
    for (i=1; i<=imx; i++)  {
      for(m=firstpass; (m<=lastpass); m++){
        if (s[m][i] > (nlstate+ndeath)) {
-         *nberr++;
+         (*nberr)++;
          printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
          fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
          return 1;
- Line 5428  calandcheckages(int imx, int maxwav, dou
+ Line 11320  calandcheckages(int imx, int maxwav, dou
      return (1);
  }
- syscompilerinfo()
+ #if defined(_MSC_VER)
-  {
+ /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-    /* #include "syscompilerinfo.h"*/
+ /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
- #include <gnu/libc-version.h>
+ //#include "stdafx.h"
+ //#include <stdio.h>
+ //#include <tchar.h>
+ //#include <windows.h>
+ //#include <iostream>
+ typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
+ LPFN_ISWOW64PROCESS fnIsWow64Process;
+ BOOL IsWow64()
+ {
+         BOOL bIsWow64 = FALSE;
+         //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
+         //  (HANDLE, PBOOL);
+         //LPFN_ISWOW64PROCESS fnIsWow64Process;
+         HMODULE module = GetModuleHandle(_T("kernel32"));
+         const char funcName[] = "IsWow64Process";
+         fnIsWow64Process = (LPFN_ISWOW64PROCESS)
+                 GetProcAddress(module, funcName);
+         if (NULL != fnIsWow64Process)
+         {
+                 if (!fnIsWow64Process(GetCurrentProcess(),
+                         &bIsWow64))
+                         //throw std::exception("Unknown error");
+                         printf("Unknown error\n");
+         }
+         return bIsWow64 != FALSE;
+ }
+ #endif
+ void syscompilerinfo(int logged)
+ {
+ #include <stdint.h>
+   /* #include "syscompilerinfo.h"*/
+    /* command line Intel compiler 32bit windows, XP compatible:*/
+    /* /GS /W3 /Gy
+       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
+       "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
+       "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
+       /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
+    */
+    /* 64 bits */
+    /*
+      /GS /W3 /Gy
+      /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
+      /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
+      /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
+      "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
+    /* Optimization are useless and O3 is slower than O2 */
+    /*
+      /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
+      /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
+      /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
+      /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
+    */
+    /* Link is */ /* /OUT:"visual studio
+\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
+       /PDB:"visual studio
+\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
+       "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
+       "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
+       "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
+       /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
+       /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
+       uiAccess='false'"
+       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
+       /NOLOGO /TLBID:1
+    */
+ #if defined __INTEL_COMPILER
  #if defined(__GNUC__)
- # if defined(__GNUC_PATCHLEVEL__)
+         struct utsname sysInfo;  /* For Intel on Linux and OS/X */
- #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+ #endif
-                             + __GNUC_MINOR__ * 100 \
+ #elif defined(__GNUC__)
-                             + __GNUC_PATCHLEVEL__)
+ #ifndef  __APPLE__
- # else
+ #include <gnu/libc-version.h>  /* Only on gnu */
- #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+ #endif
-                             + __GNUC_MINOR__ * 100)
+    struct utsname sysInfo;
- # endif
+    int cross = CROSS;
+    if (cross){
+            printf("Cross-");
+            if(logged) fprintf(ficlog, "Cross-");
+    }
  #endif
+    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
+ #if defined(__clang__)
+    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
+ #endif
+ #if defined(__ICC) || defined(__INTEL_COMPILER)
+    printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
+ #endif
+ #if defined(__GNUC__) || defined(__GNUG__)
+    printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
+ #endif
+ #if defined(__HP_cc) || defined(__HP_aCC)
+    printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
+ #endif
+ #if defined(__IBMC__) || defined(__IBMCPP__)
+    printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
+ #endif
+ #if defined(_MSC_VER)
+    printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
+ #endif
+ #if defined(__PGI)
+    printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
+ #endif
+ #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
+    printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
+ #endif
+    printf(" for "); if (logged) fprintf(ficlog, " for ");
  // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
  #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
      // Windows (x64 and x86)
+    printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
  #elif __unix__ // all unices, not all compilers
      // Unix
+    printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
  #elif __linux__
      // linux
+    printf("linux ");if(logged) fprintf(ficlog,"linux ");
  #elif __APPLE__
-     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
+     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
+    printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
  #endif
  /*  __MINGW32__   */
- Line 5463  syscompilerinfo()
+ Line 11465  syscompilerinfo()
  /* _WIN64  // Defined for applications for Win64. */
  /* _M_X64 // Defined for compilations that target x64 processors. */
  /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
- #include <stdint.h>
  #if UINTPTR_MAX == 0xffffffff
-    printf("32-bit \n"); /* 32-bit */
+    printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
  #elif UINTPTR_MAX == 0xffffffffffffffff
-   printf("64-bit \n");/* 64-bit */
+    printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
  #else
-  printf("wtf-bit \n"); /* wtf */
+    printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
  #endif
- struct utsname sysInfo;
+ #if defined(__GNUC__)
+ # if defined(__GNUC_PATCHLEVEL__)
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                             + __GNUC_MINOR__ * 100 \
+                             + __GNUC_PATCHLEVEL__)
+ # else
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                             + __GNUC_MINOR__ * 100)
+ # endif
+    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
+    if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
     if (uname(&sysInfo) != -1) {
-       puts(sysInfo.sysname);
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-       puts(sysInfo.nodename);
+          if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-       puts(sysInfo.release);
-       puts(sysInfo.version);
-       puts(sysInfo.machine);
     }
     else
        perror("uname() error");
-    printf("GNU C version %d\n", __GNUC_VERSION__);
+    //#ifndef __INTEL_COMPILER
-   printf("GNU libc version: %s\n", gnu_get_libc_version());
+ #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
+    printf("GNU libc version: %s\n", gnu_get_libc_version());
+    if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
+ #endif
+ #endif
+    //   void main ()
+    //   {
+ #if defined(_MSC_VER)
+    if (IsWow64()){
+            printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+            if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+    }
+    else{
+            printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+            if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+    }
+    //      printf("\nPress Enter to continue...");
+    //      getchar();
+    //   }
+ #endif
+ }
+ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
+   /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/
+   /* Computes the prevalence limit for each combination of the dummy covariates */
+   int i, j, k, i1, k4=0, nres=0 ;
+   /* double ftolpl = 1.e-10; */
+   double age, agebase, agelim;
+   double tot;
+   strcpy(filerespl,"PL_");
+   strcat(filerespl,fileresu);
+   if((ficrespl=fopen(filerespl,"w"))==NULL) {
+     printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+     fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+   }
+   printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
+   pstamp(ficrespl);
+   fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficrespl,"#Age ");
+   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+   fprintf(ficrespl,"\n");
+   /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
+   agebase=ageminpar;
+   agelim=agemaxpar;
+   /* i1=pow(2,ncoveff); */
+   i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
+   if (cptcovn < 1){i1=1;}
+   /* for(k=1; k<=i1;k++){ /\* For each combination k of dummy covariates in the model *\/ */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       k=TKresult[nres];
+       /* if(i1 != 1 && TKresult[nres]!= k) /\* We found the combination k corresponding to the resultline value of dummies *\/ */
+       /*        continue; */
+       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       /* k=k+1; */
+       /* to clean */
+       /*printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));*/
+       fprintf(ficrespl,"#******");
+       printf("#******");
+       fprintf(ficlog,"#******");
+       for(j=1;j<=cptcovs ;j++) {/**< cptcovs number of SIMPLE covariates in the model or resultline V2+V1 =2 (dummy or quantit or time varying) */
+         /* fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Here problem for varying dummy*\/ */
+         /* printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+         /* fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+         fprintf(ficrespl," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+         printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+         fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+       }
+       /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+       /*        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+       /*        fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+       /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+       /* } */
+       fprintf(ficrespl,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       if(invalidvarcomb[k]){
+         printf("\nCombination (%d) ignored because no case \n",k);
+         fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
+         fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
+         continue;
+       }
+       fprintf(ficrespl,"#Age ");
+       /* for(j=1;j<=cptcoveff;j++) { */
+       /*        fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+       /* } */
+       for(j=1;j<=cptcovs;j++) { /* New the quanti variable is added */
+         fprintf(ficrespl,"V%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+       }
+       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+       fprintf(ficrespl,"Total Years_to_converge\n");
+       for (age=agebase; age<=agelim; age++){
+         /* for (age=agebase; age<=agebase; age++){ */
+         /**< Computes the prevalence limit in each live state at age x and for covariate combination (k and) nres */
+         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres); /* Nicely done */
+         fprintf(ficrespl,"%.0f ",age );
+         /* for(j=1;j<=cptcoveff;j++) */
+         /*   fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+         for(j=1;j<=cptcovs;j++)
+           fprintf(ficrespl,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+         tot=0.;
+         for(i=1; i<=nlstate;i++){
+           tot +=  prlim[i][i];
+           fprintf(ficrespl," %.5f", prlim[i][i]);
+         }
+         fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
+       } /* Age */
+       /* was end of cptcod */
+     } /* nres */
+   /* } /\* for each combination *\/ */
+   return 0;
+ }
+ int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
+         /*--------------- Back Prevalence limit  (backward stable prevalence) --------------*/
+         /* Computes the back prevalence limit  for any combination      of covariate values
+    * at any age between ageminpar and agemaxpar
+          */
+   int i, j, k, i1, nres=0 ;
+   /* double ftolpl = 1.e-10; */
+   double age, agebase, agelim;
+   double tot;
+   /* double ***mobaverage; */
+   /* double      **dnewm, **doldm, **dsavm;  /\* for use *\/ */
+   strcpy(fileresplb,"PLB_");
+   strcat(fileresplb,fileresu);
+   if((ficresplb=fopen(fileresplb,"w"))==NULL) {
+     printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
+     fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
+   }
+   printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
+   fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
+   pstamp(ficresplb);
+   fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficresplb,"#Age ");
+   for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
+   fprintf(ficresplb,"\n");
+   /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
+   agebase=ageminpar;
+   agelim=agemaxpar;
+   i1=pow(2,cptcoveff);
+   if (cptcovn < 1){i1=1;}
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+      if(i1 != 1 && TKresult[nres]!= k)
+         continue;
+      /*printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));*/
+       fprintf(ficresplb,"#******");
+       printf("#******");
+       fprintf(ficlog,"#******");
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+       }
+       fprintf(ficresplb,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       if(invalidvarcomb[k]){
+         printf("\nCombination (%d) ignored because no cases \n",k);
+         fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
+         fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+         continue;
+       }
+       fprintf(ficresplb,"#Age ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+       }
+       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
+       fprintf(ficresplb,"Total Years_to_converge\n");
+       for (age=agebase; age<=agelim; age++){
+         /* for (age=agebase; age<=agebase; age++){ */
+         if(mobilavproj > 0){
+           /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
+           /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+           bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
+         }else if (mobilavproj == 0){
+           printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+           fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+           exit(1);
+         }else{
+           /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+           bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
+           /* printf("TOTOT\n"); */
+           /* exit(1); */
+         }
+         fprintf(ficresplb,"%.0f ",age );
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+         tot=0.;
+         for(i=1; i<=nlstate;i++){
+           tot +=  bprlim[i][i];
+           fprintf(ficresplb," %.5f", bprlim[i][i]);
+         }
+         fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
+       } /* Age */
+       /* was end of cptcod */
+       /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
+     } /* end of any combination */
+   } /* end of nres */
+   /* hBijx(p, bage, fage); */
+   /* fclose(ficrespijb); */
+   return 0;
+ }
+ int hPijx(double *p, int bage, int fage){
+     /*------------- h Pij x at various ages ------------*/
+   /* to be optimized with precov */
+   int stepsize;
+   int agelim;
+   int hstepm;
+   int nhstepm;
+   int h, i, i1, j, k, k4, nres=0;
+   double agedeb;
+   double ***p3mat;
+   strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
+   if((ficrespij=fopen(filerespij,"w"))==NULL) {
+     printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
+     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
+   }
+   printf("Computing pij: result on file '%s' \n", filerespij);
+   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   /*if (stepm<=24) stepsize=2;*/
+   agelim=AGESUP;
+   hstepm=stepsize*YEARM; /* Every year of age */
+   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+   /* hstepm=1;   aff par mois*/
+   pstamp(ficrespij);
+   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+   i1= pow(2,cptcoveff);
+   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+   /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
+   /*    k=k+1;  */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     k=TKresult[nres];
+     /* for(k=1; k<=i1;k++){ */
+     /* if(i1 != 1 && TKresult[nres]!= k) */
+     /*  continue; */
+     fprintf(ficrespij,"\n#****** ");
+     for(j=1;j<=cptcovs;j++){
+       fprintf(ficrespij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+       /* fprintf(ficrespij,"@wV%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+       /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+       /*        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+       /*        fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+     }
+     fprintf(ficrespij,"******\n");
+     for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+       nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+       /*          nhstepm=nhstepm*YEARM; aff par mois*/
+       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       oldm=oldms;savm=savms;
+       hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
+       fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+       for(i=1; i<=nlstate;i++)
+         for(j=1; j<=nlstate+ndeath;j++)
+           fprintf(ficrespij," %1d-%1d",i,j);
+       fprintf(ficrespij,"\n");
+       for (h=0; h<=nhstepm; h++){
+         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+         fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
+         for(i=1; i<=nlstate;i++)
+           for(j=1; j<=nlstate+ndeath;j++)
+             fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+         fprintf(ficrespij,"\n");
+       }
+       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       fprintf(ficrespij,"\n");
+     }
+   }
+   /*}*/
+   return 0;
+ }
+  int hBijx(double *p, int bage, int fage, double ***prevacurrent){
+     /*------------- h Bij x at various ages ------------*/
+     /* To be optimized with precov */
+   int stepsize;
+   /* int agelim; */
+         int ageminl;
+   int hstepm;
+   int nhstepm;
+   int h, i, i1, j, k, nres;
+   double agedeb;
+   double ***p3mat;
+   strcpy(filerespijb,"PIJB_");  strcat(filerespijb,fileresu);
+   if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
+     printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
+     fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
+   }
+   printf("Computing pij back: result on file '%s' \n", filerespijb);
+   fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   /*if (stepm<=24) stepsize=2;*/
+   /* agelim=AGESUP; */
+   ageminl=AGEINF; /* was 30 */
+   hstepm=stepsize*YEARM; /* Every year of age */
+   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+   /* hstepm=1;   aff par mois*/
+   pstamp(ficrespijb);
+   fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
+   i1= pow(2,cptcoveff);
+   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+   /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
+   /*    k=k+1;  */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     k=TKresult[nres];
+     /* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying *\/ */
+     /*    if(i1 != 1 && TKresult[nres]!= k) */
+     /*  continue; */
+     fprintf(ficrespijb,"\n#****** ");
+     for(j=1;j<=cptcovs;j++){
+       fprintf(ficrespij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+       /* for(j=1;j<=cptcoveff;j++) */
+       /*        fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+       /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
+       /*        fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+     }
+     fprintf(ficrespijb,"******\n");
+     if(invalidvarcomb[k]){  /* Is it necessary here? */
+       fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
+       continue;
+     }
+     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
+       /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
+       nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
+       nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
+       /*          nhstepm=nhstepm*YEARM; aff par mois*/
+       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
+       /* and memory limitations if stepm is small */
+       /* oldm=oldms;savm=savms; */
+       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
+       hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */
+       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
+       fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
+       for(i=1; i<=nlstate;i++)
+         for(j=1; j<=nlstate+ndeath;j++)
+           fprintf(ficrespijb," %1d-%1d",i,j);
+       fprintf(ficrespijb,"\n");
+       for (h=0; h<=nhstepm; h++){
+         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+         fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
+         /* fprintf(ficrespijb,"%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(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */
+         fprintf(ficrespijb,"\n");
+       }
+       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       fprintf(ficrespijb,"\n");
+     } /* end age deb */
+     /* } /\* end combination *\/ */
+   } /* end nres */
+   return 0;
+  } /*  hBijx */
-  }
  /***********************************************/
  /**************** Main Program *****************/
- Line 5502  int main(int argc, char *argv[])
+ Line 11915  int main(int argc, char *argv[])
    double ssval;
  #endif
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
+   int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
+   /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
+   int ncvyear=0; /* Number of years needed for the period prevalence to converge */
    int jj, ll, li, lj, lk;
    int numlinepar=0; /* Current linenumber of parameter file */
+   int num_filled;
    int itimes;
    int NDIM=2;
    int vpopbased=0;
+   int nres=0;
+   int endishere=0;
+   int noffset=0;
+   int ncurrv=0; /* Temporary variable */
    char ca[32], cb[32];
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
    struct stat info;
-   double agedeb;
+   double agedeb=0.;
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
+   double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
    double fret;
-   double dum; /* Dummy variable */
+   double dum=0.; /* Dummy variable */
    double ***p3mat;
-   double ***mobaverage;
+   /* double ***mobaverage; */
+   double wald;
    char line[MAXLINE];
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
+   char  modeltemp[MAXLINE];
+   char resultline[MAXLINE], resultlineori[MAXLINE];
    char pathr[MAXLINE], pathimach[MAXLINE];
    char *tok, *val; /* pathtot */
-   int firstobs=1, lastobs=10;
+   /* int firstobs=1, lastobs=10; /\* nobs = lastobs-firstobs declared globally ;*\/ */
-   int c,  h , cpt;
+   int c,  h , cpt, c2;
-   int jl;
+   int jl=0;
-   int i1, j1, jk, stepsize;
+   int i1, j1, jk, stepsize=0;
+   int count=0;
    int *tab;
    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
+   /* double anprojf, mprojf, jprojf; */
+   /* double jintmean,mintmean,aintmean;   */
+   int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
+   int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
+   double yrfproj= 10.0; /* Number of years of forward projections */
+   double yrbproj= 10.0; /* Number of years of backward projections */
+   int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
    int mobilav=0,popforecast=0;
-   int hstepm, nhstepm;
+   int hstepm=0, nhstepm=0;
    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=0, fage=110, age, agelim, agebase;
+   double bage=0, fage=110., age, agelim=0., agebase=0.;
    double ftolpl=FTOL;
    double **prlim;
-   double ***param; /* Matrix of parameters */
+   double **bprlim;
-   double  *p;
+   double ***param; /* Matrix of parameters, param[i][j][k] param=ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel)
+                     state of origin, state of destination including death, for each covariate: constante, age, and V1 V2 etc. */
+   double ***paramstart; /* Matrix of starting parameter values */
+   double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
    double **matcov; /* Matrix of covariance */
+   double **hess; /* Hessian matrix */
    double ***delti3; /* Scale */
    double *delti; /* Scale */
    double ***eij, ***vareij;
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double dateprev1, dateprev2;
+   double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
+   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
    double **ximort;
    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
    int *dcwave;
- Line 5595  int main(int argc, char *argv[])
+ Line 12040  int main(int argc, char *argv[])
    nberr=0; /* Number of errors and warnings */
    nbwarn=0;
+ #ifdef WIN32
+   _getcwd(pathcd, size);
+ #else
    getcwd(pathcd, size);
+ #endif
-   printf("\n%s\n%s",version,fullversion);
+   syscompilerinfo(0);
+   printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
    if(argc <=1){
      printf("\nEnter the parameter file name: ");
-     fgets(pathr,FILENAMELENGTH,stdin);
+     if(!fgets(pathr,FILENAMELENGTH,stdin)){
+       printf("ERROR Empty parameter file name\n");
+       goto end;
+     }
      i=strlen(pathr);
      if(pathr[i-1]=='\n')
        pathr[i-1]='\0';
      i=strlen(pathr);
-     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
+     if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
        pathr[i-1]='\0';
-    for (tok = pathr; tok != NULL; ){
+     }
+     i=strlen(pathr);
+     if( i==0 ){
+       printf("ERROR Empty parameter file name\n");
+       goto end;
+     }
+     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);
- Line 5615  int main(int argc, char *argv[])
+ Line 12073  int main(int argc, char *argv[])
        if(pathr[0] == '\0') break; /* Dirty */
      }
    }
+   else if (argc<=2){
+     strcpy(pathtot,argv[1]);
+   }
    else{
      strcpy(pathtot,argv[1]);
+     strcpy(z,argv[2]);
+     printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
    }
    /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
    /*cygwin_split_path(pathtot,path,optionfile);
- Line 5631  int main(int argc, char *argv[])
+ Line 12094  int main(int argc, char *argv[])
    /* 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);
+ #ifdef WIN32
+   _chdir(path); /* Can be a relative path */
+   if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+ #else
    chdir(path); /* Can be a relative path */
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+   if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
-     printf("Current directory %s!\n",pathcd);
+ #endif
+   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);
+     printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
      /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
      /* fclose(ficlog); */
  /*     exit(1); */
- Line 5648  int main(int argc, char *argv[])
+ Line 12116  int main(int argc, char *argv[])
    /*-------- arguments in the command line --------*/
-   /* Log file */
+   /* Main Log file */
    strcat(filelog, optionfilefiname);
    strcat(filelog,".log");    /* */
    if((ficlog=fopen(filelog,"w"))==NULL)    {
- Line 5656  int main(int argc, char *argv[])
+ Line 12124  int main(int argc, char *argv[])
      goto end;
    }
    fprintf(ficlog,"Log filename:%s\n",filelog);
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+   fprintf(ficlog,"Version %s %s",version,fullversion);
    fprintf(ficlog,"\nEnter the parameter file name: \n");
    fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
   path=%s \n\
- Line 5664  int main(int argc, char *argv[])
+ Line 12132  int main(int argc, char *argv[])
   optionfilext=%s\n\
   optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-   syscompilerinfo();
+   syscompilerinfo(1);
    printf("Local time (at start):%s",strstart);
    fprintf(ficlog,"Local time (at start): %s",strstart);
- Line 5675  int main(int argc, char *argv[])
+ Line 12143  int main(int argc, char *argv[])
    /* */
    strcpy(fileres,"r");
    strcat(fileres, optionfilefiname);
+   strcat(fileresu, optionfilefiname); /* Without r in front */
    strcat(fileres,".txt");    /* Other files have txt extension */
+   strcat(fileresu,".txt");    /* Other files have txt extension */
-   /*---------arguments file --------*/
+   /* Main ---------arguments file --------*/
    if((ficpar=fopen(optionfile,"r"))==NULL)    {
      printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
- Line 5687  int main(int argc, char *argv[])
+ Line 12157  int main(int argc, char *argv[])
      exit(70);
    }
    strcpy(filereso,"o");
-   strcat(filereso,fileres);
+   strcat(filereso,fileresu);
    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;
    }
+       /*-------- 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", rfileres);goto end;
+     fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
+     fflush(ficlog);
+     goto end;
+   }
+   fprintf(ficres,"#IMaCh %s\n",version);
    /* Reads comments: lines beginning with '#' */
    numlinepar=0;
-   while((c=getc(ficpar))=='#' && c!= EOF){
+   /* Is it a BOM UTF-8 Windows file? */
-     ungetc(c,ficpar);
+   /* First parameter line */
-     fgets(line, MAXLINE, ficpar);
+   while(fgets(line, MAXLINE, ficpar)) {
+     noffset=0;
+     if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
+     {
+       noffset=noffset+3;
+       printf("# File is an UTF8 Bom.\n"); // 0xBF
+     }
+ /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
+     else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
+     {
+       noffset=noffset+2;
+       printf("# File is an UTF16BE BOM file\n");
+     }
+     else if( line[0] == 0 && line[1] == 0)
+     {
+       if( line[2] == (char)0xFE && line[3] == (char)0xFF){
+         noffset=noffset+4;
+         printf("# File is an UTF16BE BOM file\n");
+       }
+     } else{
+       ;/*printf(" Not a BOM file\n");*/
+     }
+     /* If line starts with a # it is a comment */
+     if (line[noffset] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficres);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
+                         title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
+     if (num_filled != 5) {
+       printf("Should be 5 parameters\n");
+       fprintf(ficlog,"Should be 5 parameters\n");
+     }
      numlinepar++;
-     fputs(line,stdout);
+     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
-     fputs(line,ficparo);
+     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
-     fputs(line,ficlog);
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+   }
+   /* Second parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* while(fscanf(ficpar,"%[^\n]", line)) { */
+     /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
+     if (line[0] == '#') {
+       numlinepar++;
+       printf("%s",line);
+       fprintf(ficres,"%s",line);
+       fprintf(ficparo,"%s",line);
+       fprintf(ficlog,"%s",line);
+       continue;
+     }else
+       break;
    }
-   ungetc(c,ficpar);
+   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
+                         &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
-   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);
+     if (num_filled != 11) {
-   numlinepar++;
+       printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
-   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);
+       printf("but line=%s\n",line);
-   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,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
-   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);
+       fprintf(ficlog,"but line=%s\n",line);
+     }
+     if( lastpass > maxwav){
+       printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
+       fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
+       fflush(ficlog);
+       goto end;
+     }
+       printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+     fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+     fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
+     fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+   }
+   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
+   /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
+   /* Third parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       printf("%s",line);
+       fprintf(ficres,"%s",line);
+       fprintf(ficparo,"%s",line);
+       fprintf(ficlog,"%s",line);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
+     if (num_filled != 1){
+       printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
+       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
+       model[0]='\0';
+       goto end;
+     }
+     else{
+       if (model[0]=='+'){
+         for(i=1; i<=strlen(model);i++)
+           modeltemp[i-1]=model[i];
+         strcpy(model,modeltemp);
+       }
+     }
+     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
+     printf("model=1+age+%s\n",model);fflush(stdout);
+     fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
+     fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
+     fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
+   }
+   /* 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=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
+   /* numlinepar=numlinepar+3; /\* In general *\/ */
+   /* 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=1+age+%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 nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
+   /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
    fflush(ficlog);
+   /* if(model[0]=='#'|| model[0]== '\0'){ */
+   if(model[0]=='#'){
+     printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
+  'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
+  'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n");            \
+     if(mle != -1){
+       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
+       exit(1);
+     }
+   }
    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
      numlinepar++;
+     if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
+       z[0]=line[1];
+     }
+     /* printf("****line [1] = %c \n",line[1]); */
      fputs(line, stdout);
      //puts(line);
      fputs(line,ficparo);
- Line 5728  int main(int argc, char *argv[])
+ Line 12329  int main(int argc, char *argv[])
    ungetc(c,ficpar);
-   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
+   covar=matrix(0,NCOVMAX,firstobs,lastobs);  /**< used in readdata */
+   if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs);  /**< Fixed quantitative covariate */
+   if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs);  /**< Time varying quantitative covariate */
+   if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs);  /**< Time varying covariate (dummy and quantitative)*/
    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*/
+     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,age*age makes 3*/
    else
-     ncovmodel=2;
+     ncovmodel=2; /* Constant and age */
-   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){
- Line 5751  int main(int argc, char *argv[])
+ Line 12354  int main(int argc, char *argv[])
    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 */
+ /* We could also provide initial parameters values giving by simple logistic regression
+  * only one way, that is without matrix product. We will have nlstate maximizations */
+       /* for(i=1;i<nlstate;i++){ */
+       /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
+       /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
+       /* } */
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     printf(" You chose 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);
+     fprintf(ficlog," You chose 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==-5) { /* Main Wizard */
-   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);
+     printf(" You chose 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);
+     fprintf(ficlog," You chose 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);
-   }
+     hess=matrix(1,npar,1,npar);
-   else{
+   }  else{ /* Begin of mle != -1 or -5 */
      /* Read guessed parameters */
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
- Line 5781  int main(int argc, char *argv[])
+ Line 12389  int main(int argc, char *argv[])
      ungetc(c,ficpar);
      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     paramstart= 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++;
+         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,"%1d%1d",&i1,&j1);
-         if ((i1 != i) && (j1 != j)){
+         if ((i1 != i) || (j1 != jj)){
            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);
- Line 5795  run imach with mle=-1 to get a correct t
+ Line 12413  run imach with mle=-1 to get a correct t
          }
          fprintf(ficparo,"%1d%1d",i1,j1);
          if(mle==1)
-           printf("%1d%1d",i,j);
+           printf("%1d%1d",i,jj);
-         fprintf(ficlog,"%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i,jj);
          for(k=1; k<=ncovmodel;k++){
            fscanf(ficpar," %lf",&param[i][j][k]);
            if(mle==1){
- Line 5816  run imach with mle=-1 to get a correct t
+ Line 12434  run imach with mle=-1 to get a correct t
        }
      }
      fflush(ficlog);
-     /* Reads scales values */
+     /* Reads parameters values */
      p=param[1][1];
+     pstart=paramstart[1][1];
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
- Line 5855  run imach with mle=-1 to get a correct t
+ Line 12474  run imach with mle=-1 to get a correct t
        }
      }
      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);
- Line 5872  run imach with mle=-1 to get a correct t
+ Line 12491  run imach with mle=-1 to get a correct t
        fputs(line,ficlog);
      }
      ungetc(c,ficpar);
      matcov=matrix(1,npar,1,npar);
+     hess=matrix(1,npar,1,npar);
      for(i=1; i <=npar; i++)
        for(j=1; j <=npar; j++) matcov[i][j]=0.;
+     /* Scans npar lines */
      for(i=1; i <=npar; i++){
-       fscanf(ficpar,"%s",str);
+       count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
-       if(mle==1)
+       if(count != 3){
-         printf("%s",str);
+         printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
-       fprintf(ficlog,"%s",str);
+ This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
-       fprintf(ficparo,"%s",str);
+ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+         fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+ This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+         exit(1);
+       }else{
+         if(mle==1)
+           printf("%1d%1d%d",i1,j1,jk);
+       }
+       fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
+       fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
        for(j=1; j <=i; j++){
          fscanf(ficpar," %le",&matcov[i][j]);
          if(mle==1){
- Line 5894  run imach with mle=-1 to get a correct t
+ Line 12525  run imach with mle=-1 to get a correct t
        fscanf(ficpar,"\n");
        numlinepar++;
        if(mle==1)
-         printf("\n");
+                                 printf("\n");
        fprintf(ficlog,"\n");
        fprintf(ficparo,"\n");
      }
+     /* End of read covariance matrix npar lines */
      for(i=1; i <=npar; i++)
        for(j=i+1;j<=npar;j++)
          matcov[i][j]=matcov[j][i];
- Line 5908  run imach with mle=-1 to get a correct t
+ Line 12540  run imach with mle=-1 to get a correct t
      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 */
+   /*  Main data
-   n= lastobs;
+    */
-   num=lvector(1,n);
+   nobs=lastobs-firstobs+1; /* was = lastobs;*/
-   moisnais=vector(1,n);
+   /* num=lvector(1,n); */
-   annais=vector(1,n);
+   /* moisnais=vector(1,n); */
-   moisdc=vector(1,n);
+   /* annais=vector(1,n); */
-   andc=vector(1,n);
+   /* moisdc=vector(1,n); */
-   agedc=vector(1,n);
+   /* andc=vector(1,n); */
-   cod=ivector(1,n);
+   /* weight=vector(1,n); */
-   weight=vector(1,n);
+   /* agedc=vector(1,n); */
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   /* cod=ivector(1,n); */
-   mint=matrix(1,maxwav,1,n);
+   /* for(i=1;i<=n;i++){ */
-   anint=matrix(1,maxwav,1,n);
+   num=lvector(firstobs,lastobs);
-   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
+   moisnais=vector(firstobs,lastobs);
+   annais=vector(firstobs,lastobs);
+   moisdc=vector(firstobs,lastobs);
+   andc=vector(firstobs,lastobs);
+   weight=vector(firstobs,lastobs);
+   agedc=vector(firstobs,lastobs);
+   cod=ivector(firstobs,lastobs);
+   for(i=firstobs;i<=lastobs;i++){
+     num[i]=0;
+     moisnais[i]=0;
+     annais[i]=0;
+     moisdc[i]=0;
+     andc[i]=0;
+     agedc[i]=0;
+     cod[i]=0;
+     weight[i]=1.0; /* Equal weights, 1 by default */
+   }
+   mint=matrix(1,maxwav,firstobs,lastobs);
+   anint=matrix(1,maxwav,firstobs,lastobs);
+   s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
+   /* printf("BUG ncovmodel=%d NCOVMAX=%d 2**ncovmodel=%f BUG\n",ncovmodel,NCOVMAX,pow(2,ncovmodel)); */
    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 */
+   ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 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
+   /*    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. */
+   TvarsDind=ivector(1,NCOVMAX); /*  */
+   TnsdVar=ivector(1,NCOVMAX); /*  */
+     /* for(i=1; i<=NCOVMAX;i++) TnsdVar[i]=3; */
+   TvarsD=ivector(1,NCOVMAX); /*  */
+   TvarsQind=ivector(1,NCOVMAX); /*  */
+   TvarsQ=ivector(1,NCOVMAX); /*  */
+   TvarF=ivector(1,NCOVMAX); /*  */
+   TvarFind=ivector(1,NCOVMAX); /*  */
+   TvarV=ivector(1,NCOVMAX); /*  */
+   TvarVind=ivector(1,NCOVMAX); /*  */
+   TvarA=ivector(1,NCOVMAX); /*  */
+   TvarAind=ivector(1,NCOVMAX); /*  */
+   TvarFD=ivector(1,NCOVMAX); /*  */
+   TvarFDind=ivector(1,NCOVMAX); /*  */
+   TvarFQ=ivector(1,NCOVMAX); /*  */
+   TvarFQind=ivector(1,NCOVMAX); /*  */
+   TvarVD=ivector(1,NCOVMAX); /*  */
+   TvarVDind=ivector(1,NCOVMAX); /*  */
+   TvarVQ=ivector(1,NCOVMAX); /*  */
+   TvarVQind=ivector(1,NCOVMAX); /*  */
+   Tvalsel=vector(1,NCOVMAX); /*  */
+   Tvarsel=ivector(1,NCOVMAX); /*  */
+   Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
+   Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
+   Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
    /*  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.
- Line 5958  run imach with mle=-1 to get a correct t
+ Line 12628  run imach with mle=-1 to get a correct t
      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=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
+   Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
    /* 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)
+      Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
    */
    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) */
+   Tvardk=imatrix(1,NCOVMAX,1,2);
    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
-                       */
+                            */
+   for(i=1;i<NCOVMAX;i++)
+     Tage[i]=0;
+   Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
+                                 * individual dummy, fixed or varying:
+                                 * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
+                                 * 3, 1, 0, 0, 0, 0, 0, 0},
+                                 * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
+                                 * V1 df, V2 qf, V3 & V4 dv, V5 qv
+                                 * Tmodelind[1]@9={9,0,3,2,}*/
+   TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
+   TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
+                                 * individual quantitative, fixed or varying:
+                                 * Tmodelqind[1]=1,Tvaraff[1]@9={4,
+                                 * 3, 1, 0, 0, 0, 0, 0, 0},
+                                 * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ /* Main decodemodel */
-   if(decodemodel(model, lastobs) == 1)
+   if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
      goto end;
    if((double)(lastobs-imx)/(double)imx > 1.10){
- Line 5992  run imach with mle=-1 to get a correct t
+ Line 12682  run imach with mle=-1 to get a correct t
    agegomp=(int)agemin;
-   free_vector(moisnais,1,n);
+   free_vector(moisnais,firstobs,lastobs);
-   free_vector(annais,1,n);
+   free_vector(annais,firstobs,lastobs);
    /* free_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n);*/
-   free_vector(moisdc,1,n);
+   /* free_vector(moisdc,1,n); */
-   free_vector(andc,1,n);
+   /* free_vector(andc,1,n); */
    /* */
    wav=ivector(1,imx);
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
+   dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
+   bh=imatrix(1,lastpass-firstpass+2,1,imx);
+   mw=imatrix(1,lastpass-firstpass+2,1,imx);
    /* Concatenates waves */
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+      Death is a valid wave (if date is known).
+      mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+      and mw[mi+1][i]. dh depends on stepm.
+   */
    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-   /* */
+   /* Concatenates waves */
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   free_vector(moisdc,firstobs,lastobs);
+   free_vector(andc,firstobs,lastobs);
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
    ncodemax[1]=1;
    Ndum =ivector(-1,NCOVMAX);
-   if (ncovmodel > 2)
+   cptcoveff=0;
-     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
+   if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
+     tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; as well as calculate cptcoveff or number of total effective dummy covariates*/
+   }
+   ncovcombmax=pow(2,cptcoveff);
+   invalidvarcomb=ivector(1, ncovcombmax);
+   for(i=1;i<ncovcombmax;i++)
+     invalidvarcomb[i]=0;
+   /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
+      V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
+   /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
+   /*  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],codtabm(100,10));*/
+   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
+   /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
+    * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
+    * (currently 0 or 1) in the data.
+    * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
+    * corresponding modality (h,j).
+    */
-   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++){ /* scans any effective covariate */
-     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 each modality of this covariate ncodemax=2*/
-         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)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
-            *     h     1     2     3     4
+            * For k=4 covariates, h goes from 1 to m=2**k
-            *______________________________
+            * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
-            *     1 i=1 1 i=1 1 i=1 1 i=1 1
+            * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
-            *     2     2     1     1     1
+            *     h\k   1     2     3     4   *  h-1\k-1  4  3  2  1
-            *     3 i=2 1     2     1     1
+            *______________________________   *______________________
-            *     4     2     2     1     1
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1   *     0     0  0  0  0
-            *     5 i=3 1 i=2 1     2     1
+            *     2     2     1     1     1   *     1     0  0  0  1
-            *     6     2     1     2     1
+            *     3 i=2 1     2     1     1   *     2     0  0  1  0
-            *     7 i=4 1     2     2     1
+            *     4     2     2     1     1   *     3     0  0  1  1
-            *     8     2     2     2     1
+            *     5 i=3 1 i=2 1     2     1   *     4     0  1  0  0
-            *     9 i=5 1 i=3 1 i=2 1     1
+            *     6     2     1     2     1   *     5     0  1  0  1
-            *    10     2     1     1     1
+            *     7 i=4 1     2     2     1   *     6     0  1  1  0
-            *    11 i=6 1     2     1     1
+            *     8     2     2     2     1   *     7     0  1  1  1
-            *    12     2     2     1     1
+            *     9 i=5 1 i=3 1 i=2 1     2   *     8     1  0  0  0
-            *    13 i=7 1 i=4 1     2     1
+            *    10     2     1     1     2   *     9     1  0  0  1
-            *    14     2     1     2     1
+            *    11 i=6 1     2     1     2   *    10     1  0  1  0
-            *    15 i=8 1     2     2     1
+            *    12     2     2     1     2   *    11     1  0  1  1
-            *    16     2     2     2     1
+            *    13 i=7 1 i=4 1     2     2   *    12     1  1  0  0
-            */
+            *    14     2     1     2     2   *    13     1  1  0  1
-           codtab[h][k]=j;
+            *    15 i=8 1     2     2     2   *    14     1  1  1  0
-           /*codtab[h][Tvar[k]]=j;*/
+            *    16     2     2     2     2   *    15     1  1  1  1
-           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]]);
+            */
-         }
+   /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
-       }
+      /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
-     }
+      * and the value of each covariate?
-   }
+      * V1=1, V2=1, V3=2, V4=1 ?
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+      * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
-      codtab[1][2]=1;codtab[2][2]=2; */
+      * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
-   /* for(i=1; i <=m ;i++){
+      * In order to get the real value in the data, we use nbcode
-      for(k=1; k <=cptcovn; k++){
+      * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
-        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+      * We are keeping this crazy system in order to be able (in the future?)
-      }
+      * to have more than 2 values (0 or 1) for a covariate.
-      printf("\n");
+      * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
-      }
+      * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
-      scanf("%d",i);*/
+      *              bbbbbbbb
+      *              76543210
+      *   h-1        00000101 (6-1=5)
+      *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
+      *           &
+      *     1        00000001 (1)
+      *              00000000        = 1 & ((h-1) >> (k-1))
+      *          +1= 00000001 =1
+      *
+      * h=14, k=3 => h'=h-1=13, k'=k-1=2
+      *          h'      1101 =2^3+2^2+0x2^1+2^0
+      *    >>k'            11
+      *          &   00000001
+      *            = 00000001
+      *      +1    = 00000010=2    =  codtabm(14,3)
+      * Reverse h=6 and m=16?
+      * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
+      * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
+      * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
+      * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
+      * V3=decodtabm(14,3,2**4)=2
+      *          h'=13   1101 =2^3+2^2+0x2^1+2^0
+      *(h-1) >> (j-1)    0011 =13 >> 2
+      *          &1 000000001
+      *           = 000000001
+      *         +1= 000000010 =2
+      *                  2211
+      *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
+      *                  V3=2
+                  * codtabm and decodtabm are identical
+      */
   free_ivector(Ndum,-1,NCOVMAX);
-   /*------------ gnuplot -------------*/
+   /* Initialisation of ----------- gnuplot -------------*/
    strcpy(optionfilegnuplot,optionfilefiname);
    if(mle==-3)
-     strcat(optionfilegnuplot,"-mort");
+     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,"\n# IMaCh-%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 --------*/
+   /* Initialisation of --------- index.htm --------*/
    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
    if(mle==-3)
-     strcat(optionfilehtm,"-mort");
+     strcat(optionfilehtm,"-MORT_");
    strcat(optionfilehtm,".htm");
    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
      printf("Problem with %s \n",optionfilehtm);
- Line 6110  run imach with mle=-1 to get a correct t
+ Line 12853  run imach with mle=-1 to get a correct t
    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",\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%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> \
+   fprintf(fichtm,"<html><head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n\
+ <title>IMaCh %s</title></head>\n\
+  <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n\
+ <font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>\
+ -EUROREVES-Institut de longévité-2013-2022-Japan Society for the Promotion of Sciences 日本学術振興会 \
+ (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - \
+ <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \n", optionfilehtm);
+   fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\"> \n\
+ <font size=\"2\">IMaCh-%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\
+ This file: <a href=\"%s\">%s</a></br>Title=%s <br>Datafile=<a href=\"%s\">%s</a> Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
  \n\
  <hr  size=\"2\" color=\"#EC5E5E\">\
   <ul><li><h4>Parameter files</h4>\n\
- Line 6125  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 12877  Title=%s <br>Datafile=%s Firstpass=%d La
   - 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,\
+           version,fullversion,optionfilehtm,optionfilehtm,title,datafile,datafile,firstpass,lastpass,stepm, weightopt, model, \
            optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
            fileres,fileres,\
            filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
- Line 6133  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 12885  Title=%s <br>Datafile=%s Firstpass=%d La
    strcpy(pathr,path);
    strcat(pathr,optionfilefiname);
+ #ifdef WIN32
+   _chdir(optionfilefiname); /* Move to directory named optionfile */
+ #else
    chdir(optionfilefiname); /* Move to directory named optionfile */
+ #endif
    /* Calculates basic frequencies. Computes observed prevalence at single age
+                  and for any valid combination of covariates
       and prints on file fileres'p'. */
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+   freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
+               firstpass, lastpass,  stepm,  weightopt, model);
    fprintf(fichtm,"\n");
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+   fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\
+           ftol, stepm);
+   fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
+   ncurrv=1;
+   for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
+   ncurrv=i;
+   for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
+   ncurrv=i;
+   for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li>Number of time varying  quantitative covariates: nqtv=%d ", nqtv);
+   ncurrv=i;
+   for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
+            nlstate, ndeath, maxwav, mle, weightopt);
+   fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
+ <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
+   fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Number of (used) 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);
+   imx,agemin,agemax,jmin,jmax,jmean);
    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     oldms= 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 */
+   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     savms= 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 */
+   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*/
+   /* For mortality only */
    if (mle==-3){
      ximort=matrix(1,NDIM,1,NDIM);
- /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
+     for(i=1;i<=NDIM;i++)
-     cens=ivector(1,n);
+       for(j=1;j<=NDIM;j++)
-     ageexmed=vector(1,n);
+         ximort[i][j]=0.;
-     agecens=vector(1,n);
+     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-     dcwave=ivector(1,n);
+     cens=ivector(firstobs,lastobs);
+     ageexmed=vector(firstobs,lastobs);
+     agecens=vector(firstobs,lastobs);
+     dcwave=ivector(firstobs,lastobs);
      for (i=1; i<=imx; i++){
        dcwave[i]=-1;
        for (m=firstpass; m<=lastpass; m++)
- Line 6174  Interval (in months) between two waves:
+ Line 12956  Interval (in months) between two waves:
            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;
- Line 6197  Interval (in months) between two waves:
+ Line 12979  Interval (in months) between two waves:
          ximort[i][j]=(i == j ? 1.0 : 0.0);
      }
-     /*p[1]=0.0268; p[NDIM]=0.083;*/
+     p[1]=0.0268; p[NDIM]=0.083;
-     /*printf("%lf %lf", p[1], p[2]);*/
+     /* printf("%lf %lf", p[1], p[2]); */
  #ifdef GSL
- Line 6206  Interval (in months) between two waves:
+ Line 12988  Interval (in months) between two waves:
  #else
      printf("Powell\n");  fprintf(ficlog,"Powell\n");
  #endif
-     strcpy(filerespow,"pow-mort");
+     strcpy(filerespow,"POW-MORT_");
-     strcat(filerespow,fileres);
+     strcat(filerespow,fileresu);
      if((ficrespow=fopen(filerespow,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", filerespow);
        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
- Line 6249  Interval (in months) between two waves:
+ Line 13031  Interval (in months) between two waves:
      /* Initialize method and iterate */
      /*     p[1]=0.0268; p[NDIM]=0.083; */
- /*     gsl_vector_set(x, 0, 0.0268); */
+     /*     gsl_vector_set(x, 0, 0.0268); */
- /*     gsl_vector_set(x, 1, 0.083); */
+     /*     gsl_vector_set(x, 1, 0.083); */
      gsl_vector_set(x, 0, p[1]);
      gsl_vector_set(x, 1, p[2]);
- Line 6303  Interval (in months) between two waves:
+ Line 13085  Interval (in months) between two waves:
  #endif
      fclose(ficrespow);
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+     hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
      for(i=1; i <=NDIM; i++)
        for(j=i+1;j<=NDIM;j++)
-         matcov[i][j]=matcov[j][i];
+                                 matcov[i][j]=matcov[j][i];
      printf("\nCovariance matrix\n ");
+     fprintf(ficlog,"\nCovariance matrix\n ");
      for(i=1; i <=NDIM; i++) {
        for(j=1;j<=NDIM;j++){
-         printf("%f ",matcov[i][j]);
+                                 printf("%f ",matcov[i][j]);
+                                 fprintf(ficlog,"%f ",matcov[i][j]);
        }
-       printf("\n ");
+       printf("\n ");  fprintf(ficlog,"\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++)
+     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]));
+       fprintf(ficlog,"%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);
+     lsurv=vector(agegomp,AGESUP);
-     tpop=vector(1,AGESUP);
+     lpop=vector(agegomp,AGESUP);
+     tpop=vector(agegomp,AGESUP);
      lsurv[agegomp]=100000;
      for (k=agegomp;k<=AGESUP;k++) {
- Line 6352  Interval (in months) between two waves:
+ Line 13137  Interval (in months) between two waves:
      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+                 ageminpar=50;
+                 agemaxpar=100;
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+     if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
+         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+     }else{
+                         printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
+                         fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
+       printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+                 }
+     printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                       stepm, weightopt,\
                       model,imx,p,matcov,agemortsup);
-     free_vector(lsurv,1,AGESUP);
+     free_vector(lsurv,agegomp,AGESUP);
-     free_vector(lpop,1,AGESUP);
+     free_vector(lpop,agegomp,AGESUP);
-     free_vector(tpop,1,AGESUP);
+     free_vector(tpop,agegomp,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);
+     free_ivector(dcwave,firstobs,lastobs);
+     free_vector(agecens,firstobs,lastobs);
+     free_vector(ageexmed,firstobs,lastobs);
+     free_ivector(cens,firstobs,lastobs);
+ #ifdef GSL
  #endif
-   } /* Endof if mle==-3 */
+   } /* Endof if mle==-3 mortality only */
+   /* Standard  */
-   else{ /* For mle >=1 */
+   else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
-     globpr=0;/* debug */
+     globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+     /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
      printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
      for (k=1; k<=npar;k++)
        printf(" %d %8.5f",k,p[k]);
      printf("\n");
-     globpr=1; /* to print the contributions */
+     if(mle>=1){ /* Could be 1 or 2, Real Maximization */
+       /* mlikeli uses func not funcone */
+       /* for(i=1;i<nlstate;i++){ */
+       /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
+       /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
+       /* } */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
+       globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+       /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
+       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     }
+     globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
      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);
+           /* exit(0); */
      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,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, 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");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); /* Printing model equation */
      fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("#model=  1      +     age ");
+     fprintf(ficres,"#model=  1      +     age ");
+     fprintf(ficlog,"#model=  1      +     age ");
+     fprintf(fichtm,"\n<ul><li> model=1+age+%s\n \
+ </ul>", model);
+     fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">\n");
+     fprintf(fichtm, "<tr><th>Model=</th><th>1</th><th>+ age</th>");
+     if(nagesqr==1){
+       printf("  + age*age  ");
+       fprintf(ficres,"  + age*age  ");
+       fprintf(ficlog,"  + age*age  ");
+       fprintf(fichtm, "<th>+ age*age</th>");
+     }
+     for(j=1;j <=ncovmodel-2;j++){
+       if(Typevar[j]==0) {
+         printf("  +      V%d  ",Tvar[j]);
+         fprintf(ficres,"  +      V%d  ",Tvar[j]);
+         fprintf(ficlog,"  +      V%d  ",Tvar[j]);
+         fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
+       }else if(Typevar[j]==1) {
+         printf("  +    V%d*age ",Tvar[j]);
+         fprintf(ficres,"  +    V%d*age ",Tvar[j]);
+         fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
+         fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
+       }else if(Typevar[j]==2) {
+         printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(ficres,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+       }
+     }
+     printf("\n");
+     fprintf(ficres,"\n");
+     fprintf(ficlog,"\n");
+     fprintf(fichtm, "</tr>");
+     fprintf(fichtm, "\n");
      for(i=1,jk=1; i <=nlstate; i++){
        for(k=1; k <=(nlstate+ndeath); k++){
          if (k != i) {
+           fprintf(fichtm, "<tr>");
            printf("%d%d ",i,k);
            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);
+           fprintf(fichtm, "<td>%1d%1d</td>",i,k);
            for(j=1; j <=ncovmodel; j++){
-             printf("%lf ",p[jk]);
+             printf("%12.7f ",p[jk]);
-             fprintf(ficlog,"%lf ",p[jk]);
+             fprintf(ficlog,"%12.7f ",p[jk]);
-             fprintf(ficres,"%lf ",p[jk]);
+             fprintf(ficres,"%12.7f ",p[jk]);
+             fprintf(fichtm, "<td>%12.7f</td>",p[jk]);
              jk++;
            }
            printf("\n");
            fprintf(ficlog,"\n");
            fprintf(ficres,"\n");
+           fprintf(fichtm, "</tr>\n");
          }
        }
      }
-     if(mle!=0){
+     /* fprintf(fichtm,"</tr>\n"); */
-       /* Computing hessian and covariance matrix */
+     fprintf(fichtm,"</table>\n");
+     fprintf(fichtm, "\n");
+     if(mle != 0){
+       /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
        ftolhess=ftol; /* Usually correct */
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+       hesscov(matcov, hess, p, npar, delti, ftolhess, func);
-     }
+       printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       fprintf(fichtm, "\n<p>The Wald test results are output only if the maximimzation of the Likelihood is performed (mle=1)\n</br>Parameters, Wald tests and Wald-based confidence intervals\n</br> W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n</br> And Wald-based confidence intervals plus and minus 1.96 * W \n </br> It might be better to visualize the covariance matrix. See the page '<a href=\"%s\">Matrix of variance-covariance of one-step probabilities and its graphs</a>'.\n</br>",optionfilehtmcov);
+       fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">");
+       fprintf(fichtm, "\n<tr><th>Model=</th><th>1</th><th>+ age</th>");
+       if(nagesqr==1){
+         printf("  + age*age  ");
+         fprintf(ficres,"  + age*age  ");
+         fprintf(ficlog,"  + age*age  ");
+         fprintf(fichtm, "<th>+ age*age</th>");
+       }
+       for(j=1;j <=ncovmodel-2;j++){
+         if(Typevar[j]==0) {
+           printf("  +      V%d  ",Tvar[j]);
+           fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
+         }else if(Typevar[j]==1) {
+           printf("  +    V%d*age ",Tvar[j]);
+           fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
+         }else if(Typevar[j]==2) {
+           fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         }
+       }
+       fprintf(fichtm, "</tr>\n");
+       for(i=1,jk=1; i <=nlstate; i++){
+         for(k=1; k <=(nlstate+ndeath); k++){
+           if (k != i) {
+             fprintf(fichtm, "<tr valign=top>");
+             printf("%d%d ",i,k);
+             fprintf(ficlog,"%d%d ",i,k);
+             fprintf(fichtm, "<td>%1d%1d</td>",i,k);
+             for(j=1; j <=ncovmodel; j++){
+               wald=p[jk]/sqrt(matcov[jk][jk]);
+               printf("%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               fprintf(ficlog,"%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               if(fabs(wald) > 1.96){
+                 fprintf(fichtm, "<td><b>%12.7f</b></br> (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
+               }else{
+                 fprintf(fichtm, "<td>%12.7f (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
+               }
+               fprintf(fichtm,"W=%8.3f</br>",wald);
+               fprintf(fichtm,"[%12.7f;%12.7f]</br></td>", p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               jk++;
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(fichtm, "</tr>\n");
+           }
+         }
+       }
+     } /* end of hesscov and Wald tests */
+     fprintf(fichtm,"</table>\n");
+     /*  */
      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
      printf("# Scales (for hessian or gradient estimation)\n");
      fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
- Line 6439  Interval (in months) between two waves:
+ Line 13350  Interval (in months) between two waves:
      }
      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) /* To big for the screen */
        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");
      /* # 121 Var(a12)\n\ */
- Line 6502  Interval (in months) between two waves:
+ Line 13413  Interval (in months) between two waves:
                          fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                        }else{
                          if(mle>=1)
-                           printf(" %.5e",matcov[jj][ll]);
+                           printf(" %.7e",matcov[jj][ll]);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.7e",matcov[jj][ll]);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.7e",matcov[jj][ll]);
                        }
                      }
                    }
- Line 6523  Interval (in months) between two waves:
+ Line 13434  Interval (in months) between two waves:
      fflush(ficlog);
      fflush(ficres);
+     while(fgets(line, MAXLINE, ficpar)) {
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       /* If line starts with a # it is a comment */
-       ungetc(c,ficpar);
+       if (line[0] == '#') {
-       fgets(line, MAXLINE, ficpar);
+         numlinepar++;
-       fputs(line,stdout);
+         fputs(line,stdout);
-       fputs(line,ficparo);
+         fputs(line,ficparo);
+         fputs(line,ficlog);
+         fputs(line,ficres);
+         continue;
+       }else
+         break;
      }
-     ungetc(c,ficpar);
+     /* while((c=getc(ficpar))=='#' && c!= EOF){ */
+     /*   ungetc(c,ficpar); */
+     /*   fgets(line, MAXLINE, ficpar); */
+     /*   fputs(line,stdout); */
+     /*   fputs(line,ficparo); */
+     /* } */
+     /* ungetc(c,ficpar); */
      estepm=0;
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
+       if (num_filled != 6) {
+         printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
+         fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
+         goto end;
+       }
+       printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
+     }
+     /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
+     /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
+     /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
      if (estepm==0 || estepm < stepm) estepm=stepm;
      if (fage <= 2) {
        bage = ageminpar;
- Line 6541  Interval (in months) between two waves:
+ Line 13476  Interval (in months) between two waves:
      }
      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     /* Other stuffs, more or less useful */
-       ungetc(c,ficpar);
+     while(fgets(line, MAXLINE, ficpar)) {
-       fgets(line, MAXLINE, ficpar);
+       /* If line starts with a # it is a comment */
-       fputs(line,stdout);
+       if (line[0] == '#') {
-       fputs(line,ficparo);
+         numlinepar++;
+         fputs(line,stdout);
+         fputs(line,ficparo);
+         fputs(line,ficlog);
+         fputs(line,ficres);
+         continue;
+       }else
+         break;
      }
-     ungetc(c,ficpar);
+     if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
-     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);
+       if (num_filled != 7) {
-     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+         printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-     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,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-     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);
+         goto end;
+       }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       printf("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);
+       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);
-       fgets(line, MAXLINE, ficpar);
+       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);
-       fputs(line,stdout);
+       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,ficparo);
+     }
+     while(fgets(line, MAXLINE, ficpar)) {
+       /* If line starts with a # it is a comment */
+       if (line[0] == '#') {
+         numlinepar++;
+         fputs(line,stdout);
+         fputs(line,ficparo);
+         fputs(line,ficlog);
+         fputs(line,ficres);
+         continue;
+       }else
+         break;
      }
-     ungetc(c,ficpar);
      dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+     if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+       if (num_filled != 1) {
-     fprintf(ficres,"pop_based=%d\n",popbased);
+         printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+         fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+         goto end;
-       ungetc(c,ficpar);
+       }
-       fgets(line, MAXLINE, ficpar);
+       printf("pop_based=%d\n",popbased);
-       fputs(line,stdout);
+       fprintf(ficlog,"pop_based=%d\n",popbased);
-       fputs(line,ficparo);
+       fprintf(ficparo,"pop_based=%d\n",popbased);
+       fprintf(ficres,"pop_based=%d\n",popbased);
      }
-     ungetc(c,ficpar);
+     /* Results */
-     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);
+     /* Value of covariate in each resultine will be compututed (if product) and sorted according to model rank */
-     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);
+     /* It is precov[] because we need the varying age in order to compute the real cov[] of the model equation */
-     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);
+     precov=matrix(1,MAXRESULTLINESPONE,1,NCOVMAX+1);
-     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);
+     endishere=0;
-     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);
+     nresult=0;
-     /* day and month of proj2 are not used but only year anproj2.*/
+     parameterline=0;
+     do{
+       if(!fgets(line, MAXLINE, ficpar)){
+         endishere=1;
+         parameterline=15;
+       }else if (line[0] == '#') {
+         /* If line starts with a # it is a comment */
+         numlinepar++;
+         fputs(line,stdout);
+         fputs(line,ficparo);
+         fputs(line,ficlog);
+         fputs(line,ficres);
+         continue;
+       }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
+         parameterline=11;
+       else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
+         parameterline=12;
+       else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
+         parameterline=13;
+       }
+       else{
+         parameterline=14;
+       }
+       switch (parameterline){ /* =0 only if only comments */
+       case 11:
+         if((num_filled=sscanf(line,"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)) !=EOF && (num_filled == 8)){
+                   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.*/
+           dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
+           dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
+           prvforecast = 1;
+         }
+         else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
+           printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+           fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+           fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+           prvforecast = 2;
+         }
+         else {
+           printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+           fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+           goto end;
+         }
+         break;
+       case 12:
+         if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){
+           fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           /* day and month of back2 are not used but only year anback2.*/
+           dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
+           dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
+           prvbackcast = 1;
+         }
+         else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
+           printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+           fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+           fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+           prvbackcast = 2;
+         }
+         else {
+           printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+           fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+           goto end;
+         }
+         break;
+       case 13:
+         num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);
+         nresult++; /* Sum of resultlines */
+         printf("Result %d: result:%s\n",nresult, resultlineori);
+         /* removefirstspace(&resultlineori); */
+         if(strstr(resultlineori,"v") !=0){
+           printf("Error. 'v' must be in upper case 'V' result: %s ",resultlineori);
+           fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultlineori);fflush(ficlog);
+           return 1;
+         }
+         trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */
+         printf("Decoderesult resultline=\"%s\" resultlineori=\"%s\"\n", resultline, resultlineori);
+         if(nresult > MAXRESULTLINESPONE-1){
+           printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
+           fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
+           goto end;
+         }
+         if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
+           fprintf(ficparo,"result: %s\n",resultline);
+           fprintf(ficres,"result: %s\n",resultline);
+           fprintf(ficlog,"result: %s\n",resultline);
+         } else
+           goto end;
+         break;
+       case 14:
+         printf("Error: Unknown command '%s'\n",line);
+         fprintf(ficlog,"Error: Unknown command '%s'\n",line);
+         if(line[0] == ' ' || line[0] == '\n'){
+           printf("It should not be an empty line '%s'\n",line);
+           fprintf(ficlog,"It should not be an empty line '%s'\n",line);
+         }
+         if(ncovmodel >=2 && nresult==0 ){
+           printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
+           fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
+         }
+         /* goto end; */
+         break;
+       case 15:
+         printf("End of resultlines.\n");
+         fprintf(ficlog,"End of resultlines.\n");
+         break;
+       default: /* parameterline =0 */
+         nresult=1;
+         decoderesult(".",nresult ); /* No covariate */
+       } /* End switch parameterline */
+     }while(endishere==0); /* End do */
-      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
+     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
+       printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+       fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+     }else{
+       /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
+       /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
+       /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
+       if(prvforecast==1){
+         dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
+         jprojd=jproj1;
+         mprojd=mproj1;
+         anprojd=anproj1;
+         dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
+         jprojf=jproj2;
+         mprojf=mproj2;
+         anprojf=anproj2;
+       } else if(prvforecast == 2){
+         dateprojd=dateintmean;
+         date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
+         dateprojf=dateintmean+yrfproj;
+         date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
+       }
+       if(prvbackcast==1){
+         datebackd=(jback1+12*mback1+365*anback1)/365;
+         jbackd=jback1;
+         mbackd=mback1;
+         anbackd=anback1;
+         datebackf=(jback2+12*mback2+365*anback2)/365;
+         jbackf=jback2;
+         mbackf=mback2;
+         anbackf=anback2;
+       } else if(prvbackcast == 2){
+         datebackd=dateintmean;
+         date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
+         datebackf=dateintmean-yrbproj;
+         date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
+       }
-    /*------------ free_vector  -------------*/
+       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
-    /*  chdir(path); */
+     }
+     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
-     free_ivector(wav,1,imx);
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+                  jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     /*------------ free_vector  -------------*/
-     free_lvector(num,1,n);
+     /*  chdir(path); */
-     free_vector(agedc,1,n);
+     /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
+     /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
+     /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
+     /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
+     free_lvector(num,firstobs,lastobs);
+     free_vector(agedc,firstobs,lastobs);
      /*free_matrix(covar,0,NCOVMAX,1,n);*/
      /*free_matrix(covar,1,NCOVMAX,1,n);*/
      fclose(ficparo);
      fclose(ficres);
+     /* Other results (useful)*/
      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
- #include "prevlim.h"  /* Use ficrespl, ficlog */
+     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
+     prlim=matrix(1,nlstate,1,nlstate);
+     /* Computes the prevalence limit for each combination k of the dummy covariates by calling prevalim(k) */
+     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
      fclose(ficrespl);
- #ifdef FREEEXIT2
- #include "freeexit2.h"
- #endif
      /*------------- h Pij x at various ages ------------*/
- #include "hpijx.h"
+     /*#include "hpijx.h"*/
+     /** h Pij x Probability to be in state j at age x+h being in i at x, for each combination k of dummies in the model line or to nres?*/
+     /* calls hpxij with combination k */
+     hPijx(p, bage, fage);
      fclose(ficrespij);
-   /*-------------- Variance of one-step probabilities---*/
+     /* ncovcombmax=  pow(2,cptcoveff); */
+     /*-------------- Variance of one-step probabilities for a combination ij or for nres ?---*/
      k=1;
      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     /* Prevalence for each covariate combination in probs[age][status][cov] */
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
-     for(i=1;i<=AGESUP;i++)
+     for(i=AGEINF;i<=AGESUP;i++)
-       for(j=1;j<=NCOVMAX;j++)
+       for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
-         for(k=1;k<=NCOVMAX;k++)
+         for(k=1;k<=ncovcombmax;k++)
            probs[i][j][k]=0.;
+     prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
+                ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     if (mobilav!=0 ||mobilavproj !=0 ) {
+       mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+       for(i=AGEINF;i<=AGESUP;i++)
+         for(j=1;j<=nlstate+ndeath;j++)
+           for(k=1;k<=ncovcombmax;k++)
+             mobaverages[i][j][k]=0.;
+       mobaverage=mobaverages;
+       if (mobilav!=0) {
+         printf("Movingaveraging observed prevalence\n");
+         fprintf(ficlog,"Movingaveraging observed prevalence\n");
+         if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
+           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+           printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         }
+       } else if (mobilavproj !=0) {
+         printf("Movingaveraging projected observed prevalence\n");
+         fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
+         if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
+           fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
+           printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
+         }
+       }else{
+         printf("Internal error moving average\n");
+         fflush(stdout);
+         exit(1);
+       }
+     }/* end if moving average */
      /*---------- Forecasting ------------------*/
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
-     if(prevfcast==1){
+       /*   /\*    if(stepm ==1){*\/ */
-       /*    if(stepm ==1){*/
+       /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /*This done previously after freqsummary.*/
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+       /*   dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
-       /*      }  */
+       /*   dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
-       /*      else{ */
-       /*        erreur=108; */
+       /* } else if (prvforecast==2){ */
-       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*   /\*    if(stepm ==1){*\/ */
-       /*        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); */
+       /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
-       /*      } */
+       /* } */
-     }
+       /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
+       prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
+     }
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     /* Prevbcasting */
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     if(prevbcast==1){
-     /*  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",\
+       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+       ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
-     */
+       ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
+       /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
+       bprlim=matrix(1,nlstate,1,nlstate);
+       back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
+       fclose(ficresplb);
+       hBijx(p, bage, fage, mobaverage);
+       fclose(ficrespijb);
+       /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
+       /* /\*                   mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
+       /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
+       /*                       mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
+       prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
+                        mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
-     if (mobilav!=0) {
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       }
-     }
+       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
+       free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
+       free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
+       free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
+     }    /* end  Prevbcasting */
+     /* ------ Other prevalence ratios------------ */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
      /*---------- Health expectancies, no variances ------------*/
-     strcpy(filerese,"e");
+     strcpy(filerese,"E_");
-     strcat(filerese,fileres);
+     strcat(filerese,fileresu);
      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);
+     printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
-     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
-         fprintf(ficreseij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         }
-         fprintf(ficreseij,"******\n");
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     pstamp(ficreseij);
-         oldm=oldms;savm=savms;
-         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
+     if (cptcovn < 1){i1=1;}
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+       if(i1 != 1 && TKresult[nres]!= k)
+         continue;
+       fprintf(ficreseij,"\n#****** ");
+       printf("\n#****** ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]); /* TvarsQ[j] gives the name of the jth quantitative (fixed or time v) */
+         fprintf(ficreseij,"V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]);
+       }
+       fprintf(ficreseij,"******\n");
+       printf("******\n");
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       /*}*/
+       oldm=oldms;savm=savms;
+       /* printf("HELLO Entering evsij bage=%d fage=%d k=%d estepm=%d nres=%d\n",(int) bage, (int)fage, k, estepm, nres); */
+       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
+       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
      }
      fclose(ficreseij);
+     printf("done evsij\n");fflush(stdout);
+     fprintf(ficlog,"done evsij\n");fflush(ficlog);
-     /*---------- Health expectancies and variances ------------*/
+     /*---------- State-specific expectancies and variances ------------*/
+     /* Should be moved in a function */
+     strcpy(filerest,"T_");
-     strcpy(filerest,"t");
+     strcat(filerest,fileresu);
-     strcat(filerest,fileres);
      if((ficrest=fopen(filerest,"w"))==NULL) {
        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
      }
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
+     strcpy(fileresstde,"STDE_");
+     strcat(fileresstde,fileresu);
-     strcpy(fileresstde,"stde");
-     strcat(fileresstde,fileres);
      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
      }
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     printf("  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
-     strcpy(filerescve,"cve");
+     strcpy(filerescve,"CVE_");
-     strcat(filerescve,fileres);
+     strcat(filerescve,fileresu);
      if((ficrescveij=fopen(filerescve,"w"))==NULL) {
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
      }
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     printf("    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
-     strcpy(fileresv,"v");
+     strcpy(fileresv,"V_");
-     strcat(fileresv,fileres);
+     strcat(fileresv,fileresu);
      if((ficresvij=fopen(fileresv,"w"))==NULL) {
        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
      }
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
-     /*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(ficrest,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficrest,"******\n");
-         fprintf(ficresstdeij,"\n#****** ");
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
-         fprintf(ficrescveij,"\n#****** ");
+     if (cptcovn < 1){i1=1;}
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for(nres=1; nres <= nresult; nres++) /* For each resultline, find the combination and output results according to the values of dummies and then quanti.  */
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying. For each nres and each value at position k
-         }
+                           * we know Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline
-         fprintf(ficresstdeij,"******\n");
+                           * Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline
-         fprintf(ficrescveij,"******\n");
+                           * and Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
+       /* */
-         fprintf(ficresvij,"\n#****** ");
+       if(i1 != 1 && TKresult[nres]!= k) /* TKresult[nres] is the combination of this nres resultline. All the i1 combinations are not output */
-         for(j=1;j<=cptcoveff;j++)
+         continue;
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       printf("\n# model %s \n#****** Result for:", model);
-         fprintf(ficresvij,"******\n");
+       fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
+       fprintf(ficlog,"\n# model %s \n#****** Result for:", model);
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       /* It might not be a good idea to mix dummies and quantitative */
-         oldm=oldms;savm=savms;
+       /* for(j=1;j<=cptcoveff;j++){ /\* j=resultpos. Could be a loop on cptcovs: number of single dummy covariate in the result line as well as in the model *\/ */
-         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+       for(j=1;j<=cptcovs;j++){ /* j=resultpos. Could be a loop on cptcovs: number of single covariate (dummy or quantitative) in the result line as well as in the model */
-         /*
+         /* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /\* Output by variables in the resultline *\/ */
+         /* Tvaraff[j] is the name of the dummy variable in position j in the equation model:
+          * Tvaraff[1]@9={4, 3, 0, 0, 0, 0, 0, 0, 0}, in model=V5+V4+V3+V4*V3+V5*age
+          * (V5 is quanti) V4 and V3 are dummies
+          * TnsdVar[4] is the position 1 and TnsdVar[3]=2 in codtabm(k,l)(V4  V3)=V4  V3
+          *                                                              l=1 l=2
+          *                                                           k=1  1   1   0   0
+          *                                                           k=2  2   1   1   0
+          *                                                           k=3 [1] [2]  0   1
+          *                                                           k=4  2   2   1   1
+          * If nres=1 result: V3=1 V4=0 then k=3 and outputs
+          * If nres=2 result: V4=1 V3=0 then k=2 and outputs
+          * nres=1 =>k=3 j=1 V4= nbcode[4][codtabm(3,1)=1)=0; j=2  V3= nbcode[3][codtabm(3,2)=2]=1
+          * nres=2 =>k=2 j=1 V4= nbcode[4][codtabm(2,1)=2)=1; j=2  V3= nbcode[3][codtabm(2,2)=1]=0
           */
-         /* goto endfree; */
+         /* Tvresult[nres][j] Name of the variable at position j in this resultline */
+         /* Tresult[nres][j] Value of this variable at position j could be a float if quantitative  */
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+ /* We give up with the combinations!! */
-         pstamp(ficrest);
+         printf("\n j=%d In computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d Fixed[modelresult[nres][j]]=%d\n", j, nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff,Fixed[modelresult[nres][j]]);  /* end if dummy  or quanti */
+         if(Dummy[modelresult[nres][j]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to j in resultline  */
-         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+           printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
-           oldm=oldms;savm=savms; /* Segmentation fault */
+           fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
-           cptcod= 0; /* To be deleted */
+           fprintf(ficrest,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+           if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
-           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 ");
+             printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
-           if(vpopbased==1)
+           }else{
-             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);
+             printf("varyi ");fprintf(ficlog,"varyi ");fprintf(ficrest,"varyi ");
-           else
+           }
-             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           /* fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-           fprintf(ficrest,"# Age e.. (std) ");
+           /* fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         }else if(Dummy[modelresult[nres][j]]==1){ /* Quanti variable */
-           fprintf(ficrest,"\n");
+           /* For each selected (single) quantitative value */
+           printf(" V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
-           epj=vector(1,nlstate+1);
+           fprintf(ficlog," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
-           for(age=bage; age <=fage ;age++){
+           fprintf(ficrest," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
-             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
-             if (vpopbased==1) {
+             printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
-               if(mobilav ==0){
+           }else{
-                 for(i=1; i<=nlstate;i++)
+             printf("varyi ");fprintf(ficlog,"varyi ");fprintf(ficrest,"varyi ");
-                   prlim[i][i]=probs[(int)age][i][k];
+           }
-               }else{ /* mobilav */
+         }else{
-                 for(i=1; i<=nlstate;i++)
+           printf("Error in computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d \n", nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff);  /* end if dummy  or quanti */
-                   prlim[i][i]=mobaverage[(int)age][i][k];
+           fprintf(ficlog,"Error in computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d \n", nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff);  /* end if dummy  or quanti */
-               }
+           exit(1);
-             }
+         }
+       } /* End loop for each variable in the resultline */
-             fprintf(ficrest," %4.0f",age);
+       /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
-             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+       /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /\* Wrong j is not in the equation model *\/ */
-               for(i=1, epj[j]=0.;i <=nlstate;i++) {
+       /*        fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
-                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
+       /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
-                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+       /* }       */
-               }
+       fprintf(ficrest,"******\n");
-               epj[nlstate+1] +=epj[j];
+       fprintf(ficlog,"******\n");
+       printf("******\n");
+       fprintf(ficresstdeij,"\n#****** ");
+       fprintf(ficrescveij,"\n#****** ");
+       /* It could have been: for(j=1;j<=cptcoveff;j++) {printf("V=%d=%lg",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);} */
+       /* But it won't be sorted and depends on how the resultline is ordered */
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresstdeij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
+         /* fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+         /* fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value, TvarsQind gives the position of a quantitative in model equation  */
+         fprintf(ficresstdeij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
+         fprintf(ficrescveij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
+       }
+       fprintf(ficresstdeij,"******\n");
+       fprintf(ficrescveij,"******\n");
+       fprintf(ficresvij,"\n#****** ");
+       /* pstamp(ficresvij); */
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficresvij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
+         /* fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[TnsdVar[Tvaraff[j]]])]); */
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         /* fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); /\* To solve *\/ */
+         fprintf(ficresvij," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */
+       }
+       fprintf(ficresvij,"******\n");
+       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       printf(" cvevsij ");
+       fprintf(ficlog, " cvevsij ");
+       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
+       printf(" end cvevsij \n ");
+       fprintf(ficlog, " end cvevsij \n ");
+       /*
+        */
+       /* goto endfree; */
+       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       pstamp(ficrest);
+       epj=vector(1,nlstate+1);
+       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+         oldm=oldms;savm=savms; /* ZZ Segmentation fault */
+         cptcod= 0; /* To be deleted */
+         printf("varevsij vpopbased=%d \n",vpopbased);
+         fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
+         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+         if(vpopbased==1)
+           fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
+         else
+           fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
+         fprintf(ficrest,"# Age popbased mobilav e.. (std) "); /* Adding covariate values? */
+         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         fprintf(ficrest,"\n");
+         /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
+         printf("Computing age specific forward period (stable) prevalences in each health state \n");
+         fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
+         for(age=bage; age <=fage ;age++){
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
+           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];
              }
+           }
-             for(i=1, vepp=0.;i <=nlstate;i++)
-               for(j=1;j <=nlstate;j++)
+           fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
-                 vepp += vareij[i][j][(int)age];
+           /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
-             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+           /* printf(" age %4.0f ",age); */
-             for(j=1;j <=nlstate;j++){
+           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+               /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
              }
-             fprintf(ficrest,"\n");
+             epj[nlstate+1] +=epj[j];
            }
+           /* printf(" age %4.0f \n",age); */
+           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");
          }
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       } /* End vpopbased */
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       free_vector(epj,1,nlstate+1);
-         free_vector(epj,1,nlstate+1);
+       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-       /*}*/
+       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-     }
+       printf("done selection\n");fflush(stdout);
-     free_vector(weight,1,n);
+       fprintf(ficlog,"done selection\n");fflush(ficlog);
+     } /* End k selection or end covariate selection for nres */
+     printf("done State-specific expectancies\n");fflush(stdout);
+     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
+     /* variance-covariance of forward period prevalence */
+     varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
+     free_vector(weight,firstobs,lastobs);
+     free_imatrix(Tvardk,1,NCOVMAX,1,2);
      free_imatrix(Tvard,1,NCOVMAX,1,2);
-     free_imatrix(s,1,maxwav+1,1,n);
+     free_imatrix(s,1,maxwav+1,firstobs,lastobs);
-     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(anint,1,maxwav,firstobs,lastobs);
-     free_matrix(mint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,firstobs,lastobs);
-     free_ivector(cod,1,n);
+     free_ivector(cod,firstobs,lastobs);
      free_ivector(tab,1,NCOVMAX);
      fclose(ficresstdeij);
      fclose(ficrescveij);
      fclose(ficresvij);
      fclose(ficrest);
      fclose(ficpar);
-     /*------- Variance of period (stable) prevalence------*/
-     strcpy(fileresvpl,"vpl");
-     strcat(fileresvpl,fileres);
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
-       exit(0);
-     }
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
-     /*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(ficresvpl,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficresvpl,"******\n");
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
-       /*}*/
-     }
-     fclose(ficresvpl);
      /*---------- End : free ----------------*/
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (mobilav!=0 ||mobilavproj !=0)
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
-   }  /* mle==-3 arrives here for freeing */
+     free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
-  /* endfree:*/
      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   }  /* mle==-3 arrives here for freeing */
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   /* endfree:*/
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(covar,0,NCOVMAX,1,n);
+   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(matcov,1,npar,1,npar);
+   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     /*free_vector(delti,1,npar);*/
+   if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
-     free_matrix(agev,1,maxwav,1,imx);
+   if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
+   free_matrix(matcov,1,npar,1,npar);
+   free_matrix(hess,1,npar,1,npar);
+   /*free_vector(delti,1,npar);*/
+   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_matrix(agev,1,maxwav,1,imx);
+   free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_ivector(ncodemax,1,NCOVMAX);
+   free_ivector(ncodemaxwundef,1,NCOVMAX);
+   free_ivector(Dummy,-1,NCOVMAX);
+   free_ivector(Fixed,-1,NCOVMAX);
+   free_ivector(DummyV,1,NCOVMAX);
+   free_ivector(FixedV,1,NCOVMAX);
+   free_ivector(Typevar,-1,NCOVMAX);
+   free_ivector(Tvar,1,NCOVMAX);
+   free_ivector(TvarsQ,1,NCOVMAX);
+   free_ivector(TvarsQind,1,NCOVMAX);
+   free_ivector(TvarsD,1,NCOVMAX);
+   free_ivector(TnsdVar,1,NCOVMAX);
+   free_ivector(TvarsDind,1,NCOVMAX);
+   free_ivector(TvarFD,1,NCOVMAX);
+   free_ivector(TvarFDind,1,NCOVMAX);
+   free_ivector(TvarF,1,NCOVMAX);
+   free_ivector(TvarFind,1,NCOVMAX);
+   free_ivector(TvarV,1,NCOVMAX);
+   free_ivector(TvarVind,1,NCOVMAX);
+   free_ivector(TvarA,1,NCOVMAX);
+   free_ivector(TvarAind,1,NCOVMAX);
+   free_ivector(TvarFQ,1,NCOVMAX);
+   free_ivector(TvarFQind,1,NCOVMAX);
+   free_ivector(TvarVD,1,NCOVMAX);
+   free_ivector(TvarVDind,1,NCOVMAX);
+   free_ivector(TvarVQ,1,NCOVMAX);
+   free_ivector(TvarVQind,1,NCOVMAX);
+   free_ivector(Tvarsel,1,NCOVMAX);
+   free_vector(Tvalsel,1,NCOVMAX);
+   free_ivector(Tposprod,1,NCOVMAX);
+   free_ivector(Tprod,1,NCOVMAX);
+   free_ivector(Tvaraff,1,NCOVMAX);
+   free_ivector(invalidvarcomb,1,ncovcombmax);
+   free_ivector(Tage,1,NCOVMAX);
+   free_ivector(Tmodelind,1,NCOVMAX);
+   free_ivector(TmodelInvind,1,NCOVMAX);
+   free_ivector(TmodelInvQind,1,NCOVMAX);
-     free_ivector(ncodemax,1,NCOVMAX);
+   free_matrix(precov, 1,MAXRESULTLINESPONE,1,NCOVMAX+1); /* Could be elsewhere ?*/
-     free_ivector(Tvar,1,NCOVMAX);
-     free_ivector(Tprod,1,NCOVMAX);
-     free_ivector(Tvaraff,1,NCOVMAX);
-     free_ivector(Tage,1,NCOVMAX);
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
-     free_imatrix(codtab,1,100,1,10);
+   /* free_imatrix(codtab,1,100,1,10); */
    fflush(fichtm);
    fflush(ficgp);
    if((nberr >0) || (nbwarn>0)){
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
    }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
- Line 6911  Interval (in months) between two waves:
+ Line 14209  Interval (in months) between two waves:
    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(rend_time -rstart_time,tmpout));
    printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
    fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
    fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
- Line 6924  Interval (in months) between two waves:
+ Line 14222  Interval (in months) between two waves:
    fclose(ficgp);
    fclose(ficlog);
    /*------ End -----------*/
+ /* Executes gnuplot */
-    printf("Before Current directory %s!\n",pathcd);
-    if(chdir(pathcd) != 0)
+   printf("Before Current directory %s!\n",pathcd);
+ #ifdef WIN32
+   if (_chdir(pathcd) != 0)
      printf("Can't move to directory %s!\n",path);
-   if(getcwd(pathcd,MAXLINE) > 0)
+   if(_getcwd(pathcd,MAXLINE) > 0)
+ #else
+     if(chdir(pathcd) != 0)
+       printf("Can't move to directory %s!\n", path);
+   if (getcwd(pathcd, MAXLINE) > 0)
+ #endif
      printf("Current directory %s!\n",pathcd);
    /*strcat(plotcmd,CHARSEPARATOR);*/
    sprintf(plotcmd,"gnuplot");
- Line 6954  Interval (in months) between two waves:
+ Line 14260  Interval (in months) between two waves:
    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+   strcpy(pplotcmd,plotcmd);
    if((outcmd=system(plotcmd)) != 0){
-     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+     printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
      printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
      sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
-     if((outcmd=system(plotcmd)) != 0)
+     if((outcmd=system(plotcmd)) != 0){
        printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+       strcpy(plotcmd,pplotcmd);
+     }
    }
    printf(" Successful, please wait...");
    while (z[0] != 'q') {
- Line 6982  Interval (in months) between two waves:
+ Line 14291  Interval (in months) between two waves:
      else if (z[0] == 'g') system(plotcmd);
      else if (z[0] == 'q') exit(0);
    }
-   end:
+ end:
    while (z[0] != 'q') {
-     printf("\nType  q for exiting: ");
+     printf("\nType  q for exiting: "); fflush(stdout);
      scanf("%s",z);
    }
+   printf("End\n");
+   exit(0);
  }

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